0s autopkgtest [09:59:21]: starting date and time: 2024-10-30 09:59:21+0000 0s autopkgtest [09:59:21]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [09:59:21]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6wlphw80/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-6.secgroup --name adt-plucky-s390x-tombo-20241030-095920-juju-7f2275-prod-proposed-migration-environment-15-bf6178d7-47b9-4a88-86ed-4c05ce562492 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 136s autopkgtest [10:01:37]: testbed dpkg architecture: s390x 136s autopkgtest [10:01:37]: testbed apt version: 2.9.8 136s autopkgtest [10:01:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 139s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 139s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [2840 B] 139s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [212 kB] 139s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 139s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [28.1 kB] 139s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [42.1 kB] 139s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [234 kB] 139s Fetched 600 kB in 1s (944 kB/s) 139s Reading package lists... 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 141s Calculating upgrade... 141s The following packages were automatically installed and are no longer required: 141s libperl5.38t64 perl-modules-5.38 141s Use 'sudo apt autoremove' to remove them. 141s The following NEW packages will be installed: 141s libperl5.40 perl-modules-5.40 python3-jaraco.text 141s The following packages will be upgraded: 141s info install-info libkeyutils1 liblocale-gettext-perl libtext-charwidth-perl 141s libtext-iconv-perl perl perl-base python3-pkg-resources python3-setuptools 141s vim-common vim-tiny xxd 141s 13 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 141s Need to get 12.6 MB of archives. 141s After this operation, 50.3 MB of additional disk space will be used. 141s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x perl-modules-5.40 all 5.40.0-6 [3214 kB] 141s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libperl5.40 s390x 5.40.0-6 [4984 kB] 142s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x perl s390x 5.40.0-6 [262 kB] 142s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x perl-base s390x 5.40.0-6 [1971 kB] 142s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x liblocale-gettext-perl s390x 1.07-7build1 [15.9 kB] 142s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libtext-iconv-perl s390x 1.7-8build4 [13.8 kB] 142s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libtext-charwidth-perl s390x 0.04-11build4 [9646 B] 142s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x install-info s390x 7.1.1-1 [64.8 kB] 142s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libkeyutils1 s390x 1.6.3-4ubuntu2 [9960 B] 142s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x vim-tiny s390x 2:9.1.0777-1ubuntu1 [664 kB] 142s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x vim-common all 2:9.1.0777-1ubuntu1 [394 kB] 142s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x xxd s390x 2:9.1.0777-1ubuntu1 [66.5 kB] 142s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x info s390x 7.1.1-1 [149 kB] 142s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jaraco.text all 4.0.0-1 [11.5 kB] 142s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-pkg-resources all 75.2.0-1 [134 kB] 142s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-setuptools all 75.2.0-1 [657 kB] 142s Fetched 12.6 MB in 1s (11.2 MB/s) 142s (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 ... 55329 files and directories currently installed.) 142s Preparing to unpack .../perl_5.40.0-6_s390x.deb ... 142s Unpacking perl (5.40.0-6) over (5.38.2-5) ... 142s Selecting previously unselected package perl-modules-5.40. 142s Preparing to unpack .../perl-modules-5.40_5.40.0-6_all.deb ... 142s Unpacking perl-modules-5.40 (5.40.0-6) ... 142s Selecting previously unselected package libperl5.40:s390x. 142s Preparing to unpack .../libperl5.40_5.40.0-6_s390x.deb ... 142s Unpacking libperl5.40:s390x (5.40.0-6) ... 143s Preparing to unpack .../perl-base_5.40.0-6_s390x.deb ... 143s Unpacking perl-base (5.40.0-6) over (5.38.2-5) ... 143s Setting up perl-base (5.40.0-6) ... 143s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 57408 files and directories currently installed.) 143s Preparing to unpack .../liblocale-gettext-perl_1.07-7build1_s390x.deb ... 143s Unpacking liblocale-gettext-perl (1.07-7build1) over (1.07-7) ... 143s Preparing to unpack .../libtext-iconv-perl_1.7-8build4_s390x.deb ... 143s Unpacking libtext-iconv-perl:s390x (1.7-8build4) over (1.7-8build3) ... 143s Preparing to unpack .../libtext-charwidth-perl_0.04-11build4_s390x.deb ... 143s Unpacking libtext-charwidth-perl:s390x (0.04-11build4) over (0.04-11build3) ... 143s Preparing to unpack .../install-info_7.1.1-1_s390x.deb ... 143s Unpacking install-info (7.1.1-1) over (7.1-3build2) ... 143s Setting up install-info (7.1.1-1) ... 143s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 57408 files and directories currently installed.) 143s Preparing to unpack .../0-libkeyutils1_1.6.3-4ubuntu2_s390x.deb ... 143s Unpacking libkeyutils1:s390x (1.6.3-4ubuntu2) over (1.6.3-3build1) ... 143s Preparing to unpack .../1-vim-tiny_2%3a9.1.0777-1ubuntu1_s390x.deb ... 143s Unpacking vim-tiny (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 143s Preparing to unpack .../2-vim-common_2%3a9.1.0777-1ubuntu1_all.deb ... 143s Unpacking vim-common (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 143s Preparing to unpack .../3-xxd_2%3a9.1.0777-1ubuntu1_s390x.deb ... 143s Unpacking xxd (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 143s Preparing to unpack .../4-info_7.1.1-1_s390x.deb ... 143s Unpacking info (7.1.1-1) over (7.1-3build2) ... 143s Selecting previously unselected package python3-jaraco.text. 143s Preparing to unpack .../5-python3-jaraco.text_4.0.0-1_all.deb ... 143s Unpacking python3-jaraco.text (4.0.0-1) ... 143s Preparing to unpack .../6-python3-pkg-resources_75.2.0-1_all.deb ... 143s Unpacking python3-pkg-resources (75.2.0-1) over (74.1.2-1) ... 143s Preparing to unpack .../7-python3-setuptools_75.2.0-1_all.deb ... 143s Unpacking python3-setuptools (75.2.0-1) over (74.1.2-1) ... 143s Setting up python3-pkg-resources (75.2.0-1) ... 143s Setting up libtext-iconv-perl:s390x (1.7-8build4) ... 143s Setting up libtext-charwidth-perl:s390x (0.04-11build4) ... 143s Setting up libkeyutils1:s390x (1.6.3-4ubuntu2) ... 143s Setting up xxd (2:9.1.0777-1ubuntu1) ... 143s Setting up vim-common (2:9.1.0777-1ubuntu1) ... 143s Installing new version of config file /etc/vim/vimrc ... 143s Setting up python3-jaraco.text (4.0.0-1) ... 143s Setting up perl-modules-5.40 (5.40.0-6) ... 143s Setting up info (7.1.1-1) ... 143s Setting up liblocale-gettext-perl (1.07-7build1) ... 143s Setting up python3-setuptools (75.2.0-1) ... 144s Setting up vim-tiny (2:9.1.0777-1ubuntu1) ... 144s Setting up libperl5.40:s390x (5.40.0-6) ... 144s Setting up perl (5.40.0-6) ... 144s Processing triggers for libc-bin (2.40-1ubuntu3) ... 144s Processing triggers for man-db (2.12.1-3) ... 145s Processing triggers for install-info (7.1.1-1) ... 