0s autopkgtest [10:51:58]: starting date and time: 2024-10-30 10:51:58+0000 0s autopkgtest [10:51:58]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [10:51:58]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.h47hc5pp/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:setuptools --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=setuptools/75.2.0-1 -- lxd -r lxd-armhf-10.145.243.242 lxd-armhf-10.145.243.242:autopkgtest/ubuntu/plucky/armhf 55s autopkgtest [10:52:53]: testbed dpkg architecture: armhf 57s autopkgtest [10:52:55]: testbed apt version: 2.9.8 57s autopkgtest [10:52:55]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 66s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [30.5 kB] 66s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [2840 B] 66s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 66s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [213 kB] 66s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [38.0 kB] 66s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [236 kB] 66s Fetched 601 kB in 1s (831 kB/s) 66s Reading package lists... 85s tee: /proc/self/fd/2: Permission denied 106s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 106s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 106s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 106s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 108s Reading package lists... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s Calculating upgrade... 109s The following packages were automatically installed and are no longer required: 109s libperl5.38t64 perl-modules-5.38 109s Use 'apt autoremove' to remove them. 109s The following NEW packages will be installed: 109s libperl5.40 perl-modules-5.40 python3-jaraco.text 109s The following packages will be upgraded: 109s base-files distro-info-data fwupd gcc-14-base info install-info iproute2 109s libatomic1 libdw1t64 libelf1t64 libfwupd2 libgcc-s1 libkeyutils1 109s liblocale-gettext-perl libsgutils2-1.46-2 libstdc++6 libtext-charwidth-perl 109s libtext-iconv-perl motd-news-config perl perl-base python3-pkg-resources 109s python3-setuptools sg3-utils sg3-utils-udev vim-common vim-tiny xxd 109s 28 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 19.2 MB of archives. 109s After this operation, 42.7 MB of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf motd-news-config all 13.5ubuntu2 [5274 B] 110s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf base-files armhf 13.5ubuntu2 [68.6 kB] 110s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf perl-modules-5.40 all 5.40.0-6 [3214 kB] 110s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libperl5.40 armhf 5.40.0-6 [4140 kB] 110s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf perl armhf 5.40.0-6 [262 kB] 110s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf perl-base armhf 5.40.0-6 [1674 kB] 110s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf liblocale-gettext-perl armhf 1.07-7build1 [15.0 kB] 110s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-iconv-perl armhf 1.7-8build4 [12.8 kB] 110s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-charwidth-perl armhf 0.04-11build4 [9128 B] 110s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libatomic1 armhf 14.2.0-7ubuntu1 [7842 B] 110s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-base armhf 14.2.0-7ubuntu1 [51.2 kB] 110s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++6 armhf 14.2.0-7ubuntu1 [711 kB] 110s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-s1 armhf 14.2.0-7ubuntu1 [40.8 kB] 110s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf install-info armhf 7.1.1-1 [61.4 kB] 110s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf distro-info-data all 0.63 [6588 B] 110s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libdw1t64 armhf 0.192-4 [243 kB] 110s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libelf1t64 armhf 0.192-4 [50.2 kB] 110s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf iproute2 armhf 6.10.0-2ubuntu1 [1082 kB] 110s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libkeyutils1 armhf 1.6.3-4ubuntu2 [8712 B] 110s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf vim-tiny armhf 2:9.1.0777-1ubuntu1 [693 kB] 110s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf vim-common all 2:9.1.0777-1ubuntu1 [394 kB] 110s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf xxd armhf 2:9.1.0777-1ubuntu1 [66.8 kB] 110s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf info armhf 7.1.1-1 [126 kB] 110s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd2 armhf 1.9.26-2 [125 kB] 110s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 1.9.26-2 [4404 kB] 111s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libsgutils2-1.46-2 armhf 1.46-3ubuntu5 [82.5 kB] 111s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jaraco.text all 4.0.0-1 [11.5 kB] 111s Get:28 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-pkg-resources all 75.2.0-1 [134 kB] 111s Get:29 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-setuptools all 75.2.0-1 [657 kB] 111s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils armhf 1.46-3ubuntu5 [816 kB] 111s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils-udev all 1.46-3ubuntu5 [5916 B] 111s Preconfiguring packages ... 111s Fetched 19.2 MB in 1s (14.2 MB/s) 111s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59386 files and directories currently installed.) 111s Preparing to unpack .../motd-news-config_13.5ubuntu2_all.deb ... 111s Unpacking motd-news-config (13.5ubuntu2) over (13.3ubuntu6) ... 111s Preparing to unpack .../base-files_13.5ubuntu2_armhf.deb ... 111s Unpacking base-files (13.5ubuntu2) over (13.3ubuntu6) ... 111s Setting up base-files (13.5ubuntu2) ... 111s Installing new version of config file /etc/issue ... 111s Installing new version of config file /etc/issue.net ... 111s Installing new version of config file /etc/lsb-release ... 112s motd-news.service is a disabled or a static unit not running, not starting it. 112s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59386 files and directories currently installed.) 112s Preparing to unpack .../perl_5.40.0-6_armhf.deb ... 112s Unpacking perl (5.40.0-6) over (5.38.2-5) ... 112s Selecting previously unselected package perl-modules-5.40. 112s Preparing to unpack .../perl-modules-5.40_5.40.0-6_all.deb ... 112s Unpacking perl-modules-5.40 (5.40.0-6) ... 113s Selecting previously unselected package libperl5.40:armhf. 113s Preparing to unpack .../libperl5.40_5.40.0-6_armhf.deb ... 113s Unpacking libperl5.40:armhf (5.40.0-6) ... 113s Preparing to unpack .../perl-base_5.40.0-6_armhf.deb ... 113s Unpacking perl-base (5.40.0-6) over (5.38.2-5) ... 113s Setting up perl-base (5.40.0-6) ... 113s (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 ... 61462 files and directories currently installed.) 113s Preparing to unpack .../liblocale-gettext-perl_1.07-7build1_armhf.deb ... 113s Unpacking liblocale-gettext-perl (1.07-7build1) over (1.07-7) ... 113s Preparing to unpack .../libtext-iconv-perl_1.7-8build4_armhf.deb ... 113s Unpacking libtext-iconv-perl:armhf (1.7-8build4) over (1.7-8build3) ... 113s Preparing to unpack .../libtext-charwidth-perl_0.04-11build4_armhf.deb ... 113s Unpacking libtext-charwidth-perl:armhf (0.04-11build4) over (0.04-11build3) ... 113s Preparing to unpack .../libatomic1_14.2.0-7ubuntu1_armhf.deb ... 113s Unpacking libatomic1:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 113s Preparing to unpack .../gcc-14-base_14.2.0-7ubuntu1_armhf.deb ... 113s Unpacking gcc-14-base:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 113s Setting up gcc-14-base:armhf (14.2.0-7ubuntu1) ... 113s (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 ... 61462 files and directories currently installed.) 113s Preparing to unpack .../libstdc++6_14.2.0-7ubuntu1_armhf.deb ... 113s Unpacking libstdc++6:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 113s Setting up libstdc++6:armhf (14.2.0-7ubuntu1) ... 113s (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 ... 61462 files and directories currently installed.) 113s Preparing to unpack .../libgcc-s1_14.2.0-7ubuntu1_armhf.deb ... 113s Unpacking libgcc-s1:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 113s Setting up libgcc-s1:armhf (14.2.0-7ubuntu1) ... 113s (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 ... 61462 files and directories currently installed.) 113s Preparing to unpack .../install-info_7.1.1-1_armhf.deb ... 113s Unpacking install-info (7.1.1-1) over (7.1-3build2) ... 114s Setting up install-info (7.1.1-1) ... 114s (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 ... 61462 files and directories currently installed.) 114s Preparing to unpack .../00-distro-info-data_0.63_all.deb ... 114s Unpacking distro-info-data (0.63) over (0.62) ... 114s Preparing to unpack .../01-libdw1t64_0.192-4_armhf.deb ... 114s Unpacking libdw1t64:armhf (0.192-4) over (0.191-2) ... 114s Preparing to unpack .../02-libelf1t64_0.192-4_armhf.deb ... 114s Unpacking libelf1t64:armhf (0.192-4) over (0.191-2) ... 114s Preparing to unpack .../03-iproute2_6.10.0-2ubuntu1_armhf.deb ... 114s Unpacking iproute2 (6.10.0-2ubuntu1) over (6.10.0-2) ... 114s Preparing to unpack .../04-libkeyutils1_1.6.3-4ubuntu2_armhf.deb ... 114s Unpacking libkeyutils1:armhf (1.6.3-4ubuntu2) over (1.6.3-3build1) ... 114s Preparing to unpack .../05-vim-tiny_2%3a9.1.0777-1ubuntu1_armhf.deb ... 114s Unpacking vim-tiny (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 114s Preparing to unpack .../06-vim-common_2%3a9.1.0777-1ubuntu1_all.deb ... 114s Unpacking vim-common (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 114s Preparing to unpack .../07-xxd_2%3a9.1.0777-1ubuntu1_armhf.deb ... 114s Unpacking xxd (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 114s Preparing to unpack .../08-info_7.1.1-1_armhf.deb ... 114s Unpacking info (7.1.1-1) over (7.1-3build2) ... 114s Preparing to unpack .../09-libfwupd2_1.9.26-2_armhf.deb ... 114s Unpacking libfwupd2:armhf (1.9.26-2) over (1.9.24-1) ... 114s Preparing to unpack .../10-fwupd_1.9.26-2_armhf.deb ... 114s Unpacking fwupd (1.9.26-2) over (1.9.24-1) ... 115s Preparing to unpack .../11-libsgutils2-1.46-2_1.46-3ubuntu5_armhf.deb ... 115s Unpacking libsgutils2-1.46-2:armhf (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 115s Selecting previously unselected package python3-jaraco.text. 115s Preparing to unpack .../12-python3-jaraco.text_4.0.0-1_all.deb ... 115s Unpacking python3-jaraco.text (4.0.0-1) ... 115s Preparing to unpack .../13-python3-pkg-resources_75.2.0-1_all.deb ... 115s Unpacking python3-pkg-resources (75.2.0-1) over (74.1.2-1) ... 115s Preparing to unpack .../14-python3-setuptools_75.2.0-1_all.deb ... 115s Unpacking python3-setuptools (75.2.0-1) over (74.1.2-1) ... 115s Preparing to unpack .../15-sg3-utils_1.46-3ubuntu5_armhf.deb ... 115s Unpacking sg3-utils (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 115s Preparing to unpack .../16-sg3-utils-udev_1.46-3ubuntu5_all.deb ... 115s Unpacking sg3-utils-udev (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 115s Setting up python3-pkg-resources (75.2.0-1) ... 115s Setting up motd-news-config (13.5ubuntu2) ... 115s Setting up libtext-iconv-perl:armhf (1.7-8build4) ... 115s Setting up libtext-charwidth-perl:armhf (0.04-11build4) ... 115s Setting up libkeyutils1:armhf (1.6.3-4ubuntu2) ... 115s Setting up distro-info-data (0.63) ... 115s Setting up libfwupd2:armhf (1.9.26-2) ... 115s Setting up libsgutils2-1.46-2:armhf (1.46-3ubuntu5) ... 115s Setting up xxd (2:9.1.0777-1ubuntu1) ... 115s Setting up libelf1t64:armhf (0.192-4) ... 115s Setting up libdw1t64:armhf (0.192-4) ... 115s Setting up vim-common (2:9.1.0777-1ubuntu1) ... 115s Installing new version of config file /etc/vim/vimrc ... 115s Setting up python3-jaraco.text (4.0.0-1) ... 116s Setting up libatomic1:armhf (14.2.0-7ubuntu1) ... 116s Setting up perl-modules-5.40 (5.40.0-6) ... 116s Setting up fwupd (1.9.26-2) ... 116s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 116s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 116s fwupd.service is a disabled or a static unit not running, not starting it. 116s Setting up info (7.1.1-1) ... 116s Setting up liblocale-gettext-perl (1.07-7build1) ... 116s Setting up sg3-utils (1.46-3ubuntu5) ... 116s Setting up python3-setuptools (75.2.0-1) ... 117s Setting up iproute2 (6.10.0-2ubuntu1) ... 117s Setting up vim-tiny (2:9.1.0777-1ubuntu1) ... 