0s autopkgtest [06:36:38]: starting date and time: 2024-11-14 06:36:38+0000 0s autopkgtest [06:36:38]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [06:36:38]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gyp4sk7o/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- lxd -r lxd-armhf-10.145.243.158 lxd-armhf-10.145.243.158:autopkgtest/ubuntu/plucky/armhf 55s autopkgtest [06:37:33]: testbed dpkg architecture: armhf 57s autopkgtest [06:37:35]: testbed apt version: 2.9.8 57s autopkgtest [06:37:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 65s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [98.6 kB] 65s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.4 kB] 65s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [987 kB] 65s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 65s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [103 kB] 65s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [684 kB] 65s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [5040 B] 66s Fetched 1973 kB in 1s (1990 kB/s) 66s Reading package lists... 83s tee: /proc/self/fd/2: Permission denied 105s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 105s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 105s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 105s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 107s Reading package lists... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s Calculating upgrade... 108s The following packages were automatically installed and are no longer required: 108s libperl5.38t64 perl-modules-5.38 python3-netifaces 108s Use 'apt autoremove' to remove them. 108s The following NEW packages will be installed: 108s libperl5.40 perl-modules-5.40 python3.13-gdbm systemd-cryptsetup 108s The following packages will be upgraded: 108s apport apport-core-dump-handler base-files base-passwd bash-completion 108s dhcpcd-base distro-info-data dpkg dpkg-dev fwupd gcc-14-base info 108s install-info iproute2 libarchive13t64 libatomic1 libattr1 108s libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 libblockdev-mdraid3 108s libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 libblockdev-utils3 108s libblockdev3 libbpf1 libbsd0 libbytesize-common libbytesize1 libdb5.3t64 108s libdpkg-perl libdrm-common libdrm2 libdw1t64 libedit2 libelf1t64 libevdev2 108s libfastjson4 libflashrom1 libftdi1-2 libfwupd2 libgcc-s1 libgnutls30t64 108s libgpgme11t64 libinih1 libjson-c5 libjson-glib-1.0-0 libjson-glib-1.0-common 108s libkeyutils1 libldap-common libldap2 liblocale-gettext-perl libmaxminddb0 108s libmnl0 libnetfilter-conntrack3 libnetplan1 libnewt0.52 libnghttp2-14 108s libnspr4 libnss-systemd libnvme1t64 libpam-systemd libpipeline1 libplymouth5 108s libpng16-16t64 libpopt0 libpython3-stdlib libpython3.12-minimal 108s libpython3.12-stdlib libsgutils2-1.46-2 libssh2-1t64 libstdc++6 108s libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl 108s libtraceevent1 libtraceevent1-plugin libudev1 libudisks2-0 liburcu8t64 108s libutempter0 libuv1t64 libx11-6 libx11-data libxau6 libxmlb2 mawk 108s motd-news-config nano netplan-generator netplan.io openssh-client 108s openssh-server openssh-sftp-server pci.ids perl perl-base plymouth 108s plymouth-theme-ubuntu-text python3 python3-apport python3-certifi 108s python3-cffi-backend python3-configobj python3-gdbm python3-gi python3-idna 108s python3-jaraco.functools python3-json-pointer python3-jsonpatch 108s python3-lazr.restfulclient python3-lazr.uri python3-minimal 108s python3-more-itertools python3-netplan python3-newt python3-oauthlib 108s python3-problem-report python3-typeguard python3-urllib3 python3-wadllib 108s python3-zipp python3.12 python3.12-gdbm python3.12-minimal sg3-utils 108s sg3-utils-udev ssh-import-id systemd systemd-resolved systemd-sysv 108s systemd-timesyncd tzdata udev udisks2 ufw usbutils vim-common vim-tiny 108s whiptail xxd 108s 143 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 108s Need to get 45.5 MB of archives. 108s After this operation, 43.2 MB of additional disk space will be used. 108s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf motd-news-config all 13.5ubuntu3 [5190 B] 108s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf base-files armhf 13.5ubuntu3 [75.1 kB] 108s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf dpkg armhf 1.22.11ubuntu3 [1247 kB] 109s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf perl-modules-5.40 all 5.40.0-7 [3214 kB] 109s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libperl5.40 armhf 5.40.0-7 [4139 kB] 109s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf perl armhf 5.40.0-7 [263 kB] 109s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf perl-base armhf 5.40.0-7 [1674 kB] 109s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf liblocale-gettext-perl armhf 1.07-7build1 [15.0 kB] 109s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-iconv-perl armhf 1.7-8build4 [12.8 kB] 109s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-charwidth-perl armhf 0.04-11build4 [9128 B] 109s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-9 [655 kB] 109s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf base-passwd armhf 3.6.5 [53.2 kB] 109s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 109s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 109s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf tzdata all 2024b-1ubuntu2 [274 kB] 109s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12 armhf 3.12.7-3 [661 kB] 109s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-stdlib armhf 3.12.7-3 [1934 kB] 109s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-minimal armhf 3.12.7-3 [2012 kB] 109s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-minimal armhf 3.12.7-3 [822 kB] 109s Get:20 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 109s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libnss-systemd armhf 256.5-2ubuntu4 [155 kB] 109s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-timesyncd armhf 256.5-2ubuntu4 [40.7 kB] 109s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-resolved armhf 256.5-2ubuntu4 [309 kB] 109s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libsystemd-shared armhf 256.5-2ubuntu4 [2129 kB] 109s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libsystemd0 armhf 256.5-2ubuntu4 [428 kB] 109s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-sysv armhf 256.5-2ubuntu4 [11.9 kB] 109s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libpam-systemd armhf 256.5-2ubuntu4 [226 kB] 109s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf systemd armhf 256.5-2ubuntu4 [3442 kB] 109s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf udev armhf 256.5-2ubuntu4 [1949 kB] 109s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libudev1 armhf 256.5-2ubuntu4 [188 kB] 109s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf python3-problem-report all 2.30.0-0ubuntu5 [25.0 kB] 109s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf python3-apport all 2.30.0-0ubuntu5 [93.2 kB] 109s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf python3-gi armhf 3.50.0-3 [227 kB] 109s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf apport-core-dump-handler all 2.30.0-0ubuntu5 [17.9 kB] 109s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf apport all 2.30.0-0ubuntu5 [83.0 kB] 109s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libbsd0 armhf 0.12.2-2 [36.8 kB] 109s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libedit2 armhf 3.1-20240808-1 [79.0 kB] 109s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf openssh-sftp-server armhf 1:9.7p1-7ubuntu5 [35.4 kB] 109s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf openssh-server armhf 1:9.7p1-7ubuntu5 [505 kB] 109s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf openssh-client armhf 1:9.7p1-7ubuntu5 [889 kB] 109s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libatomic1 armhf 14.2.0-8ubuntu1 [7846 B] 109s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-base armhf 14.2.0-8ubuntu1 [51.5 kB] 109s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++6 armhf 14.2.0-8ubuntu1 [711 kB] 109s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-s1 armhf 14.2.0-8ubuntu1 [40.8 kB] 109s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libattr1 armhf 1:2.5.2-2 [10.5 kB] 109s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 109s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf install-info armhf 7.1.1-1 [61.4 kB] 109s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf mawk armhf 1.3.4.20240905-1 [116 kB] 110s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf dhcpcd-base armhf 1:10.1.0-2 [188 kB] 110s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf distro-info-data all 0.63 [6588 B] 110s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf libdw1t64 armhf 0.192-4 [243 kB] 110s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libelf1t64 armhf 0.192-4 [50.2 kB] 110s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libbpf1 armhf 1:1.5.0-1 [158 kB] 110s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libmnl0 armhf 1.0.5-3 [10.7 kB] 110s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf iproute2 armhf 6.10.0-2ubuntu1 [1082 kB] 110s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf libfastjson4 armhf 1.2304.0-2 [20.2 kB] 110s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-c5 armhf 0.18+ds-1 [33.2 kB] 110s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf libkeyutils1 armhf 1.6.3-4ubuntu2 [8712 B] 110s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf netplan-generator armhf 1.1.1-1 [60.4 kB] 110s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cffi-backend armhf 1.17.1-2 [68.7 kB] 110s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf python3-netplan armhf 1.1.1-1 [24.1 kB] 110s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf netplan.io armhf 1.1.1-1 [66.4 kB] 110s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf libnetplan1 armhf 1.1.1-1 [122 kB] 110s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-2ubuntu4 [19.7 kB] 110s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-2ubuntu4 [39.2 kB] 110s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf libpopt0 armhf 1.19+dfsg-2 [25.4 kB] 110s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf vim-tiny armhf 2:9.1.0777-1ubuntu1 [693 kB] 110s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf vim-common all 2:9.1.0777-1ubuntu1 [394 kB] 110s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-2ubuntu4 [17.2 kB] 110s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf xxd armhf 2:9.1.0777-1ubuntu1 [66.8 kB] 110s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf bash-completion all 1:2.14.0-2 [210 kB] 110s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf info armhf 7.1.1-1 [126 kB] 110s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf libdrm-common all 2.4.123-1 [8436 B] 110s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf libdrm2 armhf 2.4.123-1 [36.5 kB] 110s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libevdev2 armhf 1.13.3+dfsg-1 [29.7 kB] 110s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libmaxminddb0 armhf 1.11.0-1 [16.8 kB] 110s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf libnetfilter-conntrack3 armhf 1.1.0-1 [38.4 kB] 110s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf libnghttp2-14 armhf 1.64.0-1 [68.9 kB] 110s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf libpipeline1 armhf 1.5.8-1 [26.9 kB] 110s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf libpng16-16t64 armhf 1.6.44-2 [168 kB] 110s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf libplymouth5 armhf 24.004.60-1ubuntu11 [140 kB] 110s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1-plugin armhf 1:1.8.3-1ubuntu1 [18.1 kB] 110s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1 armhf 1:1.8.3-1ubuntu1 [52.1 kB] 110s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf liburcu8t64 armhf 0.14.1-1 [56.6 kB] 110s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf libuv1t64 armhf 1.48.0-7 [83.3 kB] 110s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf libx11-data all 2:1.8.10-2 [116 kB] 110s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf libx11-6 armhf 2:1.8.10-2 [587 kB] 110s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf libxau6 armhf 1:1.0.11-1 [6558 B] 110s Get:89 http://ftpmaster.internal/ubuntu plucky/main armhf nano armhf 8.2-1 [276 kB] 110s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf pci.ids all 0.0~2024.10.24-1 [279 kB] 110s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf plymouth-theme-ubuntu-text armhf 24.004.60-1ubuntu11 [9920 B] 110s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf plymouth armhf 24.004.60-1ubuntu11 [142 kB] 110s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-gdbm armhf 3.12.7-3 [28.7 kB] 110s Get:94 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 110s Get:95 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 110s Get:96 http://ftpmaster.internal/ubuntu plucky/main armhf ufw all 0.36.2-8 [170 kB] 110s Get:97 http://ftpmaster.internal/ubuntu plucky/main armhf usbutils armhf 1:018-1 [76.1 kB] 110s Get:98 http://ftpmaster.internal/ubuntu plucky/main armhf dpkg-dev all 1.22.11ubuntu3 [1088 kB] 110s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf libdpkg-perl all 1.22.11ubuntu3 [279 kB] 110s Get:100 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive13t64 armhf 3.7.4-1.1 [331 kB] 110s Get:101 http://ftpmaster.internal/ubuntu plucky/main armhf libftdi1-2 armhf 1.5-7 [25.7 kB] 111s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf libflashrom1 armhf 1.4.0-3ubuntu1 [141 kB] 111s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 111s Get:104 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 111s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd2 armhf 1.9.26-2 [125 kB] 111s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf libxmlb2 armhf 0.3.21-1 [57.7 