145s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s The following packages will be REMOVED: 146s libperl5.38t64* perl-modules-5.38* 146s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 146s After this operation, 49.5 MB disk space will be freed. 146s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 57417 files and directories currently installed.) 146s Removing libperl5.38t64:s390x (5.38.2-5) ... 146s Removing perl-modules-5.38 (5.38.2-5) ... 146s Processing triggers for man-db (2.12.1-3) ... 146s Processing triggers for libc-bin (2.40-1ubuntu3) ... 147s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 147s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 147s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 147s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 148s Reading package lists... 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 148s Calculating upgrade... 148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 151s autopkgtest [10:01:52]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 151s autopkgtest [10:01:52]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 154s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (dsc) [2291 B] 154s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (tar) [22.3 MB] 154s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (diff) [7100 B] 154s gpgv: Signature made Wed Apr 10 17:15:32 2024 UTC 154s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 154s gpgv: Can't check signature: No public key 154s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6build1.dsc: no acceptable signature found 154s autopkgtest [10:01:55]: testing package tombo version 1.5.1-6build1 155s autopkgtest [10:01:56]: build not needed 156s autopkgtest [10:01:57]: test run-unit-test: preparing testbed 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 160s Starting 2 pkgProblemResolver with broken count: 0 160s Done 161s The following additional packages will be installed: 161s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 161s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 161s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 161s python3-decorator python3-h5py python3-h5py-serial python3-mappy 161s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 161s tombo-doc 161s Suggested packages: 161s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 161s gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 161s Recommended packages: 161s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 161s python3-rpy2 161s The following NEW packages will be installed: 161s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 161s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 161s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 161s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 161s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 161s tombo-doc 161s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 161s Need to get 63.4 MB/63.4 MB of archives. 161s After this operation, 200 MB of additional disk space will be used. 161s Get:1 /tmp/autopkgtest.C2SnA8/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [708 B] 161s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-lato all 2.015-1 [2781 kB] 161s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 161s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 161s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 161s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 161s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-7ubuntu1 [587 kB] 161s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 161s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-103-1t64 s390x 1.10.10+repack-4ubuntu3 [1426 kB] 162s Get:10 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-100t64 s390x 1.10.10+repack-4ubuntu3 [58.0 kB] 162s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 162s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 162s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-sphinxdoc all 7.4.7-3 [157 kB] 162s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 162s Get:15 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 162s Get:16 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B] 162s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 162s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11build1 [4113 kB] 162s Get:19 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py-serial s390x 3.11.0-5ubuntu1 [1151 kB] 162s Get:20 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py all 3.11.0-5ubuntu1 [7974 B] 162s Get:21 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mappy s390x 2.27+dfsg-1 [208 kB] 162s Get:22 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-tqdm all 4.66.5-1 [91.4 kB] 162s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x sphinx-rtd-theme-common all 2.0.0+dfsg-2 [1012 kB] 162s Get:24 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.13.1-3 [17.5 MB] 162s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x tombo s390x 1.5.1-6build1 [465 kB] 162s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 163s Get:27 http://ftpmaster.internal/ubuntu plucky/universe s390x tombo-doc all 1.5.1-6build1 [21.7 MB] 163s Fetched 63.4 MB in 3s (25.1 MB/s) 163s Selecting previously unselected package fonts-lato. 163s (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 ... 55484 files and directories currently installed.) 163s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 163s Unpacking fonts-lato (2.015-1) ... 164s Selecting previously unselected package fonts-font-awesome. 164s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 164s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 164s Selecting previously unselected package fonts-mathjax. 164s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 164s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 164s Selecting previously unselected package libaec0:s390x. 164s Preparing to unpack .../03-libaec0_1.1.3-1_s390x.deb ... 164s Unpacking libaec0:s390x (1.1.3-1) ... 164s Selecting previously unselected package libblas3:s390x. 164s Preparing to unpack .../04-libblas3_3.12.0-3build2_s390x.deb ... 164s Unpacking libblas3:s390x (3.12.0-3build2) ... 164s Selecting previously unselected package libgfortran5:s390x. 164s Preparing to unpack .../05-libgfortran5_14.2.0-7ubuntu1_s390x.deb ... 164s Unpacking libgfortran5:s390x (14.2.0-7ubuntu1) ... 164s Selecting previously unselected package libsz2:s390x. 164s Preparing to unpack .../06-libsz2_1.1.3-1_s390x.deb ... 164s Unpacking libsz2:s390x (1.1.3-1) ... 164s Selecting previously unselected package libhdf5-103-1t64:s390x. 164s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_s390x.deb ... 164s Unpacking libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 164s Selecting previously unselected package libhdf5-hl-100t64:s390x. 164s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_s390x.deb ... 164s Unpacking libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ... 164s Selecting previously unselected package libjs-jquery. 164s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 164s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 164s Selecting previously unselected package libjs-underscore. 164s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 164s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 164s Selecting previously unselected package libjs-sphinxdoc. 164s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-3_all.deb ... 