117s Setting up sg3-utils-udev (1.46-3ubuntu5) ... 117s update-initramfs: deferring update (trigger activated) 117s Setting up libperl5.40:armhf (5.40.0-6) ... 117s Setting up perl (5.40.0-6) ... 117s Processing triggers for dbus (1.14.10-4ubuntu5) ... 117s Processing triggers for install-info (7.1.1-1) ... 118s Processing triggers for initramfs-tools (0.142ubuntu34) ... 118s Processing triggers for libc-bin (2.40-1ubuntu3) ... 118s Processing triggers for man-db (2.12.1-3) ... 119s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-1ubuntu10) ... 119s update-initramfs: deferring update (trigger activated) 119s Processing triggers for initramfs-tools (0.142ubuntu34) ... 119s Reading package lists... 120s Building dependency tree... 120s Reading state information... 120s The following packages will be REMOVED: 120s libperl5.38t64* perl-modules-5.38* 121s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 121s After this operation, 41.6 MB disk space will be freed. 121s (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 ... 61471 files and directories currently installed.) 121s Removing libperl5.38t64:armhf (5.38.2-5) ... 121s Removing perl-modules-5.38 (5.38.2-5) ... 121s Processing triggers for man-db (2.12.1-3) ... 121s Processing triggers for libc-bin (2.40-1ubuntu3) ... 124s autopkgtest [10:54:02]: rebooting testbed after setup commands that affected boot 195s autopkgtest [10:55:13]: 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 226s autopkgtest [10:55:44]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 242s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (dsc) [2291 B] 242s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (tar) [22.3 MB] 242s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (diff) [7100 B] 242s gpgv: Signature made Wed Apr 10 17:15:32 2024 UTC 242s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 242s gpgv: Can't check signature: No public key 243s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6build1.dsc: no acceptable signature found 243s autopkgtest [10:56:01]: testing package tombo version 1.5.1-6build1 245s autopkgtest [10:56:03]: build not needed 249s autopkgtest [10:56:07]: test run-unit-test: preparing testbed 259s Reading package lists... 259s Building dependency tree... 259s Reading state information... 260s Starting pkgProblemResolver with broken count: 0 260s Starting 2 pkgProblemResolver with broken count: 0 260s Done 260s The following additional packages will be installed: 260s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 260s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 260s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 260s python3-decorator python3-h5py python3-h5py-serial python3-mappy 260s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 260s tombo-doc 260s Suggested packages: 260s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 260s gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 260s Recommended packages: 260s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 260s python3-rpy2 261s The following NEW packages will be installed: 261s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 261s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 261s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 261s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 261s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 261s tombo-doc 261s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 261s Need to get 60.2 MB/60.2 MB of archives. 261s After this operation, 174 MB of additional disk space will be used. 261s Get:1 /tmp/autopkgtest.Kf945t/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [704 B] 261s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-lato all 2.015-1 [2781 kB] 261s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 261s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 261s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 261s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 261s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-7ubuntu1 [311 kB] 261s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 261s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB] 261s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4ubuntu3 [55.9 kB] 261s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 261s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 261s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-3 [157 kB] 261s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 262s Get:15 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 262s Get:16 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 262s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 262s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 262s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.11.0-5ubuntu1 [1061 kB] 262s Get:20 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.11.0-5ubuntu1 [7974 B] 262s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mappy armhf 2.27+dfsg-1 [172 kB] 262s Get:22 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-tqdm all 4.66.5-1 [91.4 kB] 262s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-rtd-theme-common all 2.0.0+dfsg-2 [1012 kB] 262s Get:24 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-3 [16.4 MB] 262s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf tombo armhf 1.5.1-6build1 [448 kB] 262s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 262s Get:27 http://ftpmaster.internal/ubuntu plucky/universe armhf tombo-doc all 1.5.1-6build1 [21.7 MB] 264s Fetched 60.2 MB in 3s (23.6 MB/s) 264s Selecting previously unselected package fonts-lato. 264s (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 ... 59541 files and directories currently installed.) 264s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 264s Unpacking fonts-lato (2.015-1) ... 264s Selecting previously unselected package fonts-font-awesome. 264s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 264s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 264s Selecting previously unselected package fonts-mathjax. 264s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 264s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 264s Selecting previously unselected package libaec0:armhf. 264s Preparing to unpack .../03-libaec0_1.1.3-1_armhf.deb ... 264s Unpacking libaec0:armhf (1.1.3-1) ... 264s Selecting previously unselected package libblas3:armhf. 264s Preparing to unpack .../04-libblas3_3.12.0-3build2_armhf.deb ... 264s Unpacking libblas3:armhf (3.12.0-3build2) ... 264s Selecting previously unselected package libgfortran5:armhf. 264s Preparing to unpack .../05-libgfortran5_14.2.0-7ubuntu1_armhf.deb ... 264s Unpacking libgfortran5:armhf (14.2.0-7ubuntu1) ... 264s Selecting previously unselected package libsz2:armhf. 264s Preparing to unpack .../06-libsz2_1.1.3-1_armhf.deb ... 264s Unpacking libsz2:armhf (1.1.3-1) ... 264s Selecting previously unselected package libhdf5-103-1t64:armhf. 264s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ... 264s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 264s Selecting previously unselected package libhdf5-hl-100t64:armhf. 264s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_armhf.deb ... 264s Unpacking libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 264s Selecting previously unselected package libjs-jquery. 264s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 264s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 264s Selecting previously unselected package libjs-underscore. 264s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 264s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 264s Selecting previously unselected package libjs-sphinxdoc. 264s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-3_all.deb ... 264s Unpacking libjs-sphinxdoc (7.4.7-3) ... 264s Selecting previously unselected package liblapack3:armhf. 264s Preparing to unpack .../12-liblapack3_3.12.0-3build2_armhf.deb ... 264s Unpacking liblapack3:armhf (3.12.0-3build2) ... 264s Selecting previously unselected package liblbfgsb0:armhf. 265s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 265s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 265s Selecting previously unselected package liblzf1:armhf. 265s Preparing to unpack .../14-liblzf1_3.6-4_armhf.deb ... 265s Unpacking liblzf1:armhf (3.6-4) ... 265s Selecting previously unselected package python3-decorator. 265s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 265s Unpacking python3-decorator (5.1.1-5) ... 265s Selecting previously unselected package python3-numpy. 265s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 265s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 265s Selecting previously unselected package python3-h5py-serial. 265s Preparing to unpack .../17-python3-h5py-serial_3.11.0-5ubuntu1_armhf.deb ... 265s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 265s Selecting previously unselected package python3-h5py. 265s Preparing to unpack .../18-python3-h5py_3.11.0-5ubuntu1_all.deb ... 265s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 265s Selecting previously unselected package python3-mappy. 265s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1_armhf.deb ... 265s Unpacking python3-mappy (2.27+dfsg-1) ... 265s Selecting previously unselected package python3-tqdm. 265s Preparing to unpack .../20-python3-tqdm_4.66.5-1_all.deb ... 265s Unpacking python3-tqdm (4.66.5-1) ... 265s Selecting previously unselected package sphinx-rtd-theme-common. 265s Preparing to unpack .../21-sphinx-rtd-theme-common_2.0.0+dfsg-2_all.deb ... 265s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-2) ... 265s Selecting previously unselected package python3-scipy. 265s Preparing to unpack .../22-python3-scipy_1.13.1-3_armhf.deb ... 265s Unpacking python3-scipy (1.13.1-3) ... 266s Selecting previously unselected package tombo. 266s Preparing to unpack .../23-tombo_1.5.1-6build1_armhf.deb ... 266s Unpacking tombo (1.5.1-6build1) ... 266s Selecting previously unselected package libjs-mathjax. 266s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 266s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 267s Selecting previously unselected package tombo-doc. 267s Preparing to unpack .../25-tombo-doc_1.5.1-6build1_all.deb ... 267s Unpacking tombo-doc (1.5.1-6build1) ... 267s Selecting previously unselected package autopkgtest-satdep. 267s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 267s Unpacking autopkgtest-satdep (0) ... 267s Setting up fonts-lato (2.015-1) ... 267s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 267s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 267s Setting up python3-tqdm (4.66.5-1) ... 267s Setting up python3-mappy (2.27+dfsg-1) ... 267s Setting up libaec0:armhf (1.1.3-1) ... 267s Setting up python3-decorator (5.1.1-5) ... 267s Setting up libblas3:armhf (3.12.0-3build2) ... 267s 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 267s Setting up liblzf1:armhf (3.6-4) ... 267s Setting up libgfortran5:armhf (14.2.0-7ubuntu1) ... 267s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 267s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 267s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-2) ... 267s Setting up libsz2:armhf (1.1.3-1) ... 267s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 267s Setting up liblapack3:armhf (3.12.0-3build2) ... 268s 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 268s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 270s Setting up libjs-sphinxdoc (7.4.7-3) ... 270s Setting up tombo-doc (1.5.1-6build1) ... 270s Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 270s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 270s Setting up libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 270s Setting up python3-scipy (1.13.1-3) ... 274s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 275s Setting up python3-h5py (3.11.0-5ubuntu1) ... 275s Setting up tombo (1.5.1-6build1) ... 275s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 275s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 275s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 275s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 275s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 275s re.match('\+', fastq_rec[2]) is None): 275s Setting up autopkgtest-satdep (0) ... 275s Processing triggers for man-db (2.12.1-3) ... 276s Processing triggers for libc-bin (2.40-1ubuntu3) ... 291s (Reading database ... 