kB] 111s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 1.9.26-2 [4404 kB] 111s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-utils3 armhf 3.2.1-1 [17.4 kB] 111s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-crypto3 armhf 3.2.1-1 [22.4 kB] 111s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-fs3 armhf 3.2.1-1 [34.3 kB] 111s Get:111 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-loop3 armhf 3.2.1-1 [6552 B] 111s Get:112 http://ftpmaster.internal/ubuntu plucky/main armhf libbytesize1 armhf 2.11-1ubuntu1 [12.0 kB] 111s Get:113 http://ftpmaster.internal/ubuntu plucky/main armhf libbytesize-common all 2.11-1ubuntu1 [3584 B] 111s Get:114 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-mdraid3 armhf 3.2.1-1 [13.4 kB] 111s Get:115 http://ftpmaster.internal/ubuntu plucky/main armhf libnvme1t64 armhf 1.11-1 [73.8 kB] 111s Get:116 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-nvme3 armhf 3.2.1-1 [17.6 kB] 111s Get:117 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-part3 armhf 3.2.1-1 [16.5 kB] 111s Get:118 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-swap3 armhf 3.2.1-1 [8952 B] 111s Get:119 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev3 armhf 3.2.1-1 [44.2 kB] 111s Get:120 http://ftpmaster.internal/ubuntu plucky/main armhf libgpgme11t64 armhf 1.23.2-5ubuntu4 [123 kB] 111s Get:121 http://ftpmaster.internal/ubuntu plucky/main armhf libinih1 armhf 58-1ubuntu1 [6750 B] 111s Get:122 http://ftpmaster.internal/ubuntu plucky/main armhf libldap-common all 2.6.8+dfsg-1~exp4ubuntu3 [32.3 kB] 111s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf libldap2 armhf 2.6.8+dfsg-1~exp4ubuntu3 [173 kB] 111s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf libnspr4 armhf 2:4.35-1.1ubuntu2 [94.1 kB] 111s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf libsgutils2-1.46-2 armhf 1.46-3ubuntu5 [82.5 kB] 111s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf libssh2-1t64 armhf 1.11.1-1 [116 kB] 111s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf udisks2 armhf 2.10.1-11ubuntu1 [278 kB] 111s Get:128 http://ftpmaster.internal/ubuntu plucky/main armhf libudisks2-0 armhf 2.10.1-11ubuntu1 [142 kB] 111s Get:129 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 111s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf python3-certifi all 2024.8.30+dfsg-1 [9742 B] 111s Get:131 http://ftpmaster.internal/ubuntu plucky/main armhf python3-configobj all 5.0.9-1 [33.9 kB] 111s Get:132 http://ftpmaster.internal/ubuntu plucky/main armhf python3-idna all 3.8-2 [47.0 kB] 111s Get:133 http://ftpmaster.internal/ubuntu plucky/main armhf python3-more-itertools all 10.5.0-1 [56.2 kB] 111s Get:134 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jaraco.functools all 4.1.0-1 [11.8 kB] 111s Get:135 http://ftpmaster.internal/ubuntu plucky/main armhf python3-json-pointer all 2.4-2 [8396 B] 111s Get:136 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jsonpatch all 1.32-4 [12.2 kB] 112s Get:137 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.uri all 1.0.6-4 [13.6 kB] 112s Get:138 http://ftpmaster.internal/ubuntu plucky/main armhf python3-wadllib all 2.0.0-1 [36.7 kB] 112s Get:139 http://ftpmaster.internal/ubuntu plucky/main armhf python3-oauthlib all 3.2.2-2 [89.8 kB] 112s Get:140 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.restfulclient all 0.14.6-2 [50.9 kB] 112s Get:141 http://ftpmaster.internal/ubuntu plucky/main armhf python3-typeguard all 4.4.1-1 [29.0 kB] 112s Get:142 http://ftpmaster.internal/ubuntu plucky/main armhf python3-urllib3 all 2.0.7-2ubuntu0.1 [93.1 kB] 112s Get:143 http://ftpmaster.internal/ubuntu plucky/main armhf python3-zipp all 3.21.0-1 [10.2 kB] 112s Get:144 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils armhf 1.46-3ubuntu5 [816 kB] 112s Get:145 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils-udev all 1.46-3ubuntu5 [5916 B] 112s Get:146 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-cryptsetup armhf 256.5-2ubuntu4 [122 kB] 112s Get:147 http://ftpmaster.internal/ubuntu plucky/main armhf ssh-import-id all 5.11-0ubuntu3 [10.1 kB] 112s Preconfiguring packages ... 112s Fetched 45.5 MB in 4s (12.6 MB/s) 112s (Reading database ... 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(0.18+ds-1) ... 127s Setting up libevdev2:armhf (1.13.3+dfsg-1) ... 127s Setting up libldap2:armhf (2.6.8+dfsg-1~exp4ubuntu3) ... 127s Setting up info (7.1.1-1) ... 127s Setting up liblocale-gettext-perl (1.07-7build1) ... 127s Setting up libbpf1:armhf (1:1.5.0-1) ... 127s Setting up libudisks2-0:armhf (2.10.1-11ubuntu1) ... 127s Setting up python3.13-gdbm (3.13.0-2) ... 127s Setting up libpopt0:armhf (1.19+dfsg-2) ... 127s Setting up sg3-utils (1.46-3ubuntu5) ... 127s Setting up python3.12-minimal (3.12.7-3) ... 128s Setting up libpython3.12-stdlib:armhf (3.12.7-3) ... 128s Setting up libblockdev-mdraid3:armhf (3.2.1-1) ... 128s Setting up libblockdev-crypto3:armhf (3.2.1-1) ... 128s Setting up libblockdev-swap3:armhf (3.2.1-1) ... 128s Setting up iproute2 (6.10.0-2ubuntu1) ... 128s Setting up openssh-client (1:9.7p1-7ubuntu5) ... 128s Setting up python3.12 (3.12.7-3) ... 129s Setting up libblockdev-loop3:armhf (3.2.1-1) ... 129s Setting up systemd (256.5-2ubuntu4) ... 129s /usr/lib/tmpfiles.d/legacy.conf:13: Duplicate line for path "/run/lock", ignoring. 129s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 129s /usr/lib/tmpfiles.d/legacy.conf:13: Duplicate line for path "/run/lock", ignoring. 130s Setting up vim-tiny (2:9.1.0777-1ubuntu1) ... 130s Setting up libblockdev3:armhf (3.2.1-1) ... 130s Installing new version of config file /etc/libblockdev/3/conf.d/00-default.cfg ... 130s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 130s Setting up libblockdev-part3:armhf (3.2.1-1) ... 130s Setting up sg3-utils-udev (1.46-3ubuntu5) ... 130s update-initramfs: deferring update (trigger activated) 130s Setting up libperl5.40:armhf (5.40.0-7) ... 130s Setting up perl (5.40.0-7) ... 130s Setting up systemd-cryptsetup (256.5-2ubuntu4) ... 130s Setting up libnvme1t64 (1.11-1) ... 130s Setting up systemd-timesyncd (256.5-2ubuntu4) ... 131s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 131s Setting up udev (256.5-2ubuntu4) ... 131s Setting up libdpkg-perl (1.22.11ubuntu3) ... 131s Setting up libblockdev-nvme3:armhf (3.2.1-1) ... 131s Setting up libdrm2:armhf (2.4.123-1) ... 131s Setting up whiptail (0.52.24-2ubuntu4) ... 131s Setting up libtraceevent1-plugin:armhf (1:1.8.3-1ubuntu1) ... 131s Setting up libplymouth5:armhf (24.004.60-1ubuntu11) ... 131s Setting up netplan-generator (1.1.1-1) ... 131s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 131s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 131s Setting up systemd-resolved (256.5-2ubuntu4) ... 132s Setting up openssh-sftp-server (1:9.7p1-7ubuntu5) ... 132s Setting up udisks2 (2.10.1-11ubuntu1) ... 132s vda: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/uevent': Permission denied 132s vda1: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda1/uevent': Permission denied 132s vda15: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda15/uevent': Permission denied 132s vda2: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda2/uevent': Permission denied 132s loop0: Failed to write 'change' to '/sys/devices/virtual/block/loop0/uevent': Permission denied 132s loop1: Failed to write 'change' to '/sys/devices/virtual/block/loop1/uevent': Permission denied 132s loop2: Failed to write 'change' to '/sys/devices/virtual/block/loop2/uevent': Permission denied 132s loop3: Failed to write 'change' to '/sys/devices/virtual/block/loop3/uevent': Permission denied 132s loop4: Failed to write 'change' to '/sys/devices/virtual/block/loop4/uevent': Permission denied 132s loop5: Failed to write 'change' to '/sys/devices/virtual/block/loop5/uevent': Permission denied 132s loop6: Failed to write 'change' to '/sys/devices/virtual/block/loop6/uevent': Permission denied 132s loop7: Failed to write 'change' to '/sys/devices/virtual/block/loop7/uevent': Permission denied 132s loop8: Failed to write 'change' to '/sys/devices/virtual/block/loop8/uevent': Permission denied 132s Setting up systemd-sysv (256.5-2ubuntu4) ... 132s Setting up openssh-server (1:9.7p1-7ubuntu5) ... 134s Setting up plymouth (24.004.60-1ubuntu11) ... 134s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 134s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 134s Setting up libfwupd2:armhf (1.9.26-2) ... 134s Setting up libnss-systemd:armhf (256.5-2ubuntu4) ... 134s Setting up python3 (3.12.7-1) ... 134s Setting up python3-zipp (3.21.0-1) ... 134s Setting up python3-newt:armhf (0.52.24-2ubuntu4) ... 135s Setting up dpkg-dev (1.22.11ubuntu3) ... 135s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu11) ... 135s update-initramfs: deferring update (trigger activated) 135s Setting up python3-oauthlib (3.2.2-2) ... 135s Setting up python3-configobj (5.0.9-1) ... 135s Setting up python3-certifi (2024.8.30+dfsg-1) ... 135s Setting up python3-gi (3.50.0-3) ... 135s Setting up python3-idna (3.8-2) ... 135s Setting up python3-urllib3 (2.0.7-2ubuntu0.1) ... 136s Setting up python3-json-pointer (2.4-2) ... 136s Setting up libpam-systemd:armhf (256.5-2ubuntu4) ... 136s Setting up fwupd (1.9.26-2) ... 136s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 136s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 136s fwupd.service is a disabled or a static unit not running, not starting it. 136s Setting up python3-cffi-backend:armhf (1.17.1-2) ... 136s Setting up python3-more-itertools (10.5.0-1) ... 137s Setting up python3-jaraco.functools (4.1.0-1) ... 137s Setting up python3-gdbm:armhf (3.12.7-1) ... 137s Setting up python3-problem-report (2.30.0-0ubuntu5) ... 137s Setting up ssh-import-id (5.11-0ubuntu3) ... 137s Setting up python3-jsonpatch (1.32-4) ... 137s Setting up python3-typeguard (4.4.1-1) ... 137s Setting up ufw (0.36.2-8) ... 138s Setting up python3-lazr.uri (1.0.6-4) ... 138s Setting up python3-apport (2.30.0-0ubuntu5) ... 139s Setting up python3-wadllib (2.0.0-1) ... 139s Setting up python3-netplan (1.1.1-1) ... 139s Setting up python3-lazr.restfulclient (0.14.6-2) ... 139s Setting up netplan.io (1.1.1-1) ... 139s Setting up apport-core-dump-handler (2.30.0-0ubuntu5) ... 140s Setting up apport (2.30.0-0ubuntu5) ... 140s Installing new version of config file /etc/apport/crashdb.conf ... 140s apport-autoreport.service is a disabled or a static unit not running, not starting it. 140s Processing triggers for dbus (1.14.10-4ubuntu5) ... 140s Processing triggers for shared-mime-info (2.4-5) ... 141s Processing triggers for install-info (7.1.1-1) ... 141s Processing triggers for initramfs-tools (0.142ubuntu34) ... 141s Processing triggers for libc-bin (2.40-1ubuntu3) ... 141s Processing triggers for rsyslog (8.2406.0-1ubuntu2) ... 141s Processing triggers for man-db (2.12.1-3) ... 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 144s The following packages will be REMOVED: 144s libperl5.38t64* perl-modules-5.38* python3-netifaces* 144s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 144s After this operation, 41.7 MB disk space will be freed. 144s (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 ... 61507 files and directories currently installed.) 144s Removing libperl5.38t64:armhf (5.38.2-5) ... 144s Removing perl-modules-5.38 (5.38.2-5) ... 145s Removing python3-netifaces:armhf (0.11.0-2build3) ... 145s Processing triggers for man-db (2.12.1-3) ... 145s Processing triggers for libc-bin (2.40-1ubuntu3) ... 147s autopkgtest [06:39:05]: rebooting testbed after setup commands that affected boot 215s autopkgtest [06:40:13]: testbed running kernel: Linux 6.8.0-47-generic #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Oct 2 16:39:14 UTC 2 242s autopkgtest [06:40:40]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 258s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (dsc) [2291 B] 258s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (tar) [22.3 MB] 258s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (diff) [7100 B] 258s gpgv: Signature made Wed Apr 10 17:15:32 2024 UTC 258s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 258s gpgv: Can't check signature: No public key 258s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6build1.dsc: no acceptable signature found 259s autopkgtest [06:40:57]: testing package tombo version 1.5.1-6build1 260s autopkgtest [06:40:58]: build not needed 264s autopkgtest [06:41:02]: test run-unit-test: preparing testbed 274s Reading package lists... 274s Building dependency tree... 274s Reading state information... 274s Starting pkgProblemResolver with broken count: 0 274s Starting 2 pkgProblemResolver with broken count: 0 274s Done 275s The following additional packages will be installed: 275s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 275s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 275s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 275s python3-decorator python3-h5py python3-h5py-serial python3-mappy 275s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 275s tombo-doc 275s Suggested packages: 275s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 275s gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 275s Recommended packages: 275s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 275s python3-rpy2 275s The following NEW packages will be installed: 275s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 275s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 275s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 275s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 275s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 275s tombo-doc 275s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 275s Need to get 60.2 MB/60.2 MB of archives. 