164s Unpacking libjs-sphinxdoc (7.4.7-3) ... 164s Selecting previously unselected package liblapack3:s390x. 164s Preparing to unpack .../12-liblapack3_3.12.0-3build2_s390x.deb ... 164s Unpacking liblapack3:s390x (3.12.0-3build2) ... 164s Selecting previously unselected package liblbfgsb0:s390x. 164s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 164s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 164s Selecting previously unselected package liblzf1:s390x. 164s Preparing to unpack .../14-liblzf1_3.6-4_s390x.deb ... 164s Unpacking liblzf1:s390x (3.6-4) ... 164s Selecting previously unselected package python3-decorator. 164s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 164s Unpacking python3-decorator (5.1.1-5) ... 164s Selecting previously unselected package python3-numpy. 164s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-11build1_s390x.deb ... 164s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 164s Selecting previously unselected package python3-h5py-serial. 164s Preparing to unpack .../17-python3-h5py-serial_3.11.0-5ubuntu1_s390x.deb ... 164s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 164s Selecting previously unselected 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/usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 166s Setting up liblzf1:s390x (3.6-4) ... 166s Setting up libgfortran5:s390x (14.2.0-7ubuntu1) ... 166s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 166s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 166s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-2) ... 166s Setting up libsz2:s390x (1.1.3-1) ... 166s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 166s Setting up liblapack3:s390x (3.12.0-3build2) ... 166s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 166s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 168s Setting up libjs-sphinxdoc (7.4.7-3) ... 168s Setting up tombo-doc (1.5.1-6build1) ... 168s Setting up libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 168s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 168s Setting up libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ... 168s Setting up python3-scipy (1.13.1-3) ... 171s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 171s Setting up python3-h5py (3.11.0-5ubuntu1) ... 172s Setting up tombo (1.5.1-6build1) ... 172s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 172s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 172s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 172s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 172s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 172s re.match('\+', fastq_rec[2]) is None): 172s Setting up autopkgtest-satdep (0) ... 172s Processing triggers for man-db (2.12.1-3) ... 172s Processing triggers for libc-bin (2.40-1ubuntu3) ... 174s (Reading database ... 62686 files and directories currently installed.) 174s Removing autopkgtest-satdep (0) ... 175s autopkgtest [10:02:16]: test run-unit-test: [----------------------- 175s ********* Testing help commands ********** 175s usage: tombo [-h] [-v] 175s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 175s ... 175s 175s ********** Tombo ********* 175s 175s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 175s 175s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 175s 175s Tombo command groups (additional help available within each command group): 175s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 175s preprocess Pre-process nanopore reads for Tombo processing. 175s filter Apply filter to Tombo index file for specified criterion. 175s detect_modifications Perform statistical testing to detect non-standard nucleotides. 175s text_output Output Tombo results in text files. 175s build_model Create canonical and alternative base Tombo models. 175s plot Save plots to visualize raw nanopore signal or testing results. 175s 175s options: 175s -h, --help show this help message and exit 175s -v, --version show Tombo version and exit. 175s usage: tombo resquiggle [--dna] [--rna] 175s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 175s [--q-score Q_SCORE] 175s [--signal-matching-score SIGNAL_MATCHING_SCORE] 175s [--processes PROCESSES] 175s [--corrected-group CORRECTED_GROUP] 175s [--basecall-group BASECALL_GROUP] 175s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 175s [--overwrite] 175s [--failed-reads-filename FAILED_READS_FILENAME] 175s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 175s [--print-advanced-arguments] [--quiet] [--help] 175s fast5s_basedir reference 175s 175s Required Arguments: 175s fast5s_basedir Directory containing fast5 files. All files ending in 175s "fast5" found recursively within this base directory 175s will be processed. 175s reference Reference genome/transcriptome FASTA file or minimap2 175s index (with "map-ont" preset) for mapping. 175s 175s Model Parameters: 175s --dna Explicitly select canonical DNA model. Default: 175s Automatically determine from FAST5s 175s --rna Explicitly select canonical RNA model. Default: 175s Automatically determine from FAST5s 175s 175s Read Filtering Argument: 175s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 175s Filter reads based on observations per base percentile 175s thresholds. Format thresholds as "percentile:thresh 175s [pctl2:thresh2 ...]". For example to filter reads with 175s 99th pctl > 200 obs/base or max > 5k obs/base use 175s "99:200 100:5000". 175s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 175s Default: 0.000000 175s --signal-matching-score SIGNAL_MATCHING_SCORE 175s Observed to expected signal matching score (higher 175s score indicates poor matching). Sample type defaults: 175s RNA : 2 || DNA : 1.1 175s 175s Multiprocessing Arguments: 175s --processes PROCESSES 175s Number of processes. Default: 1 175s 175s FAST5 Data Arguments: 175s --corrected-group CORRECTED_GROUP 175s FAST5 group created by resquiggle command. Default: 175s RawGenomeCorrected_000 175s --basecall-group BASECALL_GROUP 175s FAST5 group obtain original basecalls (under Analyses 175s group). Default: Basecall_1D_000 175s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 175s FAST5 subgroup(s) (under /Analyses/[--basecall- 175s group]/) containing basecalls and created within 175s [--corrected-group] containing re-squiggle results. 175s Default: ['BaseCalled_template'] 175s --overwrite Overwrite previous corrected group in FAST5 files. 175s Note: only effects --corrected-group or --new- 175s corrected-group. 175s 175s Input/Output Arguments: 175s --failed-reads-filename FAILED_READS_FILENAME 175s Output failed read filenames with assoicated error. 175s Default: Do not store failed reads. 175s --num-most-common-errors NUM_MOST_COMMON_ERRORS 175s Dynamically show this many most common errors so far 175s through run. Default: 0; Just show progress 175s 175s Advanced Arguments: 175s --print-advanced-arguments 175s Print advanced re-squiggle arguments and exit. 175s 175s Miscellaneous Arguments: 175s --quiet, -q Don't print status information. 175s --help, -h Print this help message and exit 175s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 175s --fastq-filenames 175s FASTQ_FILENAMES 175s [FASTQ_FILENAMES ...] 