66744 files and directories currently installed.) 291s Removing autopkgtest-satdep (0) ... 298s autopkgtest [10:56:56]: test run-unit-test: [----------------------- 299s ********* Testing help commands ********** 300s usage: tombo [-h] [-v] 300s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 300s ... 300s 300s ********** Tombo ********* 300s 300s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 300s 300s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 300s 300s Tombo command groups (additional help available within each command group): 300s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 300s preprocess Pre-process nanopore reads for Tombo processing. 300s filter Apply filter to Tombo index file for specified criterion. 300s detect_modifications Perform statistical testing to detect non-standard nucleotides. 300s text_output Output Tombo results in text files. 300s build_model Create canonical and alternative base Tombo models. 300s plot Save plots to visualize raw nanopore signal or testing results. 300s 300s options: 300s -h, --help show this help message and exit 300s -v, --version show Tombo version and exit. 300s usage: tombo resquiggle [--dna] [--rna] 300s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 300s [--q-score Q_SCORE] 300s [--signal-matching-score SIGNAL_MATCHING_SCORE] 300s [--processes PROCESSES] 300s [--corrected-group CORRECTED_GROUP] 300s [--basecall-group BASECALL_GROUP] 300s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 300s [--overwrite] 300s [--failed-reads-filename FAILED_READS_FILENAME] 300s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 300s [--print-advanced-arguments] [--quiet] [--help] 300s fast5s_basedir reference 300s 300s Required Arguments: 300s fast5s_basedir Directory containing fast5 files. All files ending in 300s "fast5" found recursively within this base directory 300s will be processed. 300s reference Reference genome/transcriptome FASTA file or minimap2 300s index (with "map-ont" preset) for mapping. 300s 300s Model Parameters: 300s --dna Explicitly select canonical DNA model. Default: 300s Automatically determine from FAST5s 300s --rna Explicitly select canonical RNA model. Default: 300s Automatically determine from FAST5s 300s 300s Read Filtering Argument: 300s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 300s Filter reads based on observations per base percentile 300s thresholds. Format thresholds as "percentile:thresh 300s [pctl2:thresh2 ...]". For example to filter reads with 300s 99th pctl > 200 obs/base or max > 5k obs/base use 300s "99:200 100:5000". 300s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 300s Default: 0.000000 300s --signal-matching-score SIGNAL_MATCHING_SCORE 300s Observed to expected signal matching score (higher 300s score indicates poor matching). Sample type defaults: 300s RNA : 2 || DNA : 1.1 300s 300s Multiprocessing Arguments: 300s --processes PROCESSES 300s Number of processes. Default: 1 300s 300s FAST5 Data Arguments: 300s --corrected-group CORRECTED_GROUP 300s FAST5 group created by resquiggle command. Default: 300s RawGenomeCorrected_000 300s --basecall-group BASECALL_GROUP 300s FAST5 group obtain original basecalls (under Analyses 300s group). Default: Basecall_1D_000 300s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 300s FAST5 subgroup(s) (under /Analyses/[--basecall- 300s group]/) containing basecalls and created within 300s [--corrected-group] containing re-squiggle results. 300s Default: ['BaseCalled_template'] 300s --overwrite Overwrite previous corrected group in FAST5 files. 300s Note: only effects --corrected-group or --new- 300s corrected-group. 300s 300s Input/Output Arguments: 300s --failed-reads-filename FAILED_READS_FILENAME 300s Output failed read filenames with assoicated error. 300s Default: Do not store failed reads. 300s --num-most-common-errors NUM_MOST_COMMON_ERRORS 300s Dynamically show this many most common errors so far 300s through run. Default: 0; Just show progress 300s 300s Advanced Arguments: 300s --print-advanced-arguments 300s Print advanced re-squiggle arguments and exit. 300s 300s Miscellaneous Arguments: 300s --quiet, -q Don't print status information. 300s --help, -h Print this help message and exit 300s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 300s --fastq-filenames 300s FASTQ_FILENAMES 300s [FASTQ_FILENAMES ...] 300s [--basecall-group BASECALL_GROUP] 300s [--basecall-subgroup BASECALL_SUBGROUP] 300s [--overwrite] 300s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 300s [--processes PROCESSES] 300s [--quiet] [--help] 300s 300s Required Arguments: 300s --fast5-basedir FAST5_BASEDIR 300s Directory containing fast5 files. 300s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 300s FASTQ filenames containing basecalls to be added to 300s raw FAST5 files. 300s 300s FAST5 Data Arguments: 300s --basecall-group BASECALL_GROUP 300s FAST5 group obtain original basecalls (under Analyses 300s group). Default: Basecall_1D_000 300s --basecall-subgroup BASECALL_SUBGROUP 300s FAST5 subgroup (under /Analyses/[--basecall-group]/) 300s under which to store basecalls from FASTQs. Default: 300s BaseCalled_template 300s --overwrite Overwrite previous corrected group in FAST5 files. 300s Note: only effects --corrected-group or --new- 300s corrected-group. 300s 300s Sequencing Summary Argument: 300s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 300s Sequencing summary filenames produced by albacore. 300s These can make annotation of raw FAST5 files with 300s FASTQ sequence much faster. 300s 300s Multiprocessing Argument: 300s --processes PROCESSES 300s Number of processes. Default: 1 300s 300s Miscellaneous Arguments: 300s --quiet, -q Don't print status information. 300s --help, -h Print this help message and exit 300s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 300s [FAST5_BASEDIRS ...] 300s [--corrected-group CORRECTED_GROUP] 300s [--quiet] [--help] 300s 300s Required Argument: 300s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 300s Directories containing fast5 files. 300s 300s FAST5 Data Argument: 300s --corrected-group CORRECTED_GROUP 300s FAST5 group created by resquiggle command. Default: 300s RawGenomeCorrected_000 300s 300s Miscellaneous Arguments: 300s --quiet, -q Don't print status information. 300s --help, -h Print this help message and exit 300s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 300s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 300s [--corrected-group CORRECTED_GROUP] [--quiet] 300s [--help] 300s 300s Required Argument: 300s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 300s Directories containing fast5 files. 300s 300s Read Filtering Argument: 300s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 300s Filter reads based on observations per base percentile 300s thresholds. Format thresholds as "percentile:thresh 300s [pctl2:thresh2 ...]". For example to filter reads with 300s 99th pctl > 200 obs/base or max > 5k obs/base use 300s "99:200 100:5000". 300s 300s FAST5 Data Argument: 300s --corrected-group CORRECTED_GROUP 300s FAST5 group created by resquiggle command. Default: 300s RawGenomeCorrected_000 300s 300s Miscellaneous Arguments: 300s --quiet, -q Don't print status information. 300s --help, -h Print this help message and exit 300s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 300s [FAST5_BASEDIRS ...] 300s [--percent-to-filter PERCENT_TO_FILTER] 300s [--corrected-group CORRECTED_GROUP] 300s [--quiet] [--help] 300s 300s Required Arguments: 300s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 300s Directories containing fast5 files. 300s 300s Read Filtering Argument: 300s --percent-to-filter PERCENT_TO_FILTER 300s Percentage of all reads to filter. Reads are randomly 300s selected weighted according to the approximate 300s coverage at the mapped genomic location. This can be 300s useful in modeling and testing. Default: 10.000000 300s 300s FAST5 Data Arguments: 300s --corrected-group CORRECTED_GROUP 300s FAST5 group created by resquiggle command. Default: 300s RawGenomeCorrected_000 300s 300s Miscellaneous Arguments: 300s --quiet, -q Don't print status information. 300s --help, -h Print this help message and exit 300s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 300s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 300s [--corrected-group CORRECTED_GROUP] 300s [--basecall-group BASECALL_GROUP] [--quiet] 300s [--help] 300s 300s Required Arguments: 300s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 300s Directories containing fast5 files. 300s 300s Read Filtering Argument: 300s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 300s Default: 7.000000 300s 300s FAST5 Data Arguments: 300s --corrected-group CORRECTED_GROUP 300s FAST5 group created by resquiggle command. Default: 300s RawGenomeCorrected_000 300s --basecall-group BASECALL_GROUP 300s FAST5 group obtain original basecalls (under Analyses 300s group). Default: Basecall_1D_000 300s 300s Miscellaneous Arguments: 300s --quiet, -q Don't print status information. 300s --help, -h Print this help message and exit 300s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 300s [FAST5_BASEDIRS ...] 300s --signal-matching-score 300s SIGNAL_MATCHING_SCORE 300s [--corrected-group CORRECTED_GROUP] 300s [--quiet] [--help] 300s 300s Required Arguments: 300s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 300s Directories containing fast5 files. 300s --signal-matching-score SIGNAL_MATCHING_SCORE 300s Observed to expected signal matching score (higher 300s score indicates poor matching). Sample type defaults: 300s RNA : 2 || DNA : 1.1 300s 300s FAST5 Data Arguments: 300s --corrected-group CORRECTED_GROUP 300s FAST5 group created by resquiggle command. Default: 300s RawGenomeCorrected_000 300s 300s Miscellaneous Arguments: 300s --quiet, -q Don't print status information. 300s --help, -h Print this help message and exit 300s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 300s [FAST5_BASEDIRS ...] 300s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 300s [--include-partial-overlap] 300s [--corrected-group CORRECTED_GROUP] 300s [--quiet] [--help] 300s 300s Required Arguments: 300s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 300s Directories containing fast5 files. 300s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 300s Filter out reads not falling completely within include 300s regions. Omit start and end coordinates to include an 300s entire chromosome/sequence record. Format regions as 300s "chrm[:start-end] [chrm2[:start2-end2] ...]". 300s 300s Filter Argument: 300s --include-partial-overlap 300s Include reads that partially overlap the specified 300s region. Default: Only include reads completely 300s contained in a specified region 300s 300s FAST5 Data Argument: 300s --corrected-group CORRECTED_GROUP 300s FAST5 group created by resquiggle command. Default: 300s RawGenomeCorrected_000 300s 300s Miscellaneous Arguments: 300s --quiet, -q Don't print status information. 300s --help, -h Print this help message and exit 301s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 301s [FAST5_BASEDIRS ...] 301s --statistics-file-basename 301s STATISTICS_FILE_BASENAME [--dna] 301s [--rna] 301s [--fishers-method-context FISHERS_METHOD_CONTEXT] 301s [--minimum-test-reads MINIMUM_TEST_READS] 301s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 301s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 301s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 301s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 301s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 301s [--processes PROCESSES] 301s [--corrected-group CORRECTED_GROUP] 301s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 301s [--quiet] [--help] 301s 301s Required Argument: 301s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 301s Directories containing fast5 files. 301s --statistics-file-basename STATISTICS_FILE_BASENAME 301s File base name to save base by base statistics from 301s testing. Filenames will be [--statistics-file- 301s basename].[--alternate-bases]?.tombo.stats 301s 301s Comparison Model Arguments: 301s --dna Explicitly select canonical DNA model. Default: 301s Automatically determine from FAST5s 301s --rna Explicitly select canonical RNA model. Default: 301s Automatically determine from FAST5s 301s 301s Significance Test Arguments: 301s --fishers-method-context FISHERS_METHOD_CONTEXT 301s Number of context bases up and downstream over which 301s to compute Fisher's method combined p-values. Note: 301s Not applicable for alternative model likelihood ratio 301s tests. Default: 1. 