275s After this operation, 174 MB of additional disk space will be used. 275s Get:1 /tmp/autopkgtest.2My0Pl/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [708 B] 275s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-lato all 2.015-1 [2781 kB] 276s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 276s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 276s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 276s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 276s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 276s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 276s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB] 276s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4ubuntu3 [55.9 kB] 276s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 276s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 276s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] 276s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 276s Get:15 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 276s Get:16 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 276s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 276s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 276s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.11.0-5ubuntu1 [1061 kB] 277s Get:20 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.11.0-5ubuntu1 [7974 B] 277s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mappy armhf 2.27+dfsg-1 [172 kB] 277s Get:22 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-tqdm all 4.67.0-1 [91.6 kB] 277s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 277s Get:24 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5 [16.4 MB] 277s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf tombo armhf 1.5.1-6build1 [448 kB] 277s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 277s Get:27 http://ftpmaster.internal/ubuntu plucky/universe armhf tombo-doc all 1.5.1-6build1 [21.7 MB] 278s Fetched 60.2 MB in 3s (20.9 MB/s) 278s Selecting previously unselected package fonts-lato. 279s (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 ... 59567 files and directories currently installed.) 279s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 279s Unpacking fonts-lato (2.015-1) ... 279s Selecting previously unselected package fonts-font-awesome. 279s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 279s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 279s Selecting previously unselected package fonts-mathjax. 279s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 279s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 279s Selecting previously unselected package libaec0:armhf. 279s Preparing to unpack .../03-libaec0_1.1.3-1_armhf.deb ... 279s Unpacking libaec0:armhf (1.1.3-1) ... 279s Selecting previously unselected package libblas3:armhf. 279s Preparing to unpack .../04-libblas3_3.12.0-3build2_armhf.deb ... 279s Unpacking libblas3:armhf (3.12.0-3build2) ... 279s Selecting previously unselected package libgfortran5:armhf. 279s Preparing to unpack .../05-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 279s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 279s Selecting previously unselected package libsz2:armhf. 279s Preparing to unpack .../06-libsz2_1.1.3-1_armhf.deb ... 279s Unpacking libsz2:armhf (1.1.3-1) ... 279s Selecting previously unselected package libhdf5-103-1t64:armhf. 279s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ... 279s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 279s Selecting previously unselected package libhdf5-hl-100t64:armhf. 279s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_armhf.deb ... 279s Unpacking libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 279s Selecting previously unselected package libjs-jquery. 279s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 279s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 279s Selecting previously unselected package libjs-underscore. 279s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 279s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 279s Selecting previously unselected package libjs-sphinxdoc. 279s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-4_all.deb ... 279s Unpacking libjs-sphinxdoc (7.4.7-4) ... 279s Selecting previously unselected package liblapack3:armhf. 279s Preparing to unpack .../12-liblapack3_3.12.0-3build2_armhf.deb ... 279s Unpacking liblapack3:armhf (3.12.0-3build2) ... 279s Selecting previously unselected package liblbfgsb0:armhf. 279s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 279s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 279s Selecting previously unselected package liblzf1:armhf. 279s Preparing to unpack .../14-liblzf1_3.6-4_armhf.deb ... 279s Unpacking liblzf1:armhf (3.6-4) ... 279s Selecting previously unselected package python3-decorator. 279s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 279s Unpacking python3-decorator (5.1.1-5) ... 279s Selecting previously unselected package python3-numpy. 279s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 279s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 280s Selecting previously unselected package python3-h5py-serial. 280s Preparing to unpack .../17-python3-h5py-serial_3.11.0-5ubuntu1_armhf.deb ... 280s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 280s Selecting previously unselected package python3-h5py. 280s Preparing to unpack .../18-python3-h5py_3.11.0-5ubuntu1_all.deb ... 280s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 280s Selecting previously unselected package python3-mappy. 280s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1_armhf.deb ... 280s Unpacking python3-mappy (2.27+dfsg-1) ... 280s Selecting previously unselected package python3-tqdm. 280s Preparing to unpack .../20-python3-tqdm_4.67.0-1_all.deb ... 280s Unpacking python3-tqdm (4.67.0-1) ... 280s Selecting previously unselected package sphinx-rtd-theme-common. 280s Preparing to unpack .../21-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 280s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 280s Selecting previously unselected package python3-scipy. 280s Preparing to unpack .../22-python3-scipy_1.13.1-5_armhf.deb ... 280s Unpacking python3-scipy (1.13.1-5) ... 280s Selecting previously unselected package tombo. 280s Preparing to unpack .../23-tombo_1.5.1-6build1_armhf.deb ... 280s Unpacking tombo (1.5.1-6build1) ... 280s Selecting previously unselected package libjs-mathjax. 280s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 280s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 281s Selecting previously unselected package tombo-doc. 281s Preparing to unpack .../25-tombo-doc_1.5.1-6build1_all.deb ... 281s Unpacking tombo-doc (1.5.1-6build1) ... 281s Selecting previously unselected package autopkgtest-satdep. 281s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 281s Unpacking autopkgtest-satdep (0) ... 281s Setting up fonts-lato (2.015-1) ... 281s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 281s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 281s Setting up python3-tqdm (4.67.0-1) ... 281s Setting up python3-mappy (2.27+dfsg-1) ... 281s Setting up libaec0:armhf (1.1.3-1) ... 281s Setting up python3-decorator (5.1.1-5) ... 282s Setting up libblas3:armhf (3.12.0-3build2) ... 282s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 282s Setting up liblzf1:armhf (3.6-4) ... 282s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 282s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 282s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 282s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 282s Setting up libsz2:armhf (1.1.3-1) ... 282s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 282s Setting up liblapack3:armhf (3.12.0-3build2) ... 282s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 282s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 284s Setting up libjs-sphinxdoc (7.4.7-4) ... 284s Setting up tombo-doc (1.5.1-6build1) ... 284s Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 284s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 284s Setting up libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 284s Setting up python3-scipy (1.13.1-5) ... 287s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 287s Setting up python3-h5py (3.11.0-5ubuntu1) ... 287s Setting up tombo (1.5.1-6build1) ... 288s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 288s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 288s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 288s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 288s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 288s re.match('\+', fastq_rec[2]) is None): 288s Setting up autopkgtest-satdep (0) ... 288s Processing triggers for man-db (2.12.1-3) ... 288s Processing triggers for libc-bin (2.40-1ubuntu3) ... 304s (Reading database ... 66770 files and directories currently installed.) 304s Removing autopkgtest-satdep (0) ... 310s autopkgtest [06:41:48]: test run-unit-test: [----------------------- 312s ********* Testing help commands ********** 313s usage: tombo [-h] [-v] 313s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 313s ... 313s 313s ********** Tombo ********* 313s 313s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 313s 313s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 313s 313s Tombo command groups (additional help available within each command group): 313s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 313s preprocess Pre-process nanopore reads for Tombo processing. 313s filter Apply filter to Tombo index file for specified criterion. 313s detect_modifications Perform statistical testing to detect non-standard nucleotides. 313s text_output Output Tombo results in text files. 313s build_model Create canonical and alternative base Tombo models. 313s plot Save plots to visualize raw nanopore signal or testing results. 313s 313s options: 313s -h, --help show this help message and exit 313s -v, --version show Tombo version and exit. 313s usage: tombo resquiggle [--dna] [--rna] 313s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 313s [--q-score Q_SCORE] 313s [--signal-matching-score SIGNAL_MATCHING_SCORE] 313s [--processes PROCESSES] 313s [--corrected-group CORRECTED_GROUP] 313s [--basecall-group BASECALL_GROUP] 313s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 313s [--overwrite] 313s [--failed-reads-filename FAILED_READS_FILENAME] 313s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 313s [--print-advanced-arguments] [--quiet] [--help] 313s fast5s_basedir reference 313s 313s Required Arguments: 313s fast5s_basedir Directory containing fast5 files. All files ending in 313s "fast5" found recursively within this base directory 313s will be processed. 313s reference Reference genome/transcriptome FASTA file or minimap2 313s index (with "map-ont" preset) for mapping. 313s 313s Model Parameters: 313s --dna Explicitly select canonical DNA model. Default: 313s Automatically determine from FAST5s 313s --rna Explicitly select canonical RNA model. Default: 313s Automatically determine from FAST5s 313s 313s Read Filtering Argument: 313s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 313s Filter reads based on observations per base percentile 313s thresholds. Format thresholds as "percentile:thresh 313s [pctl2:thresh2 ...]". For example to filter reads with 313s 99th pctl > 200 obs/base or max > 5k obs/base use 313s "99:200 100:5000". 313s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 313s Default: 0.000000 313s --signal-matching-score SIGNAL_MATCHING_SCORE 313s Observed to expected signal matching score (higher 313s score indicates poor matching). Sample type defaults: 313s RNA : 2 || DNA : 1.1 313s 313s Multiprocessing Arguments: 313s --processes PROCESSES 313s Number of processes. Default: 1 313s 313s FAST5 Data Arguments: 313s --corrected-group CORRECTED_GROUP 313s FAST5 group created by resquiggle command. Default: 313s RawGenomeCorrected_000 313s --basecall-group BASECALL_GROUP 313s FAST5 group obtain original basecalls (under Analyses 313s group). Default: Basecall_1D_000 313s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 313s FAST5 subgroup(s) (under /Analyses/[--basecall- 313s group]/) containing basecalls and created within 313s [--corrected-group] containing re-squiggle results. 313s Default: ['BaseCalled_template'] 313s --overwrite Overwrite previous corrected group in FAST5 files. 313s Note: only effects --corrected-group or --new- 313s corrected-group. 313s 313s Input/Output Arguments: 313s --failed-reads-filename FAILED_READS_FILENAME 313s Output failed read filenames with assoicated error. 313s Default: Do not store failed reads. 313s --num-most-common-errors NUM_MOST_COMMON_ERRORS 313s Dynamically show this many most common errors so far 313s through run. Default: 0; Just show progress 313s 313s Advanced Arguments: 313s --print-advanced-arguments 313s Print advanced re-squiggle arguments and exit. 313s 313s Miscellaneous Arguments: 313s --quiet, -q Don't print status information. 313s --help, -h Print this help message and exit 313s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 313s --fastq-filenames 313s FASTQ_FILENAMES 313s [FASTQ_FILENAMES ...] 313s [--basecall-group BASECALL_GROUP] 313s [--basecall-subgroup BASECALL_SUBGROUP] 313s [--overwrite] 313s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 313s [--processes PROCESSES] 313s [--quiet] [--help] 313s 313s Required Arguments: 313s --fast5-basedir FAST5_BASEDIR 313s Directory containing fast5 files. 313s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 313s FASTQ filenames containing basecalls to be added to 313s raw FAST5 files. 313s 313s FAST5 Data Arguments: 313s --basecall-group BASECALL_GROUP 313s FAST5 group obtain original basecalls (under Analyses 313s group). Default: Basecall_1D_000 313s --basecall-subgroup BASECALL_SUBGROUP 313s FAST5 subgroup (under /Analyses/[--basecall-group]/) 313s under which to store basecalls from FASTQs. Default: 313s BaseCalled_template 313s --overwrite Overwrite previous corrected group in FAST5 files. 