175s [--basecall-group BASECALL_GROUP] 175s [--basecall-subgroup BASECALL_SUBGROUP] 175s [--overwrite] 175s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 175s [--processes PROCESSES] 175s [--quiet] [--help] 175s 175s Required Arguments: 175s --fast5-basedir FAST5_BASEDIR 175s Directory containing fast5 files. 175s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 175s FASTQ filenames containing basecalls to be added to 175s raw FAST5 files. 175s 175s FAST5 Data Arguments: 175s --basecall-group BASECALL_GROUP 175s FAST5 group obtain original basecalls (under Analyses 175s group). Default: Basecall_1D_000 175s --basecall-subgroup BASECALL_SUBGROUP 175s FAST5 subgroup (under /Analyses/[--basecall-group]/) 175s under which to store basecalls from FASTQs. Default: 175s BaseCalled_template 175s --overwrite Overwrite previous corrected group in FAST5 files. 175s Note: only effects --corrected-group or --new- 175s corrected-group. 175s 175s Sequencing Summary Argument: 175s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 175s Sequencing summary filenames produced by albacore. 175s These can make annotation of raw FAST5 files with 175s FASTQ sequence much faster. 175s 175s Multiprocessing Argument: 175s --processes PROCESSES 175s Number of processes. Default: 1 175s 175s Miscellaneous Arguments: 175s --quiet, -q Don't print status information. 175s --help, -h Print this help message and exit 175s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 175s [FAST5_BASEDIRS ...] 175s [--corrected-group CORRECTED_GROUP] 175s [--quiet] [--help] 175s 175s Required Argument: 175s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 175s Directories containing fast5 files. 175s 175s FAST5 Data Argument: 175s --corrected-group CORRECTED_GROUP 175s FAST5 group created by resquiggle command. Default: 175s RawGenomeCorrected_000 175s 175s Miscellaneous Arguments: 175s --quiet, -q Don't print status information. 175s --help, -h Print this help message and exit 175s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 175s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 175s [--corrected-group CORRECTED_GROUP] [--quiet] 175s [--help] 175s 175s Required Argument: 175s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 175s Directories containing fast5 files. 175s 175s Read Filtering Argument: 175s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 175s Filter reads based on observations per base percentile 175s thresholds. Format thresholds as "percentile:thresh 175s [pctl2:thresh2 ...]". For example to filter reads with 175s 99th pctl > 200 obs/base or max > 5k obs/base use 175s "99:200 100:5000". 175s 175s FAST5 Data Argument: 175s --corrected-group CORRECTED_GROUP 175s FAST5 group created by resquiggle command. Default: 175s RawGenomeCorrected_000 175s 175s Miscellaneous Arguments: 175s --quiet, -q Don't print status information. 175s --help, -h Print this help message and exit 175s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 175s [FAST5_BASEDIRS ...] 175s [--percent-to-filter PERCENT_TO_FILTER] 175s [--corrected-group CORRECTED_GROUP] 175s [--quiet] [--help] 175s 175s Required Arguments: 175s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 175s Directories containing fast5 files. 175s 175s Read Filtering Argument: 175s --percent-to-filter PERCENT_TO_FILTER 175s Percentage of all reads to filter. Reads are randomly 175s selected weighted according to the approximate 175s coverage at the mapped genomic location. This can be 175s useful in modeling and testing. Default: 10.000000 175s 175s FAST5 Data Arguments: 175s --corrected-group CORRECTED_GROUP 175s FAST5 group created by resquiggle command. Default: 175s RawGenomeCorrected_000 175s 175s Miscellaneous Arguments: 175s --quiet, -q Don't print status information. 175s --help, -h Print this help message and exit 175s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 175s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 175s [--corrected-group CORRECTED_GROUP] 175s [--basecall-group BASECALL_GROUP] [--quiet] 175s [--help] 175s 175s Required Arguments: 175s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 175s Directories containing fast5 files. 175s 175s Read Filtering Argument: 175s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 175s Default: 7.000000 175s 175s FAST5 Data Arguments: 175s --corrected-group CORRECTED_GROUP 175s FAST5 group created by resquiggle command. Default: 175s RawGenomeCorrected_000 175s --basecall-group BASECALL_GROUP 175s FAST5 group obtain original basecalls (under Analyses 175s group). Default: Basecall_1D_000 175s 175s Miscellaneous Arguments: 175s --quiet, -q Don't print status information. 175s --help, -h Print this help message and exit 175s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 175s [FAST5_BASEDIRS ...] 175s --signal-matching-score 175s SIGNAL_MATCHING_SCORE 175s [--corrected-group CORRECTED_GROUP] 175s [--quiet] [--help] 175s 175s Required Arguments: 175s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 175s Directories containing fast5 files. 175s --signal-matching-score SIGNAL_MATCHING_SCORE 175s Observed to expected signal matching score (higher 175s score indicates poor matching). Sample type defaults: 175s RNA : 2 || DNA : 1.1 175s 175s FAST5 Data Arguments: 175s --corrected-group CORRECTED_GROUP 175s FAST5 group created by resquiggle command. Default: 175s RawGenomeCorrected_000 175s 175s Miscellaneous Arguments: 175s --quiet, -q Don't print status information. 175s --help, -h Print this help message and exit 175s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 175s [FAST5_BASEDIRS ...] 175s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 175s [--include-partial-overlap] 175s [--corrected-group CORRECTED_GROUP] 175s [--quiet] [--help] 175s 175s Required Arguments: 175s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 175s Directories containing fast5 files. 175s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 175s Filter out reads not falling completely within include 175s regions. Omit start and end coordinates to include an 175s entire chromosome/sequence record. Format regions as 175s "chrm[:start-end] [chrm2[:start2-end2] ...]". 175s 175s Filter Argument: 175s --include-partial-overlap 175s Include reads that partially overlap the specified 175s region. Default: Only include reads completely 175s contained in a specified region 175s 175s FAST5 Data Argument: 175s --corrected-group CORRECTED_GROUP 175s FAST5 group created by resquiggle command. Default: 175s RawGenomeCorrected_000 175s 175s Miscellaneous Arguments: 175s --quiet, -q Don't print status information. 175s --help, -h Print this help message and exit 175s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 175s [FAST5_BASEDIRS ...] 175s --statistics-file-basename 175s STATISTICS_FILE_BASENAME [--dna] 175s [--rna] 175s [--fishers-method-context FISHERS_METHOD_CONTEXT] 175s [--minimum-test-reads MINIMUM_TEST_READS] 175s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 175s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 175s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 175s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 175s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 175s [--processes PROCESSES] 175s [--corrected-group CORRECTED_GROUP] 175s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 175s [--quiet] [--help] 175s 175s Required Argument: 175s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 175s Directories containing fast5 files. 