301s --minimum-test-reads MINIMUM_TEST_READS 301s Number of reads required at a position to perform 301s significance testing or contribute to model 301s estimation. Default: 1 301s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 301s P-value threshold when computing fraction of 301s significant reads at each genomic position. If two 301s values are provided, statistics between these values 301s are not considered. Default thresholds: DNA:0.15-0.5 , 301s RNA:0.05-0.4 301s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 301s Dampen fraction modified estimates for low coverage 301s sites. Two parameters are unmodified and modified 301s pseudo read counts. This is equivalent to a beta prior 301s on the fraction estimate. Set to "0 0" to disable 301s dampened fraction estimation. Default: [2, 0] 301s 301s Output Argument: 301s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 301s Base for binary files containing per-read statistics 301s from statistical testing. Filenames will be [--per- 301s read-statistics-basename].[--alternate- 301s bases]?.tombo.per_read_stats 301s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 301s Number of the most significant sites to store for 301s faster access. If a longer list of most significant 301s sites is required the list must be re-computed from 301s all batches. Very large values can increase RAM usage. 301s Default: 100000 301s 301s Multiprocessing Arguments: 301s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 301s Size of regions over which to multiprocesses statistic 301s computation. For very deep samples a smaller value is 301s recommmended in order to control memory consumption. 301s Default: 10000 301s --processes PROCESSES 301s Number of processes. Default: 1 301s 301s FAST5 Data Arguments: 301s --corrected-group CORRECTED_GROUP 301s FAST5 group created by resquiggle command. Default: 301s RawGenomeCorrected_000 301s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 301s FAST5 subgroup(s) (under /Analyses/[--basecall- 301s group]/) containing basecalls and created within 301s [--corrected-group] containing re-squiggle results. 301s Default: ['BaseCalled_template'] 301s 301s Miscellaneous Arguments: 301s --quiet, -q Don't print status information. 301s --help, -h Print this help message and exit 301s usage: tombo detect_modifications alternative_model 301s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 301s [--statistics-file-basename STATISTICS_FILE_BASENAME] 301s [--alternate-bases {dcm,CpG,5mC,6mA,dam} [{dcm,CpG,5mC,6mA,dam} ...]] 301s [--print-available-models] 301s [--dna] [--rna] 301s [--minimum-test-reads MINIMUM_TEST_READS] 301s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 301s [--standard-log-likelihood-ratio] 301s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 301s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 301s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 301s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 301s [--processes PROCESSES] 301s [--corrected-group CORRECTED_GROUP] 301s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 301s [--quiet] [--help] 301s 301s Required Argument: 301s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 301s Directories containing fast5 files. 301s --statistics-file-basename STATISTICS_FILE_BASENAME 301s File base name to save base by base statistics from 301s testing. Filenames will be [--statistics-file- 301s basename].[--alternate-bases]?.tombo.stats 301s --alternate-bases {dcm,CpG,5mC,6mA,dam} [{dcm,CpG,5mC,6mA,dam} ...] 301s Default non-standard base model for testing (not 301s required if user created --alternate-model-filenames 301s is provided). 301s 301s Comparison Arguments: 301s --print-available-models 301s Print available alternative models and exit. 301s --dna Explicitly select canonical DNA model. Default: 301s Automatically determine from FAST5s 301s --rna Explicitly select canonical RNA model. Default: 301s Automatically determine from FAST5s 301s 301s Significance Test Arguments: 301s --minimum-test-reads MINIMUM_TEST_READS 301s Number of reads required at a position to perform 301s significance testing or contribute to model 301s estimation. Default: 1 301s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 301s Log likelihood ratio threshold when computing fraction 301s of significant reads at each genomic position. If two 301s values are provided, statistics between these values 301s are not considered. Default thresholds: DNA:-1.5-2.5 , 301s RNA:-2.5-2.5 301s --standard-log-likelihood-ratio 301s Use a standard log likelihood ratio (LLR) statistic. 301s Default is to use an outlier-robust LLR-like 301s statistic. Detail in full online documentation. 301s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 301s Dampen fraction modified estimates for low coverage 301s sites. Two parameters are unmodified and modified 301s pseudo read counts. This is equivalent to a beta prior 301s on the fraction estimate. Set to "0 0" to disable 301s dampened fraction estimation. Default: [2, 0] 301s 301s Output Argument: 301s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 301s Base for binary files containing per-read statistics 301s from statistical testing. Filenames will be [--per- 301s read-statistics-basename].[--alternate- 301s bases]?.tombo.per_read_stats 301s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 301s Number of the most significant sites to store for 301s faster access. If a longer list of most significant 301s sites is required the list must be re-computed from 301s all batches. Very large values can increase RAM usage. 301s Default: 100000 301s 301s Multiprocessing Arguments: 301s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 301s Size of regions over which to multiprocesses statistic 301s computation. For very deep samples a smaller value is 301s recommmended in order to control memory consumption. 301s Default: 10000 301s --processes PROCESSES 301s Number of processes. Default: 1 301s 301s FAST5 Data Arguments: 301s --corrected-group CORRECTED_GROUP 301s FAST5 group created by resquiggle command. Default: 301s RawGenomeCorrected_000 301s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 301s FAST5 subgroup(s) (under /Analyses/[--basecall- 301s group]/) containing basecalls and created within 301s [--corrected-group] containing re-squiggle results. 301s Default: ['BaseCalled_template'] 301s 301s Miscellaneous Arguments: 301s --quiet, -q Don't print status information. 301s --help, -h Print this help message and exit 301s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 301s FAST5_BASEDIRS 301s [FAST5_BASEDIRS ...] 301s --statistics-file-basename 301s STATISTICS_FILE_BASENAME 301s --control-fast5-basedirs 301s CONTROL_FAST5_BASEDIRS 301s [CONTROL_FAST5_BASEDIRS ...] 301s [--sample-only-estimates] 301s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 301s [--dna] [--rna] 301s [--fishers-method-context FISHERS_METHOD_CONTEXT] 301s [--minimum-test-reads MINIMUM_TEST_READS] 301s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 301s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 301s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 301s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 301s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 301s [--processes PROCESSES] 301s [--corrected-group CORRECTED_GROUP] 301s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 301s [--quiet] [--help] 301s 301s Required Argument: 301s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 301s Directories containing fast5 files. 301s --statistics-file-basename STATISTICS_FILE_BASENAME 301s File base name to save base by base statistics from 301s testing. Filenames will be [--statistics-file- 301s basename].[--alternate-bases]?.tombo.stats 301s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 301s Set of directories containing fast5 files for control 301s reads, containing only canonical nucleotides. 301s 301s Model Prior Arguments: 301s --sample-only-estimates 301s Only use canonical sample to estimate expected signal 301s level and spread. Default: Use canonical model to 301s improve estimtates (esp. for low coverage regions) 301s using baysian posterior estimates. 301s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 301s Prior weights (one each for mean and spread) applied 301s to canonical base model for estimating posterior model 301s parameters for sample comparison. Default: [5, 40] 301s --dna Explicitly select canonical DNA model. Default: 301s Automatically determine from FAST5s 301s --rna Explicitly select canonical RNA model. Default: 301s Automatically determine from FAST5s 301s 301s Significance Test Arguments: 301s --fishers-method-context FISHERS_METHOD_CONTEXT 301s Number of context bases up and downstream over which 301s to compute Fisher's method combined p-values. Note: 301s Not applicable for alternative model likelihood ratio 301s tests. Default: 1. 301s --minimum-test-reads MINIMUM_TEST_READS 301s Number of reads required at a position to perform 301s significance testing or contribute to model 301s estimation. Default: 1 301s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 301s P-value threshold when computing fraction of 301s significant reads at each genomic position. If two 301s values are provided, statistics between these values 301s are not considered. Default thresholds: DNA:0.15-0.5 , 301s RNA:0.05-0.4 301s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 301s Dampen fraction modified estimates for low coverage 301s sites. Two parameters are unmodified and modified 301s pseudo read counts. This is equivalent to a beta prior 301s on the fraction estimate. Set to "0 0" to disable 301s dampened fraction estimation. Default: [2, 0] 301s 301s Output Argument: 301s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 301s Base for binary files containing per-read statistics 301s from statistical testing. Filenames will be [--per- 301s read-statistics-basename].[--alternate- 301s bases]?.tombo.per_read_stats 301s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 301s Number of the most significant sites to store for 301s faster access. If a longer list of most significant 301s sites is required the list must be re-computed from 301s all batches. Very large values can increase RAM usage. 301s Default: 100000 301s 301s Multiprocessing Arguments: 301s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 301s Size of regions over which to multiprocesses statistic 301s computation. For very deep samples a smaller value is 301s recommmended in order to control memory consumption. 301s Default: 10000 301s --processes PROCESSES 301s Number of processes. Default: 1 301s 301s FAST5 Data Arguments: 301s --corrected-group CORRECTED_GROUP 301s FAST5 group created by resquiggle command. Default: 301s RawGenomeCorrected_000 301s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 301s FAST5 subgroup(s) (under /Analyses/[--basecall- 301s group]/) containing basecalls and created within 301s [--corrected-group] containing re-squiggle results. 301s Default: ['BaseCalled_template'] 301s 301s Miscellaneous Arguments: 301s --quiet, -q Don't print status information. 301s --help, -h Print this help message and exit 301s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 301s FAST5_BASEDIRS 301s [FAST5_BASEDIRS ...] 301s --statistics-file-basename 301s STATISTICS_FILE_BASENAME 301s --alternate-fast5-basedirs 301s ALTERNATE_FAST5_BASEDIRS 301s [ALTERNATE_FAST5_BASEDIRS ...] 301s [--fishers-method-context FISHERS_METHOD_CONTEXT] 301s [--minimum-test-reads MINIMUM_TEST_READS] 301s [--statistic-type {ks,u,t}] 301s [--store-p-value] 301s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 301s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 301s [--processes PROCESSES] 301s [--corrected-group CORRECTED_GROUP] 301s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 301s [--quiet] [--help] 301s 301s Required Argument: 301s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 301s Directories containing fast5 files. 301s --statistics-file-basename STATISTICS_FILE_BASENAME 301s File base name to save base by base statistics from 301s testing. Filenames will be [--statistics-file- 301s basename].[--alternate-bases]?.tombo.stats 301s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 301s Set of directories containing fast5 files for 301s alternate set of reads. 