313s Note: only effects --corrected-group or --new- 313s corrected-group. 313s 313s Sequencing Summary Argument: 313s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 313s Sequencing summary filenames produced by albacore. 313s These can make annotation of raw FAST5 files with 313s FASTQ sequence much faster. 313s 313s Multiprocessing Argument: 313s --processes PROCESSES 313s Number of processes. Default: 1 313s 313s Miscellaneous Arguments: 313s --quiet, -q Don't print status information. 313s --help, -h Print this help message and exit 313s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 313s [FAST5_BASEDIRS ...] 313s [--corrected-group CORRECTED_GROUP] 313s [--quiet] [--help] 313s 313s Required Argument: 313s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 313s Directories containing fast5 files. 313s 313s FAST5 Data Argument: 313s --corrected-group CORRECTED_GROUP 313s FAST5 group created by resquiggle command. Default: 313s RawGenomeCorrected_000 313s 313s Miscellaneous Arguments: 313s --quiet, -q Don't print status information. 313s --help, -h Print this help message and exit 313s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 313s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 313s [--corrected-group CORRECTED_GROUP] [--quiet] 313s [--help] 313s 313s Required Argument: 313s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 313s Directories containing fast5 files. 313s 313s Read Filtering Argument: 313s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 313s Filter reads based on observations per base percentile 313s thresholds. Format thresholds as "percentile:thresh 313s [pctl2:thresh2 ...]". For example to filter reads with 313s 99th pctl > 200 obs/base or max > 5k obs/base use 313s "99:200 100:5000". 313s 313s FAST5 Data Argument: 313s --corrected-group CORRECTED_GROUP 313s FAST5 group created by resquiggle command. Default: 313s RawGenomeCorrected_000 313s 313s Miscellaneous Arguments: 313s --quiet, -q Don't print status information. 313s --help, -h Print this help message and exit 313s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 313s [FAST5_BASEDIRS ...] 313s [--percent-to-filter PERCENT_TO_FILTER] 313s [--corrected-group CORRECTED_GROUP] 313s [--quiet] [--help] 313s 313s Required Arguments: 313s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 313s Directories containing fast5 files. 313s 313s Read Filtering Argument: 313s --percent-to-filter PERCENT_TO_FILTER 313s Percentage of all reads to filter. Reads are randomly 313s selected weighted according to the approximate 313s coverage at the mapped genomic location. This can be 313s useful in modeling and testing. Default: 10.000000 313s 313s FAST5 Data Arguments: 313s --corrected-group CORRECTED_GROUP 313s FAST5 group created by resquiggle command. Default: 313s RawGenomeCorrected_000 313s 313s Miscellaneous Arguments: 313s --quiet, -q Don't print status information. 313s --help, -h Print this help message and exit 313s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 313s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 313s [--corrected-group CORRECTED_GROUP] 313s [--basecall-group BASECALL_GROUP] [--quiet] 313s [--help] 313s 313s Required Arguments: 313s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 313s Directories containing fast5 files. 313s 313s Read Filtering Argument: 313s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 313s Default: 7.000000 313s 313s FAST5 Data Arguments: 313s --corrected-group CORRECTED_GROUP 313s FAST5 group created by resquiggle command. Default: 313s RawGenomeCorrected_000 313s --basecall-group BASECALL_GROUP 313s FAST5 group obtain original basecalls (under Analyses 313s group). Default: Basecall_1D_000 313s 313s Miscellaneous Arguments: 313s --quiet, -q Don't print status information. 313s --help, -h Print this help message and exit 313s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 313s [FAST5_BASEDIRS ...] 313s --signal-matching-score 313s SIGNAL_MATCHING_SCORE 313s [--corrected-group CORRECTED_GROUP] 313s [--quiet] [--help] 313s 313s Required Arguments: 313s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 313s Directories containing fast5 files. 313s --signal-matching-score SIGNAL_MATCHING_SCORE 313s Observed to expected signal matching score (higher 313s score indicates poor matching). Sample type defaults: 313s RNA : 2 || DNA : 1.1 313s 313s FAST5 Data Arguments: 313s --corrected-group CORRECTED_GROUP 313s FAST5 group created by resquiggle command. Default: 313s RawGenomeCorrected_000 313s 313s Miscellaneous Arguments: 313s --quiet, -q Don't print status information. 313s --help, -h Print this help message and exit 313s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 313s [FAST5_BASEDIRS ...] 313s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 313s [--include-partial-overlap] 313s [--corrected-group CORRECTED_GROUP] 313s [--quiet] [--help] 313s 313s Required Arguments: 313s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 313s Directories containing fast5 files. 313s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 313s Filter out reads not falling completely within include 313s regions. Omit start and end coordinates to include an 313s entire chromosome/sequence record. Format regions as 313s "chrm[:start-end] [chrm2[:start2-end2] ...]". 313s 313s Filter Argument: 313s --include-partial-overlap 313s Include reads that partially overlap the specified 313s region. Default: Only include reads completely 313s contained in a specified region 313s 313s FAST5 Data Argument: 313s --corrected-group CORRECTED_GROUP 313s FAST5 group created by resquiggle command. Default: 313s RawGenomeCorrected_000 313s 313s Miscellaneous Arguments: 313s --quiet, -q Don't print status information. 313s --help, -h Print this help message and exit 313s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 313s [FAST5_BASEDIRS ...] 313s --statistics-file-basename 313s STATISTICS_FILE_BASENAME [--dna] 313s [--rna] 313s [--fishers-method-context FISHERS_METHOD_CONTEXT] 313s [--minimum-test-reads MINIMUM_TEST_READS] 313s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 313s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 313s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 313s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 313s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 313s [--processes PROCESSES] 313s [--corrected-group CORRECTED_GROUP] 313s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 313s [--quiet] [--help] 313s 313s Required Argument: 313s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 313s Directories containing fast5 files. 313s --statistics-file-basename STATISTICS_FILE_BASENAME 313s File base name to save base by base statistics from 313s testing. Filenames will be [--statistics-file- 313s basename].[--alternate-bases]?.tombo.stats 313s 313s Comparison Model Arguments: 313s --dna Explicitly select canonical DNA model. Default: 313s Automatically determine from FAST5s 313s --rna Explicitly select canonical RNA model. Default: 313s Automatically determine from FAST5s 313s 313s Significance Test Arguments: 313s --fishers-method-context FISHERS_METHOD_CONTEXT 313s Number of context bases up and downstream over which 313s to compute Fisher's method combined p-values. Note: 313s Not applicable for alternative model likelihood ratio 313s tests. Default: 1. 313s --minimum-test-reads MINIMUM_TEST_READS 313s Number of reads required at a position to perform 313s significance testing or contribute to model 313s estimation. Default: 1 313s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 313s P-value threshold when computing fraction of 313s significant reads at each genomic position. If two 313s values are provided, statistics between these values 313s are not considered. Default thresholds: DNA:0.15-0.5 , 313s RNA:0.05-0.4 313s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 313s Dampen fraction modified estimates for low coverage 313s sites. Two parameters are unmodified and modified 313s pseudo read counts. This is equivalent to a beta prior 313s on the fraction estimate. Set to "0 0" to disable 313s dampened fraction estimation. Default: [2, 0] 313s 313s Output Argument: 313s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 313s Base for binary files containing per-read statistics 313s from statistical testing. Filenames will be [--per- 313s read-statistics-basename].[--alternate- 313s bases]?.tombo.per_read_stats 313s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 313s Number of the most significant sites to store for 313s faster access. If a longer list of most significant 313s sites is required the list must be re-computed from 313s all batches. Very large values can increase RAM usage. 313s Default: 100000 313s 313s Multiprocessing Arguments: 313s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 313s Size of regions over which to multiprocesses statistic 313s computation. For very deep samples a smaller value is 313s recommmended in order to control memory consumption. 313s Default: 10000 313s --processes PROCESSES 313s Number of processes. Default: 1 313s 313s FAST5 Data Arguments: 313s --corrected-group CORRECTED_GROUP 313s FAST5 group created by resquiggle command. Default: 313s RawGenomeCorrected_000 313s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 313s FAST5 subgroup(s) (under /Analyses/[--basecall- 313s group]/) containing basecalls and created within 313s [--corrected-group] containing re-squiggle results. 313s Default: ['BaseCalled_template'] 313s 313s Miscellaneous Arguments: 313s --quiet, -q Don't print status information. 313s --help, -h Print this help message and exit 313s usage: tombo detect_modifications alternative_model 313s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 313s [--statistics-file-basename STATISTICS_FILE_BASENAME] 313s [--alternate-bases {dam,5mC,6mA,dcm,CpG} [{dam,5mC,6mA,dcm,CpG} ...]] 313s [--print-available-models] 313s [--dna] [--rna] 313s [--minimum-test-reads MINIMUM_TEST_READS] 313s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 313s [--standard-log-likelihood-ratio] 313s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 313s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 313s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 313s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 313s [--processes PROCESSES] 313s [--corrected-group CORRECTED_GROUP] 313s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 313s [--quiet] [--help] 313s 313s Required Argument: 313s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 313s Directories containing fast5 files. 313s --statistics-file-basename STATISTICS_FILE_BASENAME 313s File base name to save base by base statistics from 313s testing. Filenames will be [--statistics-file- 313s basename].[--alternate-bases]?.tombo.stats 313s --alternate-bases {dam,5mC,6mA,dcm,CpG} [{dam,5mC,6mA,dcm,CpG} ...] 313s Default non-standard base model for testing (not 313s required if user created --alternate-model-filenames 313s is provided). 313s 313s Comparison Arguments: 313s --print-available-models 313s Print available alternative models and exit. 313s --dna Explicitly select canonical DNA model. Default: 313s Automatically determine from FAST5s 313s --rna Explicitly select canonical RNA model. Default: 313s Automatically determine from FAST5s 313s 313s Significance Test Arguments: 313s --minimum-test-reads MINIMUM_TEST_READS 313s Number of reads required at a position to perform 313s significance testing or contribute to model 313s estimation. Default: 1 313s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 313s Log likelihood ratio threshold when computing fraction 313s of significant reads at each genomic position. If two 313s values are provided, statistics between these values 313s are not considered. Default thresholds: DNA:-1.5-2.5 , 313s RNA:-2.5-2.5 313s --standard-log-likelihood-ratio 313s Use a standard log likelihood ratio (LLR) statistic. 313s Default is to use an outlier-robust LLR-like 313s statistic. Detail in full online documentation. 313s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 313s Dampen fraction modified estimates for low coverage 313s sites. Two parameters are unmodified and modified 313s pseudo read counts. This is equivalent to a beta prior 313s on the fraction estimate. Set to "0 0" to disable 313s dampened fraction estimation. Default: [2, 0] 313s 313s Output Argument: 313s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 313s Base for binary files containing per-read statistics 313s from statistical testing. Filenames will be [--per- 313s read-statistics-basename].[--alternate- 313s bases]?.tombo.per_read_stats 313s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 313s Number of the most significant sites to store for 313s faster access. If a longer list of most significant 313s sites is required the list must be re-computed from 313s all batches. Very large values can increase RAM usage. 313s Default: 100000 313s 313s Multiprocessing Arguments: 313s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 313s Size of regions over which to multiprocesses statistic 313s computation. For very deep samples a smaller value is 313s recommmended in order to control memory consumption. 313s Default: 10000 313s --processes PROCESSES 313s Number of processes. Default: 1 313s 313s FAST5 Data Arguments: 313s --corrected-group CORRECTED_GROUP 313s FAST5 group created by resquiggle command. Default: 313s RawGenomeCorrected_000 313s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 313s FAST5 subgroup(s) (under /Analyses/[--basecall- 313s group]/) containing basecalls and created within 313s [--corrected-group] containing re-squiggle results. 313s Default: ['BaseCalled_template'] 313s 313s Miscellaneous Arguments: 313s --quiet, -q Don't print status information. 