175s --statistics-file-basename STATISTICS_FILE_BASENAME 175s File base name to save base by base statistics from 175s testing. Filenames will be [--statistics-file- 175s basename].[--alternate-bases]?.tombo.stats 175s 175s Comparison Model Arguments: 175s --dna Explicitly select canonical DNA model. Default: 175s Automatically determine from FAST5s 175s --rna Explicitly select canonical RNA model. Default: 175s Automatically determine from FAST5s 175s 175s Significance Test Arguments: 175s --fishers-method-context FISHERS_METHOD_CONTEXT 175s Number of context bases up and downstream over which 175s to compute Fisher's method combined p-values. Note: 175s Not applicable for alternative model likelihood ratio 175s tests. Default: 1. 175s --minimum-test-reads MINIMUM_TEST_READS 175s Number of reads required at a position to perform 175s significance testing or contribute to model 175s estimation. Default: 1 175s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 175s P-value threshold when computing fraction of 175s significant reads at each genomic position. If two 175s values are provided, statistics between these values 175s are not considered. Default thresholds: DNA:0.15-0.5 , 175s RNA:0.05-0.4 175s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 175s Dampen fraction modified estimates for low coverage 175s sites. Two parameters are unmodified and modified 175s pseudo read counts. This is equivalent to a beta prior 175s on the fraction estimate. Set to "0 0" to disable 175s dampened fraction estimation. Default: [2, 0] 175s 175s Output Argument: 175s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 175s Base for binary files containing per-read statistics 175s from statistical testing. Filenames will be [--per- 175s read-statistics-basename].[--alternate- 175s bases]?.tombo.per_read_stats 175s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 175s Number of the most significant sites to store for 175s faster access. If a longer list of most significant 175s sites is required the list must be re-computed from 175s all batches. Very large values can increase RAM usage. 175s Default: 100000 175s 175s Multiprocessing Arguments: 175s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 175s Size of regions over which to multiprocesses statistic 175s computation. For very deep samples a smaller value is 175s recommmended in order to control memory consumption. 175s Default: 10000 175s --processes PROCESSES 175s Number of processes. Default: 1 175s 175s FAST5 Data Arguments: 175s --corrected-group CORRECTED_GROUP 175s FAST5 group created by resquiggle command. Default: 175s RawGenomeCorrected_000 175s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 175s FAST5 subgroup(s) (under /Analyses/[--basecall- 175s group]/) containing basecalls and created within 175s [--corrected-group] containing re-squiggle results. 175s Default: ['BaseCalled_template'] 175s 175s Miscellaneous Arguments: 175s --quiet, -q Don't print status information. 175s --help, -h Print this help message and exit 176s usage: tombo detect_modifications alternative_model 176s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 176s [--statistics-file-basename STATISTICS_FILE_BASENAME] 176s [--alternate-bases {dcm,6mA,dam,5mC,CpG} [{dcm,6mA,dam,5mC,CpG} ...]] 176s [--print-available-models] 176s [--dna] [--rna] 176s [--minimum-test-reads MINIMUM_TEST_READS] 176s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 176s [--standard-log-likelihood-ratio] 176s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 176s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 176s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 176s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 176s [--processes PROCESSES] 176s [--corrected-group CORRECTED_GROUP] 176s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 176s [--quiet] [--help] 176s 176s Required Argument: 176s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 176s Directories containing fast5 files. 176s --statistics-file-basename STATISTICS_FILE_BASENAME 176s File base name to save base by base statistics from 176s testing. Filenames will be [--statistics-file- 176s basename].[--alternate-bases]?.tombo.stats 176s --alternate-bases {dcm,6mA,dam,5mC,CpG} [{dcm,6mA,dam,5mC,CpG} ...] 176s Default non-standard base model for testing (not 176s required if user created --alternate-model-filenames 176s is provided). 176s 176s Comparison Arguments: 176s --print-available-models 176s Print available alternative models and exit. 176s --dna Explicitly select canonical DNA model. Default: 176s Automatically determine from FAST5s 176s --rna Explicitly select canonical RNA model. Default: 176s Automatically determine from FAST5s 176s 176s Significance Test Arguments: 176s --minimum-test-reads MINIMUM_TEST_READS 176s Number of reads required at a position to perform 176s significance testing or contribute to model 176s estimation. Default: 1 176s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 176s Log likelihood ratio threshold when computing fraction 176s of significant reads at each genomic position. If two 176s values are provided, statistics between these values 176s are not considered. Default thresholds: DNA:-1.5-2.5 , 176s RNA:-2.5-2.5 176s --standard-log-likelihood-ratio 176s Use a standard log likelihood ratio (LLR) statistic. 176s Default is to use an outlier-robust LLR-like 176s statistic. Detail in full online documentation. 176s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 176s Dampen fraction modified estimates for low coverage 176s sites. Two parameters are unmodified and modified 176s pseudo read counts. This is equivalent to a beta prior 176s on the fraction estimate. Set to "0 0" to disable 176s dampened fraction estimation. Default: [2, 0] 176s 176s Output Argument: 176s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 176s Base for binary files containing per-read statistics 176s from statistical testing. Filenames will be [--per- 176s read-statistics-basename].[--alternate- 176s bases]?.tombo.per_read_stats 176s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 176s Number of the most significant sites to store for 176s faster access. If a longer list of most significant 176s sites is required the list must be re-computed from 176s all batches. Very large values can increase RAM usage. 176s Default: 100000 176s 176s Multiprocessing Arguments: 176s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 176s Size of regions over which to multiprocesses statistic 176s computation. For very deep samples a smaller value is 176s recommmended in order to control memory consumption. 176s Default: 10000 176s --processes PROCESSES 176s Number of processes. Default: 1 176s 176s FAST5 Data Arguments: 176s --corrected-group CORRECTED_GROUP 176s FAST5 group created by resquiggle command. Default: 176s RawGenomeCorrected_000 176s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 176s FAST5 subgroup(s) (under /Analyses/[--basecall- 176s group]/) containing basecalls and created within 176s [--corrected-group] containing re-squiggle results. 176s Default: ['BaseCalled_template'] 176s 176s Miscellaneous Arguments: 176s --quiet, -q Don't print status information. 