301s 301s Significance Test Arguments: 301s --fishers-method-context FISHERS_METHOD_CONTEXT 301s Number of context bases up and downstream over which 301s to compute Fisher's method combined p-values. Note: 301s Not applicable for alternative model likelihood ratio 301s tests. Default: 1. 301s --minimum-test-reads MINIMUM_TEST_READS 301s Number of reads required at a position to perform 301s significance testing or contribute to model 301s estimation. Default: 50 301s --statistic-type {ks,u,t} 301s Type of statistical test to apply. Default: "ks" 301s --store-p-value Store p-value instead of effect-size statistic. 301s Statistics are D-statistic (KS-test), deviation from 301s even common language effect size (u-test), and Cohen's 301s D (t-test). 301s 301s Output Argument: 301s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 301s Number of the most significant sites to store for 301s faster access. If a longer list of most significant 301s sites is required the list must be re-computed from 301s all batches. Very large values can increase RAM usage. 301s Default: 100000 301s 301s Multiprocessing Arguments: 301s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 301s Size of regions over which to multiprocesses statistic 301s computation. For very deep samples a smaller value is 301s recommmended in order to control memory consumption. 301s Default: 10000 301s --processes PROCESSES 301s Number of processes. Default: 1 301s 301s FAST5 Data Arguments: 301s --corrected-group CORRECTED_GROUP 301s FAST5 group created by resquiggle command. Default: 301s RawGenomeCorrected_000 301s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 301s FAST5 subgroup(s) (under /Analyses/[--basecall- 301s group]/) containing basecalls and created within 301s [--corrected-group] containing re-squiggle results. 301s Default: ['BaseCalled_template'] 301s 301s Miscellaneous Arguments: 301s --quiet, -q Don't print status information. 301s --help, -h Print this help message and exit 301s usage: tombo detect_modifications aggregate_per_read_stats 301s --per-read-statistics-filename 301s PER_READ_STATISTICS_FILENAME 301s --statistics-filename 301s STATISTICS_FILENAME 301s --single-read-threshold 301s SINGLE_READ_THRESHOLD 301s [SINGLE_READ_THRESHOLD ...] 301s [--minimum-test-reads MINIMUM_TEST_READS] 301s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 301s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 301s [--processes PROCESSES] 301s [--corrected-group CORRECTED_GROUP] 301s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 301s [--quiet] [--help] 301s 301s Required Argument: 301s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 301s Binary file containing per-read statistics from 301s statistical testing. 301s --statistics-filename STATISTICS_FILENAME 301s File to save/load genomic base anchored statistics. 301s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 301s P-value or log likelihood ratio threshold when 301s computing fraction of significant reads at each 301s genomic position. If two values are provided, 301s statistics between these values are not considered. 301s 301s Significance Test Arguments: 301s --minimum-test-reads MINIMUM_TEST_READS 301s Number of reads required at a position to perform 301s significance testing or contribute to model 301s estimation. Default: 1 301s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 301s Dampen fraction modified estimates for low coverage 301s sites. Two parameters are unmodified and modified 301s pseudo read counts. This is equivalent to a beta prior 301s on the fraction estimate. Set to "0 0" to disable 301s dampened fraction estimation. Default: [2, 0] 301s 301s Output Argument: 301s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 301s Number of the most significant sites to store for 301s faster access. If a longer list of most significant 301s sites is required the list must be re-computed from 301s all batches. Very large values can increase RAM usage. 301s Default: 100000 301s 301s Multiprocessing Arguments: 301s --processes PROCESSES 301s Number of processes. Default: 1 301s 301s FAST5 Data Arguments: 301s --corrected-group CORRECTED_GROUP 301s FAST5 group created by resquiggle command. Default: 301s RawGenomeCorrected_000 301s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 301s FAST5 subgroup(s) (under /Analyses/[--basecall- 301s group]/) containing basecalls and created within 301s [--corrected-group] containing re-squiggle results. 301s Default: ['BaseCalled_template'] 301s 301s Miscellaneous Arguments: 301s --quiet, -q Don't print status information. 301s --help, -h Print this help message and exit 301s usage: tombo text_output browser_files 301s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 301s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 301s [--statistics-filename STATISTICS_FILENAME] 301s [--genome-fasta GENOME_FASTA] 301s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 301s [--browser-file-basename BROWSER_FILE_BASENAME] 301s [--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} ...]] 301s [--corrected-group CORRECTED_GROUP] 301s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 301s [--quiet] [--help] 301s 301s Data Arguments: 301s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 301s Directories containing fast5 files. 301s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 301s Set of directories containing fast5 files for control 301s reads, containing only canonical nucleotides. 301s --statistics-filename STATISTICS_FILENAME 301s File to save/load genomic base anchored statistics. 301s 301s Statistic Motif Filter Arguments: 301s --genome-fasta GENOME_FASTA 301s FASTA file used to re-squiggle. For faster sequence 301s access. 301s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 301s Ground truth, motif centered, modified base 301s descriptions for output filtering. Format descriptions 301s as: "motif:mod_pos:name". The mod_pos indicates the 301s modified base within the motif (1-based index). 301s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 301s output for identification of E. coli dam and dcm 301s methylation. 301s 301s Output Arguments: 301s --browser-file-basename BROWSER_FILE_BASENAME 301s Basename for output browser files. Two files (plus and 301s minus strand) will be produced for each --file-types 301s supplied. Filenames formatted as "[browser-file- 301s basename].[file- 301s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 301s Default: tombo_results 301s --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} ...] 301s Data types of genome browser files to produce. 301s Produced coverage files are in bedGraph format, while 301s all other file types will be in wiggle format 301s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 301s Default: "coverage" 301s 301s FAST5 Data Arguments: 301s --corrected-group CORRECTED_GROUP 301s FAST5 group created by resquiggle command. Default: 301s RawGenomeCorrected_000 301s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 301s FAST5 subgroup(s) (under /Analyses/[--basecall- 301s group]/) containing basecalls and created within 301s [--corrected-group] containing re-squiggle results. 301s Default: ['BaseCalled_template'] 301s 301s Miscellaneous Arguments: 301s --quiet, -q Don't print status information. 301s --help, -h Print this help message and exit 301s usage: tombo text_output signif_sequence_context --statistics-filename 301s STATISTICS_FILENAME 301s [--genome-fasta GENOME_FASTA] 301s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 301s [--num-regions NUM_REGIONS] 301s [--num-bases NUM_BASES] 301s [--sequences-filename SEQUENCES_FILENAME] 301s [--corrected-group CORRECTED_GROUP] 301s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 301s [--quiet] [--help] 301s 301s Required Argument: 301s --statistics-filename STATISTICS_FILENAME 301s File to save/load genomic base anchored statistics. 301s 301s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 301s --genome-fasta GENOME_FASTA 301s FASTA file used to re-squiggle. For faster sequence 301s access. 301s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 301s Directories containing fast5 files. 301s 301s Region Selection Arguments: 301s --num-regions NUM_REGIONS 301s Number of regions to plot. Default: 100 301s --num-bases NUM_BASES 301s Number of bases to plot/output. Default: 15 301s 301s Output Arguments: 301s --sequences-filename SEQUENCES_FILENAME 301s File for sequences from selected regions. Sequences 301s will be stored in FASTA format. Default: 301s tombo_results.significant_regions.fasta. 301s 301s FAST5 Data Arguments: 301s --corrected-group CORRECTED_GROUP 301s FAST5 group created by resquiggle command. Default: 301s RawGenomeCorrected_000 301s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 301s FAST5 subgroup(s) (under /Analyses/[--basecall- 301s group]/) containing basecalls and created within 301s [--corrected-group] containing re-squiggle results. 301s Default: ['BaseCalled_template'] 301s 301s Miscellaneous Arguments: 301s --quiet, -q Don't print status information. 301s --help, -h Print this help message and exit 301s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 301s [FAST5_BASEDIRS ...] 301s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 301s [--plot-standard-model] 301s [--plot-alternate-model {5mC,dcm,6mA,dam,CpG}] 301s [--overplot-threshold OVERPLOT_THRESHOLD] 301s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 301s [--num-regions NUM_REGIONS] 301s [--num-bases NUM_BASES] 301s [--pdf-filename PDF_FILENAME] 301s [--corrected-group CORRECTED_GROUP] 301s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 301s [--quiet] [--help] 301s 301s Required Argument: 301s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 301s Directories containing fast5 files. 301s 301s Comparison Arguments: 301s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 301s Set of directories containing fast5 files for control 301s reads, containing only canonical nucleotides. 301s --plot-standard-model 301s Add default standard model distribution to the plot. 301s --plot-alternate-model {5mC,dcm,6mA,dam,CpG} 301s Add alternative model distribution to the plot. 301s 301s Overplotting Arguments: 301s --overplot-threshold OVERPLOT_THRESHOLD 301s Coverage level to trigger alternative plot type 301s instead of raw signal. Default: 50 301s --overplot-type {Downsample,Boxplot,Quantile,Density} 301s Plot type for regions with higher coverage. Default: 301s Downsample 301s 301s Plotting Region Arguments: 301s --num-regions NUM_REGIONS 301s Number of regions to plot. Default: 10 301s --num-bases NUM_BASES 301s Number of bases to plot/output. Default: 21 301s 301s Output Argument: 301s --pdf-filename PDF_FILENAME 301s PDF filename to store plot(s). Default: 301s tombo_results.max_coverage.pdf 301s 301s FAST5 Data Arguments: 301s --corrected-group CORRECTED_GROUP 301s FAST5 group created by resquiggle command. Default: 301s RawGenomeCorrected_000 301s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 301s FAST5 subgroup(s) (under /Analyses/[--basecall- 301s group]/) containing basecalls and created within 301s [--corrected-group] containing re-squiggle results. 301s Default: ['BaseCalled_template'] 301s 301s Miscellaneous Arguments: 301s --quiet, -q Don't print status information. 301s --help, -h Print this help message and exit 302s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 302s [FAST5_BASEDIRS ...] --genome-locations 302s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 302s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 302s [--plot-standard-model] 302s [--plot-alternate-model {CpG,5mC,6mA,dam,dcm}] 302s [--overplot-threshold OVERPLOT_THRESHOLD] 302s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 302s [--num-bases NUM_BASES] 302s [--pdf-filename PDF_FILENAME] 302s [--corrected-group CORRECTED_GROUP] 302s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 302s [--quiet] [--help] 302s 302s Required Arguments: 302s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 302s Directories containing fast5 files. 302s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 302s Genomic locations at which to plot signal. Format 302s locations as "chrm:position[:strand] 302s [chrm2:position2[:strand2] ...]" (strand not 302s applicable for all applications) 302s 302s Comparison Arguments: 302s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 302s Set of directories containing fast5 files for control 302s reads, containing only canonical nucleotides. 