313s --help, -h Print this help message and exit 314s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 314s FAST5_BASEDIRS 314s [FAST5_BASEDIRS ...] 314s --statistics-file-basename 314s STATISTICS_FILE_BASENAME 314s --control-fast5-basedirs 314s CONTROL_FAST5_BASEDIRS 314s [CONTROL_FAST5_BASEDIRS ...] 314s [--sample-only-estimates] 314s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 314s [--dna] [--rna] 314s [--fishers-method-context FISHERS_METHOD_CONTEXT] 314s [--minimum-test-reads MINIMUM_TEST_READS] 314s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 314s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 314s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 314s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 314s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 314s [--processes PROCESSES] 314s [--corrected-group CORRECTED_GROUP] 314s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 314s [--quiet] [--help] 314s 314s Required Argument: 314s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 314s Directories containing fast5 files. 314s --statistics-file-basename STATISTICS_FILE_BASENAME 314s File base name to save base by base statistics from 314s testing. Filenames will be [--statistics-file- 314s basename].[--alternate-bases]?.tombo.stats 314s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 314s Set of directories containing fast5 files for control 314s reads, containing only canonical nucleotides. 314s 314s Model Prior Arguments: 314s --sample-only-estimates 314s Only use canonical sample to estimate expected signal 314s level and spread. Default: Use canonical model to 314s improve estimtates (esp. for low coverage regions) 314s using baysian posterior estimates. 314s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 314s Prior weights (one each for mean and spread) applied 314s to canonical base model for estimating posterior model 314s parameters for sample comparison. Default: [5, 40] 314s --dna Explicitly select canonical DNA model. Default: 314s Automatically determine from FAST5s 314s --rna Explicitly select canonical RNA model. Default: 314s Automatically determine from FAST5s 314s 314s Significance Test Arguments: 314s --fishers-method-context FISHERS_METHOD_CONTEXT 314s Number of context bases up and downstream over which 314s to compute Fisher's method combined p-values. Note: 314s Not applicable for alternative model likelihood ratio 314s tests. Default: 1. 314s --minimum-test-reads MINIMUM_TEST_READS 314s Number of reads required at a position to perform 314s significance testing or contribute to model 314s estimation. Default: 1 314s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 314s P-value threshold when computing fraction of 314s significant reads at each genomic position. If two 314s values are provided, statistics between these values 314s are not considered. Default thresholds: DNA:0.15-0.5 , 314s RNA:0.05-0.4 314s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 314s Dampen fraction modified estimates for low coverage 314s sites. Two parameters are unmodified and modified 314s pseudo read counts. This is equivalent to a beta prior 314s on the fraction estimate. Set to "0 0" to disable 314s dampened fraction estimation. Default: [2, 0] 314s 314s Output Argument: 314s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 314s Base for binary files containing per-read statistics 314s from statistical testing. Filenames will be [--per- 314s read-statistics-basename].[--alternate- 314s bases]?.tombo.per_read_stats 314s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 314s Number of the most significant sites to store for 314s faster access. If a longer list of most significant 314s sites is required the list must be re-computed from 314s all batches. Very large values can increase RAM usage. 314s Default: 100000 314s 314s Multiprocessing Arguments: 314s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 314s Size of regions over which to multiprocesses statistic 314s computation. For very deep samples a smaller value is 314s recommmended in order to control memory consumption. 314s Default: 10000 314s --processes PROCESSES 314s Number of processes. Default: 1 314s 314s FAST5 Data Arguments: 314s --corrected-group CORRECTED_GROUP 314s FAST5 group created by resquiggle command. Default: 314s RawGenomeCorrected_000 314s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 314s FAST5 subgroup(s) (under /Analyses/[--basecall- 314s group]/) containing basecalls and created within 314s [--corrected-group] containing re-squiggle results. 314s Default: ['BaseCalled_template'] 314s 314s Miscellaneous Arguments: 314s --quiet, -q Don't print status information. 314s --help, -h Print this help message and exit 314s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 314s FAST5_BASEDIRS 314s [FAST5_BASEDIRS ...] 314s --statistics-file-basename 314s STATISTICS_FILE_BASENAME 314s --alternate-fast5-basedirs 314s ALTERNATE_FAST5_BASEDIRS 314s [ALTERNATE_FAST5_BASEDIRS ...] 314s [--fishers-method-context FISHERS_METHOD_CONTEXT] 314s [--minimum-test-reads MINIMUM_TEST_READS] 314s [--statistic-type {ks,u,t}] 314s [--store-p-value] 314s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 314s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 314s [--processes PROCESSES] 314s [--corrected-group CORRECTED_GROUP] 314s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 314s [--quiet] [--help] 314s 314s Required Argument: 314s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 314s Directories containing fast5 files. 314s --statistics-file-basename STATISTICS_FILE_BASENAME 314s File base name to save base by base statistics from 314s testing. Filenames will be [--statistics-file- 314s basename].[--alternate-bases]?.tombo.stats 314s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 314s Set of directories containing fast5 files for 314s alternate set of reads. 314s 314s Significance Test Arguments: 314s --fishers-method-context FISHERS_METHOD_CONTEXT 314s Number of context bases up and downstream over which 314s to compute Fisher's method combined p-values. Note: 314s Not applicable for alternative model likelihood ratio 314s tests. Default: 1. 314s --minimum-test-reads MINIMUM_TEST_READS 314s Number of reads required at a position to perform 314s significance testing or contribute to model 314s estimation. Default: 50 314s --statistic-type {ks,u,t} 314s Type of statistical test to apply. Default: "ks" 314s --store-p-value Store p-value instead of effect-size statistic. 314s Statistics are D-statistic (KS-test), deviation from 314s even common language effect size (u-test), and Cohen's 314s D (t-test). 314s 314s Output Argument: 314s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 314s Number of the most significant sites to store for 314s faster access. If a longer list of most significant 314s sites is required the list must be re-computed from 314s all batches. Very large values can increase RAM usage. 314s Default: 100000 314s 314s Multiprocessing Arguments: 314s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 314s Size of regions over which to multiprocesses statistic 314s computation. For very deep samples a smaller value is 314s recommmended in order to control memory consumption. 314s Default: 10000 314s --processes PROCESSES 314s Number of processes. Default: 1 314s 314s FAST5 Data Arguments: 314s --corrected-group CORRECTED_GROUP 314s FAST5 group created by resquiggle command. Default: 314s RawGenomeCorrected_000 314s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 314s FAST5 subgroup(s) (under /Analyses/[--basecall- 314s group]/) containing basecalls and created within 314s [--corrected-group] containing re-squiggle results. 314s Default: ['BaseCalled_template'] 314s 314s Miscellaneous Arguments: 314s --quiet, -q Don't print status information. 314s --help, -h Print this help message and exit 314s usage: tombo detect_modifications aggregate_per_read_stats 314s --per-read-statistics-filename 314s PER_READ_STATISTICS_FILENAME 314s --statistics-filename 314s STATISTICS_FILENAME 314s --single-read-threshold 314s SINGLE_READ_THRESHOLD 314s [SINGLE_READ_THRESHOLD ...] 314s [--minimum-test-reads MINIMUM_TEST_READS] 314s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 314s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 314s [--processes PROCESSES] 314s [--corrected-group CORRECTED_GROUP] 314s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 314s [--quiet] [--help] 314s 314s Required Argument: 314s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 314s Binary file containing per-read statistics from 314s statistical testing. 314s --statistics-filename STATISTICS_FILENAME 314s File to save/load genomic base anchored statistics. 314s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 314s P-value or log likelihood ratio threshold when 314s computing fraction of significant reads at each 314s genomic position. If two values are provided, 314s statistics between these values are not considered. 314s 314s Significance Test Arguments: 314s --minimum-test-reads MINIMUM_TEST_READS 314s Number of reads required at a position to perform 314s significance testing or contribute to model 314s estimation. Default: 1 314s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 314s Dampen fraction modified estimates for low coverage 314s sites. Two parameters are unmodified and modified 314s pseudo read counts. This is equivalent to a beta prior 314s on the fraction estimate. Set to "0 0" to disable 314s dampened fraction estimation. Default: [2, 0] 314s 314s Output Argument: 314s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 314s Number of the most significant sites to store for 314s faster access. If a longer list of most significant 314s sites is required the list must be re-computed from 314s all batches. Very large values can increase RAM usage. 314s Default: 100000 314s 314s Multiprocessing Arguments: 314s --processes PROCESSES 314s Number of processes. Default: 1 314s 314s FAST5 Data Arguments: 314s --corrected-group CORRECTED_GROUP 314s FAST5 group created by resquiggle command. Default: 314s RawGenomeCorrected_000 314s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 314s FAST5 subgroup(s) (under /Analyses/[--basecall- 314s group]/) containing basecalls and created within 314s [--corrected-group] containing re-squiggle results. 314s Default: ['BaseCalled_template'] 314s 314s Miscellaneous Arguments: 314s --quiet, -q Don't print status information. 314s --help, -h Print this help message and exit 314s usage: tombo text_output browser_files 314s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 314s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 314s [--statistics-filename STATISTICS_FILENAME] 314s [--genome-fasta GENOME_FASTA] 314s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 314s [--browser-file-basename BROWSER_FILE_BASENAME] 314s [--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} ...]] 314s [--corrected-group CORRECTED_GROUP] 314s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 314s [--quiet] [--help] 314s 314s Data Arguments: 314s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 314s Directories containing fast5 files. 314s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 314s Set of directories containing fast5 files for control 314s reads, containing only canonical nucleotides. 314s --statistics-filename STATISTICS_FILENAME 314s File to save/load genomic base anchored statistics. 314s 314s Statistic Motif Filter Arguments: 314s --genome-fasta GENOME_FASTA 314s FASTA file used to re-squiggle. For faster sequence 314s access. 314s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 314s Ground truth, motif centered, modified base 314s descriptions for output filtering. Format descriptions 314s as: "motif:mod_pos:name". The mod_pos indicates the 314s modified base within the motif (1-based index). 314s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 314s output for identification of E. coli dam and dcm 314s methylation. 314s 314s Output Arguments: 314s --browser-file-basename BROWSER_FILE_BASENAME 314s Basename for output browser files. Two files (plus and 314s minus strand) will be produced for each --file-types 314s supplied. Filenames formatted as "[browser-file- 314s basename].[file- 314s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 314s Default: tombo_results 314s --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} ...] 314s Data types of genome browser files to produce. 314s Produced coverage files are in bedGraph format, while 314s all other file types will be in wiggle format 314s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 314s Default: "coverage" 314s 314s FAST5 Data Arguments: 314s --corrected-group CORRECTED_GROUP 314s FAST5 group created by resquiggle command. Default: 314s RawGenomeCorrected_000 314s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 314s FAST5 subgroup(s) (under /Analyses/[--basecall- 314s group]/) containing basecalls and created within 314s [--corrected-group] containing re-squiggle results. 314s Default: ['BaseCalled_template'] 314s 314s Miscellaneous Arguments: 314s --quiet, -q Don't print status information. 314s --help, -h Print this help message and exit 314s usage: tombo text_output signif_sequence_context --statistics-filename 314s STATISTICS_FILENAME 314s [--genome-fasta GENOME_FASTA] 314s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 314s [--num-regions NUM_REGIONS] 314s [--num-bases NUM_BASES] 314s [--sequences-filename SEQUENCES_FILENAME] 314s [--corrected-group CORRECTED_GROUP] 314s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 314s [--quiet] [--help] 314s 314s Required Argument: 314s --statistics-filename STATISTICS_FILENAME 314s File to save/load genomic base anchored statistics. 314s 314s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 314s --genome-fasta GENOME_FASTA 314s FASTA file used to re-squiggle. For faster sequence 314s access. 