176s --help, -h Print this help message and exit 176s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 176s FAST5_BASEDIRS 176s [FAST5_BASEDIRS ...] 176s --statistics-file-basename 176s STATISTICS_FILE_BASENAME 176s --control-fast5-basedirs 176s CONTROL_FAST5_BASEDIRS 176s [CONTROL_FAST5_BASEDIRS ...] 176s [--sample-only-estimates] 176s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 176s [--dna] [--rna] 176s [--fishers-method-context FISHERS_METHOD_CONTEXT] 176s [--minimum-test-reads MINIMUM_TEST_READS] 176s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 176s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 176s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 176s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 176s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 176s [--processes PROCESSES] 176s [--corrected-group CORRECTED_GROUP] 176s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 176s [--quiet] [--help] 176s 176s Required Argument: 176s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 176s Directories containing fast5 files. 176s --statistics-file-basename STATISTICS_FILE_BASENAME 176s File base name to save base by base statistics from 176s testing. Filenames will be [--statistics-file- 176s basename].[--alternate-bases]?.tombo.stats 176s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 176s Set of directories containing fast5 files for control 176s reads, containing only canonical nucleotides. 176s 176s Model Prior Arguments: 176s --sample-only-estimates 176s Only use canonical sample to estimate expected signal 176s level and spread. Default: Use canonical model to 176s improve estimtates (esp. for low coverage regions) 176s using baysian posterior estimates. 176s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 176s Prior weights (one each for mean and spread) applied 176s to canonical base model for estimating posterior model 176s parameters for sample comparison. Default: [5, 40] 176s --dna Explicitly select canonical DNA model. Default: 176s Automatically determine from FAST5s 176s --rna Explicitly select canonical RNA model. Default: 176s Automatically determine from FAST5s 176s 176s Significance Test Arguments: 176s --fishers-method-context FISHERS_METHOD_CONTEXT 176s Number of context bases up and downstream over which 176s to compute Fisher's method combined p-values. Note: 176s Not applicable for alternative model likelihood ratio 176s tests. Default: 1. 176s --minimum-test-reads MINIMUM_TEST_READS 176s Number of reads required at a position to perform 176s significance testing or contribute to model 176s estimation. Default: 1 176s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 176s P-value threshold when computing fraction of 176s significant reads at each genomic position. If two 176s values are provided, statistics between these values 176s are not considered. Default thresholds: DNA:0.15-0.5 , 176s RNA:0.05-0.4 176s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 176s Dampen fraction modified estimates for low coverage 176s sites. Two parameters are unmodified and modified 176s pseudo read counts. This is equivalent to a beta prior 176s on the fraction estimate. Set to "0 0" to disable 176s dampened fraction estimation. Default: [2, 0] 176s 176s Output Argument: 176s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 176s Base for binary files containing per-read statistics 176s from statistical testing. Filenames will be [--per- 176s read-statistics-basename].[--alternate- 176s bases]?.tombo.per_read_stats 176s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 176s Number of the most significant sites to store for 176s faster access. If a longer list of most significant 176s sites is required the list must be re-computed from 176s all batches. Very large values can increase RAM usage. 176s Default: 100000 176s 176s Multiprocessing Arguments: 176s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 176s Size of regions over which to multiprocesses statistic 176s computation. For very deep samples a smaller value is 176s recommmended in order to control memory consumption. 176s Default: 10000 176s --processes PROCESSES 176s Number of processes. Default: 1 176s 176s FAST5 Data Arguments: 176s --corrected-group CORRECTED_GROUP 176s FAST5 group created by resquiggle command. Default: 176s RawGenomeCorrected_000 176s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 176s FAST5 subgroup(s) (under /Analyses/[--basecall- 176s group]/) containing basecalls and created within 176s [--corrected-group] containing re-squiggle results. 176s Default: ['BaseCalled_template'] 176s 176s Miscellaneous Arguments: 176s --quiet, -q Don't print status information. 176s --help, -h Print this help message and exit 176s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 176s FAST5_BASEDIRS 176s [FAST5_BASEDIRS ...] 176s --statistics-file-basename 176s STATISTICS_FILE_BASENAME 176s --alternate-fast5-basedirs 176s ALTERNATE_FAST5_BASEDIRS 176s [ALTERNATE_FAST5_BASEDIRS ...] 176s [--fishers-method-context FISHERS_METHOD_CONTEXT] 176s [--minimum-test-reads MINIMUM_TEST_READS] 176s [--statistic-type {ks,u,t}] 176s [--store-p-value] 176s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 176s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 176s [--processes PROCESSES] 176s [--corrected-group CORRECTED_GROUP] 176s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 176s [--quiet] [--help] 176s 176s Required Argument: 176s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 176s Directories containing fast5 files. 176s --statistics-file-basename STATISTICS_FILE_BASENAME 176s File base name to save base by base statistics from 176s testing. Filenames will be [--statistics-file- 176s basename].[--alternate-bases]?.tombo.stats 176s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 176s Set of directories containing fast5 files for 176s alternate set of reads. 176s 176s Significance Test Arguments: 176s --fishers-method-context FISHERS_METHOD_CONTEXT 176s Number of context bases up and downstream over which 176s to compute Fisher's method combined p-values. Note: 176s Not applicable for alternative model likelihood ratio 176s tests. Default: 1. 176s --minimum-test-reads MINIMUM_TEST_READS 176s Number of reads required at a position to perform 176s significance testing or contribute to model 176s estimation. Default: 50 176s --statistic-type {ks,u,t} 176s Type of statistical test to apply. Default: "ks" 176s --store-p-value Store p-value instead of effect-size statistic. 176s Statistics are D-statistic (KS-test), deviation from 176s even common language effect size (u-test), and Cohen's 176s D (t-test). 176s 176s Output Argument: 176s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 176s Number of the most significant sites to store for 176s faster access. If a longer list of most significant 176s sites is required the list must be re-computed from 176s all batches. Very large values can increase RAM usage. 176s Default: 100000 176s 176s Multiprocessing Arguments: 176s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 176s Size of regions over which to multiprocesses statistic 176s computation. For very deep samples a smaller value is 176s recommmended in order to control memory consumption. 