302s --plot-standard-model 302s Add default standard model distribution to the plot. 302s --plot-alternate-model {CpG,5mC,6mA,dam,dcm} 302s Add alternative model distribution to the plot. 302s 302s Overplotting Arguments: 302s --overplot-threshold OVERPLOT_THRESHOLD 302s Coverage level to trigger alternative plot type 302s instead of raw signal. Default: 50 302s --overplot-type {Downsample,Boxplot,Quantile,Density} 302s Plot type for regions with higher coverage. Default: 302s Downsample 302s 302s Plotting Region Argument: 302s --num-bases NUM_BASES 302s Number of bases to plot/output. Default: 21 302s 302s Output Argument: 302s --pdf-filename PDF_FILENAME 302s PDF filename to store plot(s). Default: 302s tombo_results.genome_locations.pdf 302s 302s FAST5 Data Arguments: 302s --corrected-group CORRECTED_GROUP 302s FAST5 group created by resquiggle command. Default: 302s RawGenomeCorrected_000 302s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 302s FAST5 subgroup(s) (under /Analyses/[--basecall- 302s group]/) containing basecalls and created within 302s [--corrected-group] containing re-squiggle results. 302s Default: ['BaseCalled_template'] 302s 302s Miscellaneous Arguments: 302s --quiet, -q Don't print status information. 302s --help, -h Print this help message and exit 302s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 302s [FAST5_BASEDIRS ...] --motif MOTIF 302s --genome-fasta GENOME_FASTA 302s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 302s [--plot-standard-model] 302s [--plot-alternate-model {dcm,6mA,5mC,dam,CpG}] 302s [--overplot-threshold OVERPLOT_THRESHOLD] 302s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 302s [--num-regions NUM_REGIONS] 302s [--num-bases NUM_BASES] [--deepest-coverage] 302s [--pdf-filename PDF_FILENAME] 302s [--corrected-group CORRECTED_GROUP] 302s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 302s [--quiet] [--help] 302s 302s Required Arguments: 302s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 302s Directories containing fast5 files. 302s --motif MOTIF Motif of interest at which to plot signal and 302s statsitics. Supports IUPAC single letter codes (use T 302s for RNA). 302s --genome-fasta GENOME_FASTA 302s FASTA file used to re-squiggle. For faster sequence 302s access. 302s 302s Comparison Arguments: 302s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 302s Set of directories containing fast5 files for control 302s reads, containing only canonical nucleotides. 302s --plot-standard-model 302s Add default standard model distribution to the plot. 302s --plot-alternate-model {dcm,6mA,5mC,dam,CpG} 302s Add alternative model distribution to the plot. 302s 302s Overplotting Arguments: 302s --overplot-threshold OVERPLOT_THRESHOLD 302s Coverage level to trigger alternative plot type 302s instead of raw signal. Default: 50 302s --overplot-type {Downsample,Boxplot,Quantile,Density} 302s Plot type for regions with higher coverage. Default: 302s Downsample 302s 302s Plotting Region Arguments: 302s --num-regions NUM_REGIONS 302s Number of regions to plot. Default: 10 302s --num-bases NUM_BASES 302s Number of bases to plot/output. Default: 21 302s --deepest-coverage Plot the deepest coverage regions. 302s 302s Output Argument: 302s --pdf-filename PDF_FILENAME 302s PDF filename to store plot(s). Default: 302s tombo_results.motif_centered.pdf 302s 302s FAST5 Data Arguments: 302s --corrected-group CORRECTED_GROUP 302s FAST5 group created by resquiggle command. Default: 302s RawGenomeCorrected_000 302s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 302s FAST5 subgroup(s) (under /Analyses/[--basecall- 302s group]/) containing basecalls and created within 302s [--corrected-group] containing re-squiggle results. 302s Default: ['BaseCalled_template'] 302s 302s Miscellaneous Arguments: 302s --quiet, -q Don't print status information. 302s --help, -h Print this help message and exit 302s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 302s [FAST5_BASEDIRS ...] --control-fast5-basedirs 302s CONTROL_FAST5_BASEDIRS 302s [CONTROL_FAST5_BASEDIRS ...] 302s [--overplot-threshold OVERPLOT_THRESHOLD] 302s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 302s [--num-regions NUM_REGIONS] 302s [--num-bases NUM_BASES] 302s [--pdf-filename PDF_FILENAME] 302s [--sequences-filename SEQUENCES_FILENAME] 302s [--corrected-group CORRECTED_GROUP] 302s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 302s [--quiet] [--help] 302s 302s Required Arguments: 302s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 302s Directories containing fast5 files. 302s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 302s Set of directories containing fast5 files for control 302s reads, containing only canonical nucleotides. 302s 302s Overplotting Arguments: 302s --overplot-threshold OVERPLOT_THRESHOLD 302s Coverage level to trigger alternative plot type 302s instead of raw signal. Default: 50 302s --overplot-type {Downsample,Boxplot,Quantile,Density} 302s Plot type for regions with higher coverage. Default: 302s Downsample 302s 302s Plotting Region Arguments: 302s --num-regions NUM_REGIONS 302s Number of regions to plot. Default: 10 302s --num-bases NUM_BASES 302s Number of bases to plot/output. Default: 21 302s 302s Output Arguments: 302s --pdf-filename PDF_FILENAME 302s PDF filename to store plot(s). Default: 302s tombo_results.max_difference.pdf 302s --sequences-filename SEQUENCES_FILENAME 302s File for sequences from selected regions. Sequences 302s will be stored in FASTA format. Default: None. 302s 302s FAST5 Data Arguments: 302s --corrected-group CORRECTED_GROUP 302s FAST5 group created by resquiggle command. Default: 302s RawGenomeCorrected_000 302s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 302s FAST5 subgroup(s) (under /Analyses/[--basecall- 302s group]/) containing basecalls and created within 302s [--corrected-group] containing re-squiggle results. 302s Default: ['BaseCalled_template'] 302s 302s Miscellaneous Arguments: 302s --quiet, -q Don't print status information. 302s --help, -h Print this help message and exit 302s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 302s [FAST5_BASEDIRS ...] --statistics-filename 302s STATISTICS_FILENAME 302s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 302s [--plot-standard-model] 302s [--plot-alternate-model {5mC,6mA,dcm,CpG,dam}] 302s [--overplot-threshold OVERPLOT_THRESHOLD] 302s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 302s [--num-regions NUM_REGIONS] 302s [--num-bases NUM_BASES] 302s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 302s [--pdf-filename PDF_FILENAME] 302s [--sequences-filename SEQUENCES_FILENAME] 302s [--corrected-group CORRECTED_GROUP] 302s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 302s [--quiet] [--help] 302s 302s Required Arguments: 302s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 302s Directories containing fast5 files. 302s --statistics-filename STATISTICS_FILENAME 302s File to save/load genomic base anchored statistics. 302s 302s Comparison Arguments: 302s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 302s Set of directories containing fast5 files for control 302s reads, containing only canonical nucleotides. 302s --plot-standard-model 302s Add default standard model distribution to the plot. 302s --plot-alternate-model {5mC,6mA,dcm,CpG,dam} 302s Add alternative model distribution to the plot. 302s 302s Overplotting Arguments: 302s --overplot-threshold OVERPLOT_THRESHOLD 302s Coverage level to trigger alternative plot type 302s instead of raw signal. Default: 50 302s --overplot-type {Downsample,Boxplot,Quantile,Density} 302s Plot type for regions with higher coverage. Default: 302s Downsample 302s 302s Plotting Region Arguments: 302s --num-regions NUM_REGIONS 302s Number of regions to plot. Default: 10 302s --num-bases NUM_BASES 302s Number of bases to plot/output. Default: 21 302s 302s Statistical Argument: 302s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 302s Dampen fraction modified estimates for low coverage 302s sites. Two parameters are unmodified and modified 302s pseudo read counts. This is equivalent to a beta prior 302s on the fraction estimate. Set to "0 0" to disable 302s dampened fraction estimation. Default: [2, 0] 302s 302s Output Arguments: 302s --pdf-filename PDF_FILENAME 302s PDF filename to store plot(s). Default: 302s tombo_results.significant_difference.pdf 302s --sequences-filename SEQUENCES_FILENAME 302s File for sequences from selected regions. Sequences 302s will be stored in FASTA format. Default: None. 302s 302s FAST5 Data Arguments: 302s --corrected-group CORRECTED_GROUP 302s FAST5 group created by resquiggle command. Default: 302s RawGenomeCorrected_000 302s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 302s FAST5 subgroup(s) (under /Analyses/[--basecall- 302s group]/) containing basecalls and created within 302s [--corrected-group] containing re-squiggle results. 302s Default: ['BaseCalled_template'] 302s 302s Miscellaneous Arguments: 302s --quiet, -q Don't print status information. 302s --help, -h Print this help message and exit 302s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 302s [FAST5_BASEDIRS ...] --motif MOTIF 302s --statistics-filename STATISTICS_FILENAME 302s --genome-fasta GENOME_FASTA 302s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 302s [--plot-standard-model] 302s [--plot-alternate-model {CpG,5mC,6mA,dcm,dam}] 302s [--overplot-threshold OVERPLOT_THRESHOLD] 302s [--num-regions NUM_REGIONS] 302s [--num-context NUM_CONTEXT] 302s [--num-statistics NUM_STATISTICS] 302s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 302s [--pdf-filename PDF_FILENAME] 302s [--corrected-group CORRECTED_GROUP] 302s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 302s [--quiet] [--help] 302s 302s Required Arguments: 302s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 302s Directories containing fast5 files. 302s --motif MOTIF Motif of interest at which to plot signal and 302s statsitics. Supports IUPAC single letter codes (use T 302s for RNA). 302s --statistics-filename STATISTICS_FILENAME 302s File to save/load genomic base anchored statistics. 302s --genome-fasta GENOME_FASTA 302s FASTA file used to re-squiggle. For faster sequence 302s access. 302s 302s Comparison Arguments: 302s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 302s Set of directories containing fast5 files for control 302s reads, containing only canonical nucleotides. 302s --plot-standard-model 302s Add default standard model distribution to the plot. 302s --plot-alternate-model {CpG,5mC,6mA,dcm,dam} 302s Add alternative model distribution to the plot. 302s 302s Overplotting Argument: 302s --overplot-threshold OVERPLOT_THRESHOLD 302s Coverage level to trigger alternative plot type 302s instead of raw signal. Default: 50 302s 302s Plotting Region Arguments: 302s --num-regions NUM_REGIONS 302s Number of regions to plot. Default: 3 302s --num-context NUM_CONTEXT 302s Number of context bases around motif. Default: 5 302s --num-statistics NUM_STATISTICS 302s Number of motif centered regions to include in 302s statistic distributions. Default: 200 302s 302s Statistical Argument: 302s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 302s Dampen fraction modified estimates for low coverage 302s sites. Two parameters are unmodified and modified 302s pseudo read counts. This is equivalent to a beta prior 302s on the fraction estimate. Set to "0 0" to disable 302s dampened fraction estimation. Default: [2, 0] 302s 302s Output Argument: 302s --pdf-filename PDF_FILENAME 302s PDF filename to store plot(s). Default: 302s tombo_results.motif_statistics.pdf 302s 302s FAST5 Data Arguments: 302s --corrected-group CORRECTED_GROUP 302s FAST5 group created by resquiggle command. Default: 302s RawGenomeCorrected_000 302s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 302s FAST5 subgroup(s) (under /Analyses/[--basecall- 302s group]/) containing basecalls and created within 302s [--corrected-group] containing re-squiggle results. 302s Default: ['BaseCalled_template'] 302s 302s Miscellaneous Arguments: 302s --quiet, -q Don't print status information. 302s --help, -h Print this help message and exit 302s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 302s [GENOME_LOCATIONS ...] 