314s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 314s Directories containing fast5 files. 314s 314s Region Selection Arguments: 314s --num-regions NUM_REGIONS 314s Number of regions to plot. Default: 100 314s --num-bases NUM_BASES 314s Number of bases to plot/output. Default: 15 314s 314s Output Arguments: 314s --sequences-filename SEQUENCES_FILENAME 314s File for sequences from selected regions. Sequences 314s will be stored in FASTA format. Default: 314s tombo_results.significant_regions.fasta. 314s 314s FAST5 Data Arguments: 314s --corrected-group CORRECTED_GROUP 314s FAST5 group created by resquiggle command. Default: 314s RawGenomeCorrected_000 314s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 314s FAST5 subgroup(s) (under /Analyses/[--basecall- 314s group]/) containing basecalls and created within 314s [--corrected-group] containing re-squiggle results. 314s Default: ['BaseCalled_template'] 314s 314s Miscellaneous Arguments: 314s --quiet, -q Don't print status information. 314s --help, -h Print this help message and exit 314s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 314s [FAST5_BASEDIRS ...] 314s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 314s [--plot-standard-model] 314s [--plot-alternate-model {dcm,CpG,5mC,6mA,dam}] 314s [--overplot-threshold OVERPLOT_THRESHOLD] 314s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 314s [--num-regions NUM_REGIONS] 314s [--num-bases NUM_BASES] 314s [--pdf-filename PDF_FILENAME] 314s [--corrected-group CORRECTED_GROUP] 314s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 314s [--quiet] [--help] 314s 314s Required Argument: 314s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 314s Directories containing fast5 files. 314s 314s Comparison Arguments: 314s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 314s Set of directories containing fast5 files for control 314s reads, containing only canonical nucleotides. 314s --plot-standard-model 314s Add default standard model distribution to the plot. 314s --plot-alternate-model {dcm,CpG,5mC,6mA,dam} 314s Add alternative model distribution to the plot. 314s 314s Overplotting Arguments: 314s --overplot-threshold OVERPLOT_THRESHOLD 314s Coverage level to trigger alternative plot type 314s instead of raw signal. Default: 50 314s --overplot-type {Downsample,Boxplot,Quantile,Density} 314s Plot type for regions with higher coverage. Default: 314s Downsample 314s 314s Plotting Region Arguments: 314s --num-regions NUM_REGIONS 314s Number of regions to plot. Default: 10 314s --num-bases NUM_BASES 314s Number of bases to plot/output. Default: 21 314s 314s Output Argument: 314s --pdf-filename PDF_FILENAME 314s PDF filename to store plot(s). Default: 314s tombo_results.max_coverage.pdf 314s 314s FAST5 Data Arguments: 314s --corrected-group CORRECTED_GROUP 314s FAST5 group created by resquiggle command. Default: 314s RawGenomeCorrected_000 314s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 314s FAST5 subgroup(s) (under /Analyses/[--basecall- 314s group]/) containing basecalls and created within 314s [--corrected-group] containing re-squiggle results. 314s Default: ['BaseCalled_template'] 314s 314s Miscellaneous Arguments: 314s --quiet, -q Don't print status information. 314s --help, -h Print this help message and exit 314s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 314s [FAST5_BASEDIRS ...] --genome-locations 314s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 314s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 314s [--plot-standard-model] 314s [--plot-alternate-model {CpG,dam,6mA,dcm,5mC}] 314s [--overplot-threshold OVERPLOT_THRESHOLD] 314s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 314s [--num-bases NUM_BASES] 314s [--pdf-filename PDF_FILENAME] 314s [--corrected-group CORRECTED_GROUP] 314s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 314s [--quiet] [--help] 314s 314s Required Arguments: 314s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 314s Directories containing fast5 files. 314s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 314s Genomic locations at which to plot signal. Format 314s locations as "chrm:position[:strand] 314s [chrm2:position2[:strand2] ...]" (strand not 314s applicable for all applications) 314s 314s Comparison Arguments: 314s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 314s Set of directories containing fast5 files for control 314s reads, containing only canonical nucleotides. 314s --plot-standard-model 314s Add default standard model distribution to the plot. 314s --plot-alternate-model {CpG,dam,6mA,dcm,5mC} 314s Add alternative model distribution to the plot. 314s 314s Overplotting Arguments: 314s --overplot-threshold OVERPLOT_THRESHOLD 314s Coverage level to trigger alternative plot type 314s instead of raw signal. Default: 50 314s --overplot-type {Downsample,Boxplot,Quantile,Density} 314s Plot type for regions with higher coverage. Default: 314s Downsample 314s 314s Plotting Region Argument: 314s --num-bases NUM_BASES 314s Number of bases to plot/output. Default: 21 314s 314s Output Argument: 314s --pdf-filename PDF_FILENAME 314s PDF filename to store plot(s). Default: 314s tombo_results.genome_locations.pdf 314s 314s FAST5 Data Arguments: 314s --corrected-group CORRECTED_GROUP 314s FAST5 group created by resquiggle command. Default: 314s RawGenomeCorrected_000 314s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 314s FAST5 subgroup(s) (under /Analyses/[--basecall- 314s group]/) containing basecalls and created within 314s [--corrected-group] containing re-squiggle results. 314s Default: ['BaseCalled_template'] 314s 314s Miscellaneous Arguments: 314s --quiet, -q Don't print status information. 314s --help, -h Print this help message and exit 314s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 314s [FAST5_BASEDIRS ...] --motif MOTIF 314s --genome-fasta GENOME_FASTA 314s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 314s [--plot-standard-model] 314s [--plot-alternate-model {5mC,dam,CpG,6mA,dcm}] 314s [--overplot-threshold OVERPLOT_THRESHOLD] 314s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 314s [--num-regions NUM_REGIONS] 314s [--num-bases NUM_BASES] [--deepest-coverage] 314s [--pdf-filename PDF_FILENAME] 314s [--corrected-group CORRECTED_GROUP] 314s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 314s [--quiet] [--help] 314s 314s Required Arguments: 314s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 314s Directories containing fast5 files. 314s --motif MOTIF Motif of interest at which to plot signal and 314s statsitics. Supports IUPAC single letter codes (use T 314s for RNA). 314s --genome-fasta GENOME_FASTA 314s FASTA file used to re-squiggle. For faster sequence 314s access. 314s 314s Comparison Arguments: 314s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 314s Set of directories containing fast5 files for control 314s reads, containing only canonical nucleotides. 314s --plot-standard-model 314s Add default standard model distribution to the plot. 314s --plot-alternate-model {5mC,dam,CpG,6mA,dcm} 314s Add alternative model distribution to the plot. 314s 314s Overplotting Arguments: 314s --overplot-threshold OVERPLOT_THRESHOLD 314s Coverage level to trigger alternative plot type 314s instead of raw signal. Default: 50 314s --overplot-type {Downsample,Boxplot,Quantile,Density} 314s Plot type for regions with higher coverage. Default: 314s Downsample 314s 314s Plotting Region Arguments: 314s --num-regions NUM_REGIONS 314s Number of regions to plot. Default: 10 314s --num-bases NUM_BASES 314s Number of bases to plot/output. Default: 21 314s --deepest-coverage Plot the deepest coverage regions. 314s 314s Output Argument: 314s --pdf-filename PDF_FILENAME 314s PDF filename to store plot(s). Default: 314s tombo_results.motif_centered.pdf 314s 314s FAST5 Data Arguments: 314s --corrected-group CORRECTED_GROUP 314s FAST5 group created by resquiggle command. Default: 314s RawGenomeCorrected_000 314s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 314s FAST5 subgroup(s) (under /Analyses/[--basecall- 314s group]/) containing basecalls and created within 314s [--corrected-group] containing re-squiggle results. 314s Default: ['BaseCalled_template'] 314s 314s Miscellaneous Arguments: 314s --quiet, -q Don't print status information. 314s --help, -h Print this help message and exit 314s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 314s [FAST5_BASEDIRS ...] --control-fast5-basedirs 314s CONTROL_FAST5_BASEDIRS 314s [CONTROL_FAST5_BASEDIRS ...] 314s [--overplot-threshold OVERPLOT_THRESHOLD] 314s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 314s [--num-regions NUM_REGIONS] 314s [--num-bases NUM_BASES] 314s [--pdf-filename PDF_FILENAME] 314s [--sequences-filename SEQUENCES_FILENAME] 314s [--corrected-group CORRECTED_GROUP] 314s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 314s [--quiet] [--help] 314s 314s Required Arguments: 314s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 314s Directories containing fast5 files. 314s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 314s Set of directories containing fast5 files for control 314s reads, containing only canonical nucleotides. 314s 314s Overplotting Arguments: 314s --overplot-threshold OVERPLOT_THRESHOLD 314s Coverage level to trigger alternative plot type 314s instead of raw signal. Default: 50 314s --overplot-type {Downsample,Boxplot,Quantile,Density} 314s Plot type for regions with higher coverage. Default: 314s Downsample 314s 314s Plotting Region Arguments: 314s --num-regions NUM_REGIONS 314s Number of regions to plot. Default: 10 314s --num-bases NUM_BASES 314s Number of bases to plot/output. Default: 21 314s 314s Output Arguments: 314s --pdf-filename PDF_FILENAME 314s PDF filename to store plot(s). Default: 314s tombo_results.max_difference.pdf 314s --sequences-filename SEQUENCES_FILENAME 314s File for sequences from selected regions. Sequences 314s will be stored in FASTA format. Default: None. 314s 314s FAST5 Data Arguments: 314s --corrected-group CORRECTED_GROUP 314s FAST5 group created by resquiggle command. Default: 314s RawGenomeCorrected_000 314s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 314s FAST5 subgroup(s) (under /Analyses/[--basecall- 314s group]/) containing basecalls and created within 314s [--corrected-group] containing re-squiggle results. 314s Default: ['BaseCalled_template'] 314s 314s Miscellaneous Arguments: 314s --quiet, -q Don't print status information. 314s --help, -h Print this help message and exit 314s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 314s [FAST5_BASEDIRS ...] --statistics-filename 314s STATISTICS_FILENAME 314s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 314s [--plot-standard-model] 314s [--plot-alternate-model {5mC,dcm,6mA,CpG,dam}] 314s [--overplot-threshold OVERPLOT_THRESHOLD] 314s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 314s [--num-regions NUM_REGIONS] 314s [--num-bases NUM_BASES] 314s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 314s [--pdf-filename PDF_FILENAME] 314s [--sequences-filename SEQUENCES_FILENAME] 314s [--corrected-group CORRECTED_GROUP] 314s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 314s [--quiet] [--help] 314s 314s Required Arguments: 314s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 314s Directories containing fast5 files. 314s --statistics-filename STATISTICS_FILENAME 314s File to save/load genomic base anchored statistics. 314s 314s Comparison Arguments: 314s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 314s Set of directories containing fast5 files for control 314s reads, containing only canonical nucleotides. 314s --plot-standard-model 314s Add default standard model distribution to the plot. 314s --plot-alternate-model {5mC,dcm,6mA,CpG,dam} 314s Add alternative model distribution to the plot. 314s 314s Overplotting Arguments: 314s --overplot-threshold OVERPLOT_THRESHOLD 314s Coverage level to trigger alternative plot type 314s instead of raw signal. Default: 50 314s --overplot-type {Downsample,Boxplot,Quantile,Density} 314s Plot type for regions with higher coverage. Default: 314s Downsample 314s 314s Plotting Region Arguments: 314s --num-regions NUM_REGIONS 314s Number of regions to plot. Default: 10 314s --num-bases NUM_BASES 314s Number of bases to plot/output. Default: 21 314s 314s Statistical Argument: 314s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 314s Dampen fraction modified estimates for low coverage 314s sites. Two parameters are unmodified and modified 314s pseudo read counts. This is equivalent to a beta prior 314s on the fraction estimate. Set to "0 0" to disable 314s dampened fraction estimation. Default: [2, 0] 314s 314s Output Arguments: 314s --pdf-filename PDF_FILENAME 314s PDF filename to store plot(s). Default: 314s tombo_results.significant_difference.pdf 314s --sequences-filename SEQUENCES_FILENAME 314s File for sequences from selected regions. Sequences 314s will be stored in FASTA format. Default: None. 314s 314s FAST5 Data Arguments: 314s --corrected-group CORRECTED_GROUP 314s FAST5 group created by resquiggle command. Default: 314s RawGenomeCorrected_000 314s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 314s FAST5 subgroup(s) (under /Analyses/[--basecall- 314s group]/) containing basecalls and created within 314s [--corrected-group] containing re-squiggle results. 314s Default: ['BaseCalled_template'] 314s 314s Miscellaneous Arguments: 314s --quiet, -q Don't print status information. 314s --help, -h Print this help message and exit 315s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 315s [FAST5_BASEDIRS ...] --motif MOTIF 315s --statistics-filename STATISTICS_FILENAME 315s --genome-fasta GENOME_FASTA 315s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 315s [--plot-standard-model] 315s [--plot-alternate-model {dam,6mA,CpG,5mC,dcm}] 315s [--overplot-threshold OVERPLOT_THRESHOLD] 315s [--num-regions NUM_REGIONS] 315s [--num-context NUM_CONTEXT] 315s [--num-statistics NUM_STATISTICS] 315s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 315s [--pdf-filename PDF_FILENAME] 315s [--corrected-group CORRECTED_GROUP] 315s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 315s [--quiet] [--help] 315s 315s Required Arguments: 315s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 315s Directories containing fast5 files. 