176s Default: 10000 176s --processes PROCESSES 176s Number of processes. Default: 1 176s 176s FAST5 Data Arguments: 176s --corrected-group CORRECTED_GROUP 176s FAST5 group created by resquiggle command. Default: 176s RawGenomeCorrected_000 176s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 176s FAST5 subgroup(s) (under /Analyses/[--basecall- 176s group]/) containing basecalls and created within 176s [--corrected-group] containing re-squiggle results. 176s Default: ['BaseCalled_template'] 176s 176s Miscellaneous Arguments: 176s --quiet, -q Don't print status information. 176s --help, -h Print this help message and exit 176s usage: tombo detect_modifications aggregate_per_read_stats 176s --per-read-statistics-filename 176s PER_READ_STATISTICS_FILENAME 176s --statistics-filename 176s STATISTICS_FILENAME 176s --single-read-threshold 176s SINGLE_READ_THRESHOLD 176s [SINGLE_READ_THRESHOLD ...] 176s [--minimum-test-reads MINIMUM_TEST_READS] 176s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 176s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 176s [--processes PROCESSES] 176s [--corrected-group CORRECTED_GROUP] 176s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 176s [--quiet] [--help] 176s 176s Required Argument: 176s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 176s Binary file containing per-read statistics from 176s statistical testing. 176s --statistics-filename STATISTICS_FILENAME 176s File to save/load genomic base anchored statistics. 176s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 176s P-value or log likelihood ratio threshold when 176s computing fraction of significant reads at each 176s genomic position. If two values are provided, 176s statistics between these values are not considered. 176s 176s Significance Test Arguments: 176s --minimum-test-reads MINIMUM_TEST_READS 176s Number of reads required at a position to perform 176s significance testing or contribute to model 176s estimation. Default: 1 176s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 176s Dampen fraction modified estimates for low coverage 176s sites. Two parameters are unmodified and modified 176s pseudo read counts. This is equivalent to a beta prior 176s on the fraction estimate. Set to "0 0" to disable 176s dampened fraction estimation. Default: [2, 0] 176s 176s Output Argument: 176s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 176s Number of the most significant sites to store for 176s faster access. If a longer list of most significant 176s sites is required the list must be re-computed from 176s all batches. Very large values can increase RAM usage. 176s Default: 100000 176s 176s Multiprocessing Arguments: 176s --processes PROCESSES 176s Number of processes. Default: 1 176s 176s FAST5 Data Arguments: 176s --corrected-group CORRECTED_GROUP 176s FAST5 group created by resquiggle command. Default: 176s RawGenomeCorrected_000 176s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 176s FAST5 subgroup(s) (under /Analyses/[--basecall- 176s group]/) containing basecalls and created within 176s [--corrected-group] containing re-squiggle results. 176s Default: ['BaseCalled_template'] 176s 176s Miscellaneous Arguments: 176s --quiet, -q Don't print status information. 176s --help, -h Print this help message and exit 176s usage: tombo text_output browser_files 176s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 176s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 176s [--statistics-filename STATISTICS_FILENAME] 176s [--genome-fasta GENOME_FASTA] 176s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 176s [--browser-file-basename BROWSER_FILE_BASENAME] 176s [--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} ...]] 176s [--corrected-group CORRECTED_GROUP] 176s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 176s [--quiet] [--help] 176s 176s Data Arguments: 176s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 176s Directories containing fast5 files. 176s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 176s Set of directories containing fast5 files for control 176s reads, containing only canonical nucleotides. 176s --statistics-filename STATISTICS_FILENAME 176s File to save/load genomic base anchored statistics. 176s 176s Statistic Motif Filter Arguments: 176s --genome-fasta GENOME_FASTA 176s FASTA file used to re-squiggle. For faster sequence 176s access. 176s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 176s Ground truth, motif centered, modified base 176s descriptions for output filtering. Format descriptions 176s as: "motif:mod_pos:name". The mod_pos indicates the 176s modified base within the motif (1-based index). 176s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 176s output for identification of E. coli dam and dcm 176s methylation. 176s 176s Output Arguments: 176s --browser-file-basename BROWSER_FILE_BASENAME 176s Basename for output browser files. Two files (plus and 176s minus strand) will be produced for each --file-types 176s supplied. Filenames formatted as "[browser-file- 176s basename].[file- 176s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 176s Default: tombo_results 176s --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} ...] 176s Data types of genome browser files to produce. 176s Produced coverage files are in bedGraph format, while 176s all other file types will be in wiggle format 176s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 176s Default: "coverage" 176s 176s FAST5 Data Arguments: 176s --corrected-group CORRECTED_GROUP 176s FAST5 group created by resquiggle command. Default: 176s RawGenomeCorrected_000 176s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 176s FAST5 subgroup(s) (under /Analyses/[--basecall- 176s group]/) containing basecalls and created within 176s [--corrected-group] containing re-squiggle results. 176s Default: ['BaseCalled_template'] 176s 176s Miscellaneous Arguments: 176s --quiet, -q Don't print status information. 176s --help, -h Print this help message and exit 176s usage: tombo text_output signif_sequence_context --statistics-filename 176s STATISTICS_FILENAME 176s [--genome-fasta GENOME_FASTA] 176s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 176s [--num-regions NUM_REGIONS] 176s [--num-bases NUM_BASES] 176s [--sequences-filename SEQUENCES_FILENAME] 176s [--corrected-group CORRECTED_GROUP] 176s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 176s [--quiet] [--help] 176s 176s Required Argument: 176s --statistics-filename STATISTICS_FILENAME 176s File to save/load genomic base anchored statistics. 176s 176s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 176s --genome-fasta GENOME_FASTA 176s FASTA file used to re-squiggle. For faster sequence 176s access. 176s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 176s Directories containing fast5 files. 176s 176s Region Selection Arguments: 176s --num-regions NUM_REGIONS 176s Number of regions to plot. Default: 100 176s --num-bases NUM_BASES 176s Number of bases to plot/output. Default: 15 176s 176s Output Arguments: 176s --sequences-filename SEQUENCES_FILENAME 176s File for sequences from selected regions. Sequences 176s will be stored in FASTA format. Default: 176s tombo_results.significant_regions.fasta. 176s 176s FAST5 Data Arguments: 176s --corrected-group CORRECTED_GROUP 176s FAST5 group created by resquiggle command. Default: 176s RawGenomeCorrected_000 176s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 176s FAST5 subgroup(s) (under /Analyses/[--basecall- 176s group]/) containing basecalls and created within 176s [--corrected-group] containing re-squiggle results. 