302s --per-read-statistics-filename 302s PER_READ_STATISTICS_FILENAME 302s [--genome-fasta GENOME_FASTA] 302s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 302s [--num-reads NUM_READS] [--num-bases NUM_BASES] 302s [--box-center] [--pdf-filename PDF_FILENAME] 302s [--corrected-group CORRECTED_GROUP] 302s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 302s [--quiet] [--help] 302s 302s Required Arguments: 302s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 302s Genomic locations at which to plot signal. Format 302s locations as "chrm:position[:strand] 302s [chrm2:position2[:strand2] ...]" (strand not 302s applicable for all applications) 302s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 302s Binary file containing per-read statistics from 302s statistical testing. 302s 302s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 302s --genome-fasta GENOME_FASTA 302s FASTA file used to re-squiggle. For faster sequence 302s access. 302s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 302s Directories containing fast5 files. 302s 302s Plotting Region Arguments: 302s --num-reads NUM_READS 302s Number of reads to plot. Default: 100 302s --num-bases NUM_BASES 302s Number of bases to plot/output. Default: 51 302s --box-center Plot a box around the central base. 302s 302s Output Argument: 302s --pdf-filename PDF_FILENAME 302s PDF filename to store plot(s). Default: 302s tombo_results.per_read_stats.pdf 302s 302s FAST5 Data Arguments: 302s --corrected-group CORRECTED_GROUP 302s FAST5 group created by resquiggle command. Default: 302s RawGenomeCorrected_000 302s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 302s FAST5 subgroup(s) (under /Analyses/[--basecall- 302s group]/) containing basecalls and created within 302s [--corrected-group] containing re-squiggle results. 302s Default: ['BaseCalled_template'] 302s 302s Miscellaneous Arguments: 302s --quiet, -q Don't print status information. 302s --help, -h Print this help message and exit 302s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 302s [STATISTICS_FILENAMES ...] 302s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 302s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 302s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 302s [--genome-fasta GENOME_FASTA] 302s [--pdf-filename PDF_FILENAME] 302s [--statistics-per-block STATISTICS_PER_BLOCK] 302s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 302s [--quiet] [--help] 302s 302s Required Argument: 302s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 302s Files to load genomic base anchored statistics. 302s 302s Ground Truth Arguments (provide bed files or motifs): 302s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 302s Modification description and bed format files 302s containing single base locations of ground truth 302s modified sites. Bed files should contain 6 fields 302s including strand. Format descriptions as 302s "mod_name:locs.bed". Example: "CpG 302s bisulfite":bisulfite_locs.bed 302s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 302s Bed format files containing single base locations of 302s ground truth unmodified sites. Bed files should 302s contain 6 fields including strand. 302s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 302s Ground truth, motif centered, modified base 302s descriptions for computing ROC and PR curves. Each 302s statistics file is associated with a set of motif 302s descriptions. Format descriptions as: 302s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 302s mod_pos indicates the alternate-base within the motif 302s (1-based index). Example: CCWGG:2:"dcm 302s 5mC"::GATC:2:"dam 6mA" would assess the performance of 302s a single Tombo statistics file for identification of 302s E. coli dam and dcm methylation. 302s --genome-fasta GENOME_FASTA 302s FASTA file used to re-squiggle. For faster sequence 302s access. 302s 302s Output Arguments: 302s --pdf-filename PDF_FILENAME 302s PDF filename to store plot(s). Default: 302s tombo_results.roc.pdf 302s 302s Down-sampling Arguments: 302s --statistics-per-block STATISTICS_PER_BLOCK 302s Number of randomly selected per-read, per-base 302s statistics to extract from each genomic block for 302s plotting. Default: Include all stats 302s --total-statistics-limit TOTAL_STATISTICS_LIMIT 302s Total per-read statistics to be extracted for 302s plotting. Avoids memory overflow for large runs. 302s Default: 5000000 302s 302s Miscellaneous Arguments: 302s --quiet, -q Don't print status information. 302s --help, -h Print this help message and exit 302s usage: tombo plot per_read_roc --per-read-statistics-filenames 302s PER_READ_STATISTICS_FILENAMES 302s [PER_READ_STATISTICS_FILENAMES ...] 302s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 302s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 302s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 302s [--genome-fasta GENOME_FASTA] 302s [--statistics-per-block STATISTICS_PER_BLOCK] 302s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 302s [--pdf-filename PDF_FILENAME] [--quiet] 302s [--help] 302s 302s Required Argument: 302s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 302s Binary files containing per-read statistics from 302s statistical testing. 302s 302s Ground Truth Arguments (provide bed files or motifs): 302s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 302s Modification description and bed format files 302s containing single base locations of ground truth 302s modified sites. Bed files should contain 6 fields 302s including strand. Format descriptions as 302s "mod_name:locs.bed". Example: "CpG 302s bisulfite":bisulfite_locs.bed 302s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 302s Bed format files containing single base locations of 302s ground truth unmodified sites. Bed files should 302s contain 6 fields including strand. 302s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 302s Ground truth, motif centered, modified base 302s descriptions for computing ROC and PR curves. Each 302s statistics file is associated with a set of motif 302s descriptions. Format descriptions as: 302s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 302s mod_pos indicates the alternate-base within the motif 302s (1-based index). Example: CCWGG:2:"dcm 302s 5mC"::GATC:2:"dam 6mA" would assess the performance of 302s a single Tombo statistics file for identification of 302s E. coli dam and dcm methylation. 302s --genome-fasta GENOME_FASTA 302s FASTA file used to re-squiggle. For faster sequence 302s access. 302s 302s Down-sampling Arguments: 302s --statistics-per-block STATISTICS_PER_BLOCK 302s Number of randomly selected per-read, per-base 302s statistics to extract from each genomic block for 302s plotting. Default: 100000 302s --total-statistics-limit TOTAL_STATISTICS_LIMIT 302s Total per-read statistics to be extracted for 302s plotting. Avoids memory overflow for large runs. 302s Default: 5000000 302s 302s Output Arguments: 302s --pdf-filename PDF_FILENAME 302s PDF filename to store plot(s). Default: 302s tombo_results.per_reads_roc.pdf 302s 302s Miscellaneous Arguments: 302s --quiet, -q Don't print status information. 302s --help, -h Print this help message and exit 303s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 303s [--upstream-bases {0,1,2,3,4}] 303s [--downstream-bases {0,1,2,3,4}] [--read-mean] 303s [--num-kmer-threshold NUM_KMER_THRESHOLD] 303s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 303s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 303s [--corrected-group CORRECTED_GROUP] 303s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 303s [--quiet] [--help] 303s 303s Required Argument: 303s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 303s Directories containing fast5 files. 303s 303s Data Processing Arguments: 303s --upstream-bases {0,1,2,3,4} 303s Upstream bases in k-mer. Default: 1 303s --downstream-bases {0,1,2,3,4} 303s Downstream bases in k-mer. Default: 2 303s --read-mean Plot k-mer means across whole reads as opposed to 303s individual k-mer event levels. 303s --num-kmer-threshold NUM_KMER_THRESHOLD 303s Observations of each k-mer required to include a read 303s in read level averages. Default: 1 303s 303s Plotting Region Arguments: 303s --num-reads NUM_READS 303s Number of reads to plot. Default: 100 303s 303s Output Arguments: 303s --pdf-filename PDF_FILENAME 303s PDF filename to store plot(s). Default: 303s tombo_results.kmer_distribution.pdf 303s --r-data-filename R_DATA_FILENAME 303s Filename to save R data structure. Default: Don't save 303s --dont-plot Don't plot result. Useful to produce only R data file. 303s 303s FAST5 Data Arguments: 303s --corrected-group CORRECTED_GROUP 303s FAST5 group created by resquiggle command. Default: 303s RawGenomeCorrected_000 303s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 303s FAST5 subgroup(s) (under /Analyses/[--basecall- 303s group]/) containing basecalls and created within 303s [--corrected-group] containing re-squiggle results. 303s Default: ['BaseCalled_template'] 303s 303s Miscellaneous Arguments: 303s --quiet, -q Don't print status information. 303s --help, -h Print this help message and exit 303s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 303s [FAST5_BASEDIRS ...] 303s --control-fast5-basedirs 303s CONTROL_FAST5_BASEDIRS 303s [CONTROL_FAST5_BASEDIRS ...] 303s --statistics-filename 303s STATISTICS_FILENAME 303s [--genome-fasta GENOME_FASTA] 303s [--processes PROCESSES] 303s [--num-regions NUM_REGIONS] 303s [--num-bases NUM_BASES] 303s [--slide-span SLIDE_SPAN] 303s [--pdf-filename PDF_FILENAME] 303s [--r-data-filename R_DATA_FILENAME] 303s [--corrected-group CORRECTED_GROUP] 303s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 303s [--quiet] [--help] 303s 303s Required Arguments: 303s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 303s Directories containing fast5 files. 303s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 303s Set of directories containing fast5 files for control 303s reads, containing only canonical nucleotides. 303s --statistics-filename STATISTICS_FILENAME 303s File to save/load genomic base anchored statistics. 303s 303s FASTA Sequence Argument: 303s --genome-fasta GENOME_FASTA 303s FASTA file used to re-squiggle. For faster sequence 303s access. 303s 303s Multiprocessing Argument: 303s --processes PROCESSES 303s Number of processes. Default: 1 303s 303s Plotting Region Arguments: 303s --num-regions NUM_REGIONS 303s Number of regions to plot. Default: 10 303s --num-bases NUM_BASES 303s Number of bases to plot/output. Default: 21 303s --slide-span SLIDE_SPAN 303s Number of bases offset over which to search when 303s computing distances for signal cluster plotting. 303s Default: 0 (exact position) 303s 303s Output Arguments: 303s --pdf-filename PDF_FILENAME 303s PDF filename to store plot(s). Default: 303s tombo_results.signal_clusters.pdf 303s --r-data-filename R_DATA_FILENAME 303s Filename to save R data structure. Default: Don't save 303s 303s FAST5 Data Arguments: 303s --corrected-group CORRECTED_GROUP 303s FAST5 group created by resquiggle command. Default: 303s RawGenomeCorrected_000 303s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 303s FAST5 subgroup(s) (under /Analyses/[--basecall- 303s group]/) containing basecalls and created within 303s [--corrected-group] containing re-squiggle results. 303s Default: ['BaseCalled_template'] 303s 303s Miscellaneous Arguments: 303s --quiet, -q Don't print status information. 303s --help, -h Print this help message and exit 303s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 303s 303s Required Arguments: 303s fast5s_basedir Directory containing fast5 files. All files ending in 303s "fast5" found recursively within this base directory will be 303s processed. 303s 303s Miscellaneous Arguments: 303s --quiet, -q Don't print status information. 303s --help, -h Print this help message and exit 303s usage: tombo build_model event_resquiggle 303s [--minimap2-executable MINIMAP2_EXECUTABLE] 303s [--minimap2-index MINIMAP2_INDEX] 303s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 303s [--graphmap-executable GRAPHMAP_EXECUTABLE] 303s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 303s [--normalization-type {median,pA,pA_raw,none}] 303s [--pore-model-filename PORE_MODEL_FILENAME] 303s [--outlier-threshold OUTLIER_THRESHOLD] 303s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 303s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 303s [--timeout TIMEOUT] 303s [--cpts-limit CPTS_LIMIT] 303s [--skip-index] [--overwrite] 303s [--failed-reads-filename FAILED_READS_FILENAME] 303s [--include-event-stdev] 303s [--corrected-group CORRECTED_GROUP] 303s [--basecall-group BASECALL_GROUP] 303s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 303s [--processes PROCESSES] 303s [--align-processes ALIGN_PROCESSES] 303s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 303s [--resquiggle-processes RESQUIGGLE_PROCESSES] 303s [--quiet] [--help] 303s fast5s_basedir reference_fasta 303s 303s Required Arguments: 303s fast5s_basedir Directory containing fast5 files. All files ending in 303s "fast5" found recursively within this base directory 303s will be processed. 