315s --motif MOTIF Motif of interest at which to plot signal and 315s statsitics. Supports IUPAC single letter codes (use T 315s for RNA). 315s --statistics-filename STATISTICS_FILENAME 315s File to save/load genomic base anchored statistics. 315s --genome-fasta GENOME_FASTA 315s FASTA file used to re-squiggle. For faster sequence 315s access. 315s 315s Comparison Arguments: 315s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 315s Set of directories containing fast5 files for control 315s reads, containing only canonical nucleotides. 315s --plot-standard-model 315s Add default standard model distribution to the plot. 315s --plot-alternate-model {dam,6mA,CpG,5mC,dcm} 315s Add alternative model distribution to the plot. 315s 315s Overplotting Argument: 315s --overplot-threshold OVERPLOT_THRESHOLD 315s Coverage level to trigger alternative plot type 315s instead of raw signal. Default: 50 315s 315s Plotting Region Arguments: 315s --num-regions NUM_REGIONS 315s Number of regions to plot. Default: 3 315s --num-context NUM_CONTEXT 315s Number of context bases around motif. Default: 5 315s --num-statistics NUM_STATISTICS 315s Number of motif centered regions to include in 315s statistic distributions. Default: 200 315s 315s Statistical Argument: 315s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 315s Dampen fraction modified estimates for low coverage 315s sites. Two parameters are unmodified and modified 315s pseudo read counts. This is equivalent to a beta prior 315s on the fraction estimate. Set to "0 0" to disable 315s dampened fraction estimation. Default: [2, 0] 315s 315s Output Argument: 315s --pdf-filename PDF_FILENAME 315s PDF filename to store plot(s). Default: 315s tombo_results.motif_statistics.pdf 315s 315s FAST5 Data Arguments: 315s --corrected-group CORRECTED_GROUP 315s FAST5 group created by resquiggle command. Default: 315s RawGenomeCorrected_000 315s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 315s FAST5 subgroup(s) (under /Analyses/[--basecall- 315s group]/) containing basecalls and created within 315s [--corrected-group] containing re-squiggle results. 315s Default: ['BaseCalled_template'] 315s 315s Miscellaneous Arguments: 315s --quiet, -q Don't print status information. 315s --help, -h Print this help message and exit 315s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 315s [GENOME_LOCATIONS ...] 315s --per-read-statistics-filename 315s PER_READ_STATISTICS_FILENAME 315s [--genome-fasta GENOME_FASTA] 315s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 315s [--num-reads NUM_READS] [--num-bases NUM_BASES] 315s [--box-center] [--pdf-filename PDF_FILENAME] 315s [--corrected-group CORRECTED_GROUP] 315s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 315s [--quiet] [--help] 315s 315s Required Arguments: 315s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 315s Genomic locations at which to plot signal. Format 315s locations as "chrm:position[:strand] 315s [chrm2:position2[:strand2] ...]" (strand not 315s applicable for all applications) 315s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 315s Binary file containing per-read statistics from 315s statistical testing. 315s 315s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 315s --genome-fasta GENOME_FASTA 315s FASTA file used to re-squiggle. For faster sequence 315s access. 315s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 315s Directories containing fast5 files. 315s 315s Plotting Region Arguments: 315s --num-reads NUM_READS 315s Number of reads to plot. Default: 100 315s --num-bases NUM_BASES 315s Number of bases to plot/output. Default: 51 315s --box-center Plot a box around the central base. 315s 315s Output Argument: 315s --pdf-filename PDF_FILENAME 315s PDF filename to store plot(s). Default: 315s tombo_results.per_read_stats.pdf 315s 315s FAST5 Data Arguments: 315s --corrected-group CORRECTED_GROUP 315s FAST5 group created by resquiggle command. Default: 315s RawGenomeCorrected_000 315s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 315s FAST5 subgroup(s) (under /Analyses/[--basecall- 315s group]/) containing basecalls and created within 315s [--corrected-group] containing re-squiggle results. 315s Default: ['BaseCalled_template'] 315s 315s Miscellaneous Arguments: 315s --quiet, -q Don't print status information. 315s --help, -h Print this help message and exit 315s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 315s [STATISTICS_FILENAMES ...] 315s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 315s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 315s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 315s [--genome-fasta GENOME_FASTA] 315s [--pdf-filename PDF_FILENAME] 315s [--statistics-per-block STATISTICS_PER_BLOCK] 315s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 315s [--quiet] [--help] 315s 315s Required Argument: 315s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 315s Files to load genomic base anchored statistics. 315s 315s Ground Truth Arguments (provide bed files or motifs): 315s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 315s Modification description and bed format files 315s containing single base locations of ground truth 315s modified sites. Bed files should contain 6 fields 315s including strand. Format descriptions as 315s "mod_name:locs.bed". Example: "CpG 315s bisulfite":bisulfite_locs.bed 315s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 315s Bed format files containing single base locations of 315s ground truth unmodified sites. Bed files should 315s contain 6 fields including strand. 315s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 315s Ground truth, motif centered, modified base 315s descriptions for computing ROC and PR curves. Each 315s statistics file is associated with a set of motif 315s descriptions. Format descriptions as: 315s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 315s mod_pos indicates the alternate-base within the motif 315s (1-based index). Example: CCWGG:2:"dcm 315s 5mC"::GATC:2:"dam 6mA" would assess the performance of 315s a single Tombo statistics file for identification of 315s E. coli dam and dcm methylation. 315s --genome-fasta GENOME_FASTA 315s FASTA file used to re-squiggle. For faster sequence 315s access. 315s 315s Output Arguments: 315s --pdf-filename PDF_FILENAME 315s PDF filename to store plot(s). Default: 315s tombo_results.roc.pdf 315s 315s Down-sampling Arguments: 315s --statistics-per-block STATISTICS_PER_BLOCK 315s Number of randomly selected per-read, per-base 315s statistics to extract from each genomic block for 315s plotting. Default: Include all stats 315s --total-statistics-limit TOTAL_STATISTICS_LIMIT 315s Total per-read statistics to be extracted for 315s plotting. Avoids memory overflow for large runs. 315s Default: 5000000 315s 315s Miscellaneous Arguments: 315s --quiet, -q Don't print status information. 315s --help, -h Print this help message and exit 315s usage: tombo plot per_read_roc --per-read-statistics-filenames 315s PER_READ_STATISTICS_FILENAMES 315s [PER_READ_STATISTICS_FILENAMES ...] 315s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 315s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 315s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 315s [--genome-fasta GENOME_FASTA] 315s [--statistics-per-block STATISTICS_PER_BLOCK] 315s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 315s [--pdf-filename PDF_FILENAME] [--quiet] 315s [--help] 315s 315s Required Argument: 315s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 315s Binary files containing per-read statistics from 315s statistical testing. 315s 315s Ground Truth Arguments (provide bed files or motifs): 315s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 315s Modification description and bed format files 315s containing single base locations of ground truth 315s modified sites. Bed files should contain 6 fields 315s including strand. Format descriptions as 315s "mod_name:locs.bed". Example: "CpG 315s bisulfite":bisulfite_locs.bed 315s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 315s Bed format files containing single base locations of 315s ground truth unmodified sites. Bed files should 315s contain 6 fields including strand. 315s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 315s Ground truth, motif centered, modified base 315s descriptions for computing ROC and PR curves. Each 315s statistics file is associated with a set of motif 315s descriptions. Format descriptions as: 315s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 315s mod_pos indicates the alternate-base within the motif 315s (1-based index). Example: CCWGG:2:"dcm 315s 5mC"::GATC:2:"dam 6mA" would assess the performance of 315s a single Tombo statistics file for identification of 315s E. coli dam and dcm methylation. 315s --genome-fasta GENOME_FASTA 315s FASTA file used to re-squiggle. For faster sequence 315s access. 315s 315s Down-sampling Arguments: 315s --statistics-per-block STATISTICS_PER_BLOCK 315s Number of randomly selected per-read, per-base 315s statistics to extract from each genomic block for 315s plotting. Default: 100000 315s --total-statistics-limit TOTAL_STATISTICS_LIMIT 315s Total per-read statistics to be extracted for 315s plotting. Avoids memory overflow for large runs. 315s Default: 5000000 315s 315s Output Arguments: 315s --pdf-filename PDF_FILENAME 315s PDF filename to store plot(s). Default: 315s tombo_results.per_reads_roc.pdf 315s 315s Miscellaneous Arguments: 315s --quiet, -q Don't print status information. 315s --help, -h Print this help message and exit 315s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 315s [--upstream-bases {0,1,2,3,4}] 315s [--downstream-bases {0,1,2,3,4}] [--read-mean] 315s [--num-kmer-threshold NUM_KMER_THRESHOLD] 315s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 315s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 315s [--corrected-group CORRECTED_GROUP] 315s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 315s [--quiet] [--help] 315s 315s Required Argument: 315s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 315s Directories containing fast5 files. 315s 315s Data Processing Arguments: 315s --upstream-bases {0,1,2,3,4} 315s Upstream bases in k-mer. Default: 1 315s --downstream-bases {0,1,2,3,4} 315s Downstream bases in k-mer. Default: 2 315s --read-mean Plot k-mer means across whole reads as opposed to 315s individual k-mer event levels. 315s --num-kmer-threshold NUM_KMER_THRESHOLD 315s Observations of each k-mer required to include a read 315s in read level averages. Default: 1 315s 315s Plotting Region Arguments: 315s --num-reads NUM_READS 315s Number of reads to plot. Default: 100 315s 315s Output Arguments: 315s --pdf-filename PDF_FILENAME 315s PDF filename to store plot(s). Default: 315s tombo_results.kmer_distribution.pdf 315s --r-data-filename R_DATA_FILENAME 315s Filename to save R data structure. Default: Don't save 315s --dont-plot Don't plot result. Useful to produce only R data file. 315s 315s FAST5 Data Arguments: 315s --corrected-group CORRECTED_GROUP 315s FAST5 group created by resquiggle command. Default: 315s RawGenomeCorrected_000 315s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 315s FAST5 subgroup(s) (under /Analyses/[--basecall- 315s group]/) containing basecalls and created within 315s [--corrected-group] containing re-squiggle results. 315s Default: ['BaseCalled_template'] 315s 315s Miscellaneous Arguments: 315s --quiet, -q Don't print status information. 315s --help, -h Print this help message and exit 315s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 315s [FAST5_BASEDIRS ...] 315s --control-fast5-basedirs 315s CONTROL_FAST5_BASEDIRS 315s [CONTROL_FAST5_BASEDIRS ...] 315s --statistics-filename 315s STATISTICS_FILENAME 315s [--genome-fasta GENOME_FASTA] 315s [--processes PROCESSES] 315s [--num-regions NUM_REGIONS] 315s [--num-bases NUM_BASES] 315s [--slide-span SLIDE_SPAN] 315s [--pdf-filename PDF_FILENAME] 315s [--r-data-filename R_DATA_FILENAME] 315s [--corrected-group CORRECTED_GROUP] 315s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 315s [--quiet] [--help] 315s 315s Required Arguments: 315s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 315s Directories containing fast5 files. 315s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 315s Set of directories containing fast5 files for control 315s reads, containing only canonical nucleotides. 315s --statistics-filename STATISTICS_FILENAME 315s File to save/load genomic base anchored statistics. 315s 315s FASTA Sequence Argument: 315s --genome-fasta GENOME_FASTA 315s FASTA file used to re-squiggle. For faster sequence 315s access. 315s 315s Multiprocessing Argument: 315s --processes PROCESSES 315s Number of processes. Default: 1 315s 315s Plotting Region Arguments: 315s --num-regions NUM_REGIONS 315s Number of regions to plot. Default: 10 315s --num-bases NUM_BASES 315s Number of bases to plot/output. Default: 21 315s --slide-span SLIDE_SPAN 315s Number of bases offset over which to search when 315s computing distances for signal cluster plotting. 315s Default: 0 (exact position) 315s 315s Output Arguments: 315s --pdf-filename PDF_FILENAME 315s PDF filename to store plot(s). Default: 315s tombo_results.signal_clusters.pdf 315s --r-data-filename R_DATA_FILENAME 315s Filename to save R data structure. Default: Don't save 315s 315s FAST5 Data Arguments: 315s --corrected-group CORRECTED_GROUP 315s FAST5 group created by resquiggle command. Default: 315s RawGenomeCorrected_000 315s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 315s FAST5 subgroup(s) (under /Analyses/[--basecall- 315s group]/) containing basecalls and created within 315s [--corrected-group] containing re-squiggle results. 