303s reference_fasta Reference genome/transcriptome FASTA file for mapping. 303s 303s Mapper Arguments (One mapper is required): 303s --minimap2-executable MINIMAP2_EXECUTABLE 303s Path to minimap2 executable. 303s --minimap2-index MINIMAP2_INDEX 303s Path to minimap2 index (with map-ont preset) file 303s corresponding to the [genome_fasta] provided. 303s --bwa-mem-executable BWA_MEM_EXECUTABLE 303s Path to bwa-mem executable. 303s --graphmap-executable GRAPHMAP_EXECUTABLE 303s Path to graphmap executable. 303s --alignment-batch-size ALIGNMENT_BATCH_SIZE 303s Number of reads included in each alignment call. Note: 303s A new system mapping call is made for each batch 303s (including loading of the genome), so it is advised to 303s use larger values for larger genomes. Default: 1000 303s 303s Signal Processing Arguments: 303s --normalization-type {median,pA,pA_raw,none} 303s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 303s as in the ONT events (using offset, range and 303s digitization), "pA": k-mer-based correction for pA 303s drift as in nanopolish (requires [--pore-model- 303s filename]), "median": median and MAD from raw signal. 303s Default: median 303s --pore-model-filename PORE_MODEL_FILENAME 303s File containing kmer model parameters (level_mean and 303s level_stdv) used in order to compute kmer-based 303s corrected pA values. E.g. https://github.com/jts/nanop 303s olish/blob/master/etc/r9- 303s models/template_median68pA.5mers.model 303s --outlier-threshold OUTLIER_THRESHOLD 303s Windosrize the signal at this number of scale values. 303s Negative value disables outlier clipping. Default: 303s 5.000000 303s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 303s Specify the 2 parameters for segmentation 1) running 303s neighboring windows width 2) minimum raw observations 303s per genomic base. Sample type defaults: RNA : 12 6 || 303s DNA : 5 3 303s 303s Read Filtering Arguments: 303s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 303s Filter reads based on observations per base percentile 303s thresholds. Format thresholds as "percentile:thresh 303s [pctl2:thresh2 ...]". For example to filter reads with 303s 99th pctl > 200 obs/base or max > 5k obs/base use 303s "99:200 100:5000". 303s --timeout TIMEOUT Timeout in seconds for processing a single read. 303s Default: No timeout. 303s --cpts-limit CPTS_LIMIT 303s Maximum number of changepoints to find within a single 303s indel group. Default: No limit. 303s 303s Input/Output Arguments: 303s --skip-index Skip creation of tombo index. This drastically slows 303s downstream tombo commands. Default stores tombo index 303s named ".[--fast5-basedir].[--corrected- 303s group].tombo.index" to be loaded automatically for 303s downstream commands. 303s --overwrite Overwrite previous corrected group in FAST5 files. 303s Note: only effects --corrected-group or --new- 303s corrected-group. 303s --failed-reads-filename FAILED_READS_FILENAME 303s Output failed read filenames with assoicated error. 303s Default: Do not store failed reads. 303s --include-event-stdev 303s Include corrected event standard deviation in output 303s FAST5 data. 303s 303s FAST5 Data Arguments: 303s --corrected-group CORRECTED_GROUP 303s FAST5 group created by resquiggle command. Default: 303s RawGenomeCorrected_000 303s --basecall-group BASECALL_GROUP 303s FAST5 group obtain original basecalls (under Analyses 303s group). Default: Basecall_1D_000 303s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 303s FAST5 subgroup(s) (under /Analyses/[--basecall- 303s group]/) containing basecalls and created within 303s [--corrected-group] containing re-squiggle results. 303s Default: ['BaseCalled_template'] 303s 303s Multiprocessing Arguments: 303s --processes PROCESSES 303s Number of processes. Default: 2 303s --align-processes ALIGN_PROCESSES 303s Number of processes to use for parsing and aligning 303s original basecalls. Each process will independently 303s load the genome into memory, so use caution with 303s larger genomes (e.g. human). Default: 1 303s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 303s Number of threads to use for aligner system call. 303s Default: [--processes] / (2 * [--align-processes)] 303s --resquiggle-processes RESQUIGGLE_PROCESSES 303s Number of processes to use for resquiggle algorithm. 303s Default: [--processes] / 2 303s 303s Miscellaneous Arguments: 303s --quiet, -q Don't print status information. 303s --help, -h Print this help message and exit 303s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 303s [FAST5_BASEDIRS ...] 303s --tombo-model-filename 303s TOMBO_MODEL_FILENAME 303s [--estimate-mean] 303s [--kmer-specific-sd] 303s [--upstream-bases {0,1,2,3,4}] 303s [--downstream-bases {0,1,2,3,4}] 303s [--minimum-test-reads MINIMUM_TEST_READS] 303s [--coverage-threshold COVERAGE_THRESHOLD] 303s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 303s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 303s [--processes PROCESSES] 303s [--corrected-group CORRECTED_GROUP] 303s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 303s [--quiet] [--help] 303s 303s Required Arguments: 303s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 303s Directories containing fast5 files. 303s --tombo-model-filename TOMBO_MODEL_FILENAME 303s Filename to save Tombo model. 303s 303s Modeling Arguments: 303s --estimate-mean Use the mean instead of median for model level 303s estimation. Note: This can cause poor fits due to 303s outliers 303s --kmer-specific-sd Estimate standard deviation for each k-mers 303s individually. 303s --upstream-bases {0,1,2,3,4} 303s Upstream bases in k-mer. Default: 1 303s --downstream-bases {0,1,2,3,4} 303s Downstream bases in k-mer. Default: 2 303s 303s Filtering Arguments: 303s --minimum-test-reads MINIMUM_TEST_READS 303s Number of reads required at a position to perform 303s significance testing or contribute to model 303s estimation. Default: 10 303s --coverage-threshold COVERAGE_THRESHOLD 303s Maximum mean coverage per region when estimating k-mer 303s model (limits compute time for deep samples). Default: 303s 100 303s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 303s Number of each k-mer observations required in order to 303s produce a reference (genomic locations for standard 303s reference and per-read for alternative reference). 303s Default: 5 303s 303s Multiprocessing Arguments: 303s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 303s Size of regions over which to multiprocesses statistic 303s computation. For very deep samples a smaller value is 303s recommmended in order to control memory consumption. 303s Default: 10000 303s --processes PROCESSES 303s Number of processes. Default: 1 303s 303s FAST5 Data Arguments: 303s --corrected-group CORRECTED_GROUP 303s FAST5 group created by resquiggle command. Default: 303s RawGenomeCorrected_000 303s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 303s FAST5 subgroup(s) (under /Analyses/[--basecall- 303s group]/) containing basecalls and created within 303s [--corrected-group] containing re-squiggle results. 303s Default: ['BaseCalled_template'] 303s 303s Miscellaneous Arguments: 303s --quiet, -q Don't print status information. 303s --help, -h Print this help message and exit 303s usage: tombo build_model estimate_alt_reference --alternate-model-filename 303s ALTERNATE_MODEL_FILENAME 303s --alternate-model-name 303s ALTERNATE_MODEL_NAME 303s --alternate-model-base 303s {A,C,G,T} 303s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 303s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 303s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 303s [--control-density-filename CONTROL_DENSITY_FILENAME] 303s [--dna] [--rna] 303s [--tombo-model-filename TOMBO_MODEL_FILENAME] 303s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 303s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 303s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 303s [--save-density-basename SAVE_DENSITY_BASENAME] 303s [--processes PROCESSES] 303s [--corrected-group CORRECTED_GROUP] 303s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 303s [--quiet] [--help] 303s 303s Required Arguments: 303s --alternate-model-filename ALTERNATE_MODEL_FILENAME 303s Tombo model for alternative likelihood ratio 303s significance testing. 303s --alternate-model-name ALTERNATE_MODEL_NAME 303s A short name to associate with this alternate model 303s (e.g. 5mC, 6mA, etc.). This text will be included in 303s output filenames when this model is used for testing. 303s --alternate-model-base {A,C,G,T} 303s Non-standard base is an alternative to this base. 303s 303s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 303s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 303s Directories containing fast5 files. 303s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 303s Set of directories containing fast5 files for control 303s reads, containing only canonical nucleotides. 303s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 303s File containing k-mer level kernel density estimates 303s for the alternative sample saved using --save-density- 303s basename. 303s --control-density-filename CONTROL_DENSITY_FILENAME 303s File containing k-mer level kernel density estimates 303s for the control sample saved using --save-density- 303s basename. 303s 303s Standard Model Arguments: 303s --dna Explicitly select canonical DNA model. Default: 303s Automatically determine from FAST5s 303s --rna Explicitly select canonical RNA model. Default: 303s Automatically determine from FAST5s 303s --tombo-model-filename TOMBO_MODEL_FILENAME 303s Tombo model filename. If no file is provided, the 303s default DNA or RNA Tombo model will be used. 303s 303s Model Fitting Arguments: 303s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 303s When esitmating the alternative base incorporation 303s rate, this percent of k-mers are assumed to have 303s significantly shifted signal so the alternative 303s distribution minimally overlaps the standard base 303s distribution. Default: 5.000000 303s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 303s Bandwidth applied when performing Gaussian kernal 303s density esitmation on standard and alternative base 303s signal distributions. Default: 0.050000 303s 303s Filtering Argument: 303s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 303s Number of each k-mer observations required in order to 303s produce a reference (genomic locations for standard 303s reference and per-read for alternative reference). 303s Default: 1000 303s 303s Output Argument: 303s --save-density-basename SAVE_DENSITY_BASENAME 303s Basename to save alternative model estimation density 303s estimation information. See scripts/debug_est_alt.R 303s for info use example. Default: Don't save. 303s 303s Multiprocessing Arguments: 303s --processes PROCESSES 303s Number of processes. Default: 1 303s 303s FAST5 Data Arguments: 303s --corrected-group CORRECTED_GROUP 303s FAST5 group created by resquiggle command. Default: 303s RawGenomeCorrected_000 303s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 303s FAST5 subgroup(s) (under /Analyses/[--basecall- 303s group]/) containing basecalls and created within 303s [--corrected-group] containing re-squiggle results. 303s Default: ['BaseCalled_template'] 303s 303s Miscellaneous Arguments: 303s --quiet, -q Don't print status information. 303s --help, -h Print this help message and exit 303s This test only tests the help system 303s There is an extensive test in 303s 303s tombo/tests/shell_tests.sh 303s 303s but this requires to download larger data 303s sets which is not done for the moment. 304s autopkgtest [10:57:02]: test run-unit-test: -----------------------] 308s autopkgtest [10:57:06]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 308s run-unit-test PASS 311s autopkgtest [10:57:09]: @@@@@@@@@@@@@@@@@@@@ summary 311s run-unit-test PASS