315s Default: ['BaseCalled_template'] 315s 315s Miscellaneous Arguments: 315s --quiet, -q Don't print status information. 315s --help, -h Print this help message and exit 315s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 315s 315s Required Arguments: 315s fast5s_basedir Directory containing fast5 files. All files ending in 315s "fast5" found recursively within this base directory will be 315s processed. 315s 315s Miscellaneous Arguments: 315s --quiet, -q Don't print status information. 315s --help, -h Print this help message and exit 315s usage: tombo build_model event_resquiggle 315s [--minimap2-executable MINIMAP2_EXECUTABLE] 315s [--minimap2-index MINIMAP2_INDEX] 315s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 315s [--graphmap-executable GRAPHMAP_EXECUTABLE] 315s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 315s [--normalization-type {median,pA,pA_raw,none}] 315s [--pore-model-filename PORE_MODEL_FILENAME] 315s [--outlier-threshold OUTLIER_THRESHOLD] 315s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 315s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 315s [--timeout TIMEOUT] 315s [--cpts-limit CPTS_LIMIT] 315s [--skip-index] [--overwrite] 315s [--failed-reads-filename FAILED_READS_FILENAME] 315s [--include-event-stdev] 315s [--corrected-group CORRECTED_GROUP] 315s [--basecall-group BASECALL_GROUP] 315s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 315s [--processes PROCESSES] 315s [--align-processes ALIGN_PROCESSES] 315s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 315s [--resquiggle-processes RESQUIGGLE_PROCESSES] 315s [--quiet] [--help] 315s fast5s_basedir reference_fasta 315s 315s Required Arguments: 315s fast5s_basedir Directory containing fast5 files. All files ending in 315s "fast5" found recursively within this base directory 315s will be processed. 315s reference_fasta Reference genome/transcriptome FASTA file for mapping. 315s 315s Mapper Arguments (One mapper is required): 315s --minimap2-executable MINIMAP2_EXECUTABLE 315s Path to minimap2 executable. 315s --minimap2-index MINIMAP2_INDEX 315s Path to minimap2 index (with map-ont preset) file 315s corresponding to the [genome_fasta] provided. 315s --bwa-mem-executable BWA_MEM_EXECUTABLE 315s Path to bwa-mem executable. 315s --graphmap-executable GRAPHMAP_EXECUTABLE 315s Path to graphmap executable. 315s --alignment-batch-size ALIGNMENT_BATCH_SIZE 315s Number of reads included in each alignment call. Note: 315s A new system mapping call is made for each batch 315s (including loading of the genome), so it is advised to 315s use larger values for larger genomes. Default: 1000 315s 315s Signal Processing Arguments: 315s --normalization-type {median,pA,pA_raw,none} 315s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 315s as in the ONT events (using offset, range and 315s digitization), "pA": k-mer-based correction for pA 315s drift as in nanopolish (requires [--pore-model- 315s filename]), "median": median and MAD from raw signal. 315s Default: median 315s --pore-model-filename PORE_MODEL_FILENAME 315s File containing kmer model parameters (level_mean and 315s level_stdv) used in order to compute kmer-based 315s corrected pA values. E.g. https://github.com/jts/nanop 315s olish/blob/master/etc/r9- 315s models/template_median68pA.5mers.model 315s --outlier-threshold OUTLIER_THRESHOLD 315s Windosrize the signal at this number of scale values. 315s Negative value disables outlier clipping. Default: 315s 5.000000 315s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 315s Specify the 2 parameters for segmentation 1) running 315s neighboring windows width 2) minimum raw observations 315s per genomic base. Sample type defaults: RNA : 12 6 || 315s DNA : 5 3 315s 315s Read Filtering Arguments: 315s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 315s Filter reads based on observations per base percentile 315s thresholds. Format thresholds as "percentile:thresh 315s [pctl2:thresh2 ...]". For example to filter reads with 315s 99th pctl > 200 obs/base or max > 5k obs/base use 315s "99:200 100:5000". 315s --timeout TIMEOUT Timeout in seconds for processing a single read. 315s Default: No timeout. 315s --cpts-limit CPTS_LIMIT 315s Maximum number of changepoints to find within a single 315s indel group. Default: No limit. 315s 315s Input/Output Arguments: 315s --skip-index Skip creation of tombo index. This drastically slows 315s downstream tombo commands. Default stores tombo index 315s named ".[--fast5-basedir].[--corrected- 315s group].tombo.index" to be loaded automatically for 315s downstream commands. 315s --overwrite Overwrite previous corrected group in FAST5 files. 315s Note: only effects --corrected-group or --new- 315s corrected-group. 315s --failed-reads-filename FAILED_READS_FILENAME 315s Output failed read filenames with assoicated error. 315s Default: Do not store failed reads. 315s --include-event-stdev 315s Include corrected event standard deviation in output 315s FAST5 data. 315s 315s FAST5 Data Arguments: 315s --corrected-group CORRECTED_GROUP 315s FAST5 group created by resquiggle command. Default: 315s RawGenomeCorrected_000 315s --basecall-group BASECALL_GROUP 315s FAST5 group obtain original basecalls (under Analyses 315s group). Default: Basecall_1D_000 315s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 315s FAST5 subgroup(s) (under /Analyses/[--basecall- 315s group]/) containing basecalls and created within 315s [--corrected-group] containing re-squiggle results. 315s Default: ['BaseCalled_template'] 315s 315s Multiprocessing Arguments: 315s --processes PROCESSES 315s Number of processes. Default: 2 315s --align-processes ALIGN_PROCESSES 315s Number of processes to use for parsing and aligning 315s original basecalls. Each process will independently 315s load the genome into memory, so use caution with 315s larger genomes (e.g. human). Default: 1 315s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 315s Number of threads to use for aligner system call. 315s Default: [--processes] / (2 * [--align-processes)] 315s --resquiggle-processes RESQUIGGLE_PROCESSES 315s Number of processes to use for resquiggle algorithm. 315s Default: [--processes] / 2 315s 315s Miscellaneous Arguments: 315s --quiet, -q Don't print status information. 315s --help, -h Print this help message and exit 315s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 315s [FAST5_BASEDIRS ...] 315s --tombo-model-filename 315s TOMBO_MODEL_FILENAME 315s [--estimate-mean] 315s [--kmer-specific-sd] 315s [--upstream-bases {0,1,2,3,4}] 315s [--downstream-bases {0,1,2,3,4}] 315s [--minimum-test-reads MINIMUM_TEST_READS] 315s [--coverage-threshold COVERAGE_THRESHOLD] 315s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 315s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 315s [--processes PROCESSES] 315s [--corrected-group CORRECTED_GROUP] 315s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 315s [--quiet] [--help] 315s 315s Required Arguments: 315s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 315s Directories containing fast5 files. 315s --tombo-model-filename TOMBO_MODEL_FILENAME 315s Filename to save Tombo model. 315s 315s Modeling Arguments: 315s --estimate-mean Use the mean instead of median for model level 315s estimation. Note: This can cause poor fits due to 315s outliers 315s --kmer-specific-sd Estimate standard deviation for each k-mers 315s individually. 315s --upstream-bases {0,1,2,3,4} 315s Upstream bases in k-mer. Default: 1 315s --downstream-bases {0,1,2,3,4} 315s Downstream bases in k-mer. Default: 2 315s 315s Filtering Arguments: 315s --minimum-test-reads MINIMUM_TEST_READS 315s Number of reads required at a position to perform 315s significance testing or contribute to model 315s estimation. Default: 10 315s --coverage-threshold COVERAGE_THRESHOLD 315s Maximum mean coverage per region when estimating k-mer 315s model (limits compute time for deep samples). Default: 315s 100 315s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 315s Number of each k-mer observations required in order to 315s produce a reference (genomic locations for standard 315s reference and per-read for alternative reference). 315s Default: 5 315s 315s Multiprocessing Arguments: 315s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 315s Size of regions over which to multiprocesses statistic 315s computation. For very deep samples a smaller value is 315s recommmended in order to control memory consumption. 315s Default: 10000 315s --processes PROCESSES 315s Number of processes. Default: 1 315s 315s FAST5 Data Arguments: 315s --corrected-group CORRECTED_GROUP 315s FAST5 group created by resquiggle command. Default: 315s RawGenomeCorrected_000 315s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 315s FAST5 subgroup(s) (under /Analyses/[--basecall- 315s group]/) containing basecalls and created within 315s [--corrected-group] containing re-squiggle results. 315s Default: ['BaseCalled_template'] 315s 315s Miscellaneous Arguments: 315s --quiet, -q Don't print status information. 315s --help, -h Print this help message and exit 315s usage: tombo build_model estimate_alt_reference --alternate-model-filename 315s ALTERNATE_MODEL_FILENAME 315s --alternate-model-name 315s ALTERNATE_MODEL_NAME 315s --alternate-model-base 315s {A,C,G,T} 315s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 315s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 315s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 315s [--control-density-filename CONTROL_DENSITY_FILENAME] 315s [--dna] [--rna] 315s [--tombo-model-filename TOMBO_MODEL_FILENAME] 315s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 315s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 315s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 315s [--save-density-basename SAVE_DENSITY_BASENAME] 315s [--processes PROCESSES] 315s [--corrected-group CORRECTED_GROUP] 315s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 315s [--quiet] [--help] 315s 315s Required Arguments: 315s --alternate-model-filename ALTERNATE_MODEL_FILENAME 315s Tombo model for alternative likelihood ratio 315s significance testing. 315s --alternate-model-name ALTERNATE_MODEL_NAME 315s A short name to associate with this alternate model 315s (e.g. 5mC, 6mA, etc.). This text will be included in 315s output filenames when this model is used for testing. 315s --alternate-model-base {A,C,G,T} 315s Non-standard base is an alternative to this base. 315s 315s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 315s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 315s Directories containing fast5 files. 315s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 315s Set of directories containing fast5 files for control 315s reads, containing only canonical nucleotides. 315s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 315s File containing k-mer level kernel density estimates 315s for the alternative sample saved using --save-density- 315s basename. 315s --control-density-filename CONTROL_DENSITY_FILENAME 315s File containing k-mer level kernel density estimates 315s for the control sample saved using --save-density- 315s basename. 315s 315s Standard Model Arguments: 315s --dna Explicitly select canonical DNA model. Default: 315s Automatically determine from FAST5s 315s --rna Explicitly select canonical RNA model. Default: 315s Automatically determine from FAST5s 315s --tombo-model-filename TOMBO_MODEL_FILENAME 315s Tombo model filename. If no file is provided, the 315s default DNA or RNA Tombo model will be used. 315s 315s Model Fitting Arguments: 315s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 315s When esitmating the alternative base incorporation 315s rate, this percent of k-mers are assumed to have 315s significantly shifted signal so the alternative 315s distribution minimally overlaps the standard base 315s distribution. Default: 5.000000 315s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 315s Bandwidth applied when performing Gaussian kernal 315s density esitmation on standard and alternative base 315s signal distributions. Default: 0.050000 315s 315s Filtering Argument: 315s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 315s Number of each k-mer observations required in order to 315s produce a reference (genomic locations for standard 315s reference and per-read for alternative reference). 315s Default: 1000 315s 315s Output Argument: 315s --save-density-basename SAVE_DENSITY_BASENAME 315s Basename to save alternative model estimation density 315s estimation information. See scripts/debug_est_alt.R 315s for info use example. Default: Don't save. 315s 315s Multiprocessing Arguments: 315s --processes PROCESSES 315s Number of processes. Default: 1 315s 315s FAST5 Data Arguments: 315s --corrected-group CORRECTED_GROUP 315s FAST5 group created by resquiggle command. Default: 315s RawGenomeCorrected_000 315s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 315s FAST5 subgroup(s) (under /Analyses/[--basecall- 315s group]/) containing basecalls and created within 315s [--corrected-group] containing re-squiggle results. 315s Default: ['BaseCalled_template'] 315s 315s Miscellaneous Arguments: 315s --quiet, -q Don't print status information. 315s --help, -h Print this help message and exit 315s This test only tests the help system 315s There is an extensive test in 315s 315s tombo/tests/shell_tests.sh 315s 315s but this requires to download larger data 315s sets which is not done for the moment. 316s autopkgtest [06:41:54]: test run-unit-test: -----------------------] 320s autopkgtest [06:41:58]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 320s run-unit-test PASS 324s autopkgtest [06:42:02]: @@@@@@@@@@@@@@@@@@@@ summary 324s run-unit-test PASS