176s Default: ['BaseCalled_template'] 176s 176s Miscellaneous Arguments: 176s --quiet, -q Don't print status information. 176s --help, -h Print this help message and exit 176s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 176s [FAST5_BASEDIRS ...] 176s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 176s [--plot-standard-model] 176s [--plot-alternate-model {6mA,CpG,dcm,5mC,dam}] 176s [--overplot-threshold OVERPLOT_THRESHOLD] 176s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 176s [--num-regions NUM_REGIONS] 176s [--num-bases NUM_BASES] 176s [--pdf-filename PDF_FILENAME] 176s [--corrected-group CORRECTED_GROUP] 176s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 176s [--quiet] [--help] 176s 176s Required Argument: 176s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 176s Directories containing fast5 files. 176s 176s Comparison Arguments: 176s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 176s Set of directories containing fast5 files for control 176s reads, containing only canonical nucleotides. 176s --plot-standard-model 176s Add default standard model distribution to the plot. 176s --plot-alternate-model {6mA,CpG,dcm,5mC,dam} 176s Add alternative model distribution to the plot. 176s 176s Overplotting Arguments: 176s --overplot-threshold OVERPLOT_THRESHOLD 176s Coverage level to trigger alternative plot type 176s instead of raw signal. Default: 50 176s --overplot-type {Downsample,Boxplot,Quantile,Density} 176s Plot type for regions with higher coverage. Default: 176s Downsample 176s 176s Plotting Region Arguments: 176s --num-regions NUM_REGIONS 176s Number of regions to plot. Default: 10 176s --num-bases NUM_BASES 176s Number of bases to plot/output. Default: 21 176s 176s Output Argument: 176s --pdf-filename PDF_FILENAME 176s PDF filename to store plot(s). Default: 176s tombo_results.max_coverage.pdf 176s 176s FAST5 Data Arguments: 176s --corrected-group CORRECTED_GROUP 176s FAST5 group created by resquiggle command. Default: 176s RawGenomeCorrected_000 176s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 176s FAST5 subgroup(s) (under /Analyses/[--basecall- 176s group]/) containing basecalls and created within 176s [--corrected-group] containing re-squiggle results. 176s Default: ['BaseCalled_template'] 176s 176s Miscellaneous Arguments: 176s --quiet, -q Don't print status information. 176s --help, -h Print this help message and exit 176s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 176s [FAST5_BASEDIRS ...] --genome-locations 176s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 176s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 176s [--plot-standard-model] 176s [--plot-alternate-model {5mC,dam,6mA,CpG,dcm}] 176s [--overplot-threshold OVERPLOT_THRESHOLD] 176s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 176s [--num-bases NUM_BASES] 176s [--pdf-filename PDF_FILENAME] 176s [--corrected-group CORRECTED_GROUP] 176s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 176s [--quiet] [--help] 176s 176s Required Arguments: 176s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 176s Directories containing fast5 files. 176s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 176s Genomic locations at which to plot signal. Format 176s locations as "chrm:position[:strand] 176s [chrm2:position2[:strand2] ...]" (strand not 176s applicable for all applications) 176s 176s Comparison Arguments: 176s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 176s Set of directories containing fast5 files for control 176s reads, containing only canonical nucleotides. 176s --plot-standard-model 176s Add default standard model distribution to the plot. 176s --plot-alternate-model {5mC,dam,6mA,CpG,dcm} 176s Add alternative model distribution to the plot. 176s 176s Overplotting Arguments: 176s --overplot-threshold OVERPLOT_THRESHOLD 176s Coverage level to trigger alternative plot type 176s instead of raw signal. Default: 50 176s --overplot-type {Downsample,Boxplot,Quantile,Density} 176s Plot type for regions with higher coverage. Default: 176s Downsample 176s 176s Plotting Region Argument: 176s --num-bases NUM_BASES 176s Number of bases to plot/output. Default: 21 176s 176s Output Argument: 176s --pdf-filename PDF_FILENAME 176s PDF filename to store plot(s). Default: 176s tombo_results.genome_locations.pdf 176s 176s FAST5 Data Arguments: 176s --corrected-group CORRECTED_GROUP 176s FAST5 group created by resquiggle command. Default: 176s RawGenomeCorrected_000 176s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 176s FAST5 subgroup(s) (under /Analyses/[--basecall- 176s group]/) containing basecalls and created within 176s [--corrected-group] containing re-squiggle results. 176s Default: ['BaseCalled_template'] 176s 176s Miscellaneous Arguments: 176s --quiet, -q Don't print status information. 176s --help, -h Print this help message and exit 176s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 176s [FAST5_BASEDIRS ...] --motif MOTIF 176s --genome-fasta GENOME_FASTA 176s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 176s [--plot-standard-model] 176s [--plot-alternate-model {5mC,6mA,dcm,dam,CpG}] 176s [--overplot-threshold OVERPLOT_THRESHOLD] 176s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 176s [--num-regions NUM_REGIONS] 176s [--num-bases NUM_BASES] [--deepest-coverage] 176s [--pdf-filename PDF_FILENAME] 176s [--corrected-group CORRECTED_GROUP] 176s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 176s [--quiet] [--help] 176s 176s Required Arguments: 176s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 176s Directories containing fast5 files. 176s --motif MOTIF Motif of interest at which to plot signal and 176s statsitics. Supports IUPAC single letter codes (use T 176s for RNA). 176s --genome-fasta GENOME_FASTA 176s FASTA file used to re-squiggle. For faster sequence 176s access. 176s 176s Comparison Arguments: 176s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 176s Set of directories containing fast5 files for control 176s reads, containing only canonical nucleotides. 176s --plot-standard-model 176s Add default standard model distribution to the plot. 176s --plot-alternate-model {5mC,6mA,dcm,dam,CpG} 176s Add alternative model distribution to the plot. 176s 176s Overplotting Arguments: 176s --overplot-threshold OVERPLOT_THRESHOLD 176s Coverage level to trigger alternative plot type 176s instead of raw signal. Default: 50 176s --overplot-type {Downsample,Boxplot,Quantile,Density} 176s Plot type for regions with higher coverage. Default: 176s Downsample 176s 176s Plotting Region Arguments: 176s --num-regions NUM_REGIONS 176s Number of regions to plot. Default: 10 176s --num-bases NUM_BASES 176s Number of bases to plot/output. Default: 21 176s --deepest-coverage Plot the deepest coverage regions. 176s 176s Output Argument: 176s --pdf-filename PDF_FILENAME 176s PDF filename to store plot(s). Default: 176s tombo_results.motif_centered.pdf 176s 176s FAST5 Data Arguments: 176s --corrected-group CORRECTED_GROUP 176s FAST5 group created by resquiggle command. Default: 176s RawGenomeCorrected_000 176s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 176s FAST5 subgroup(s) (under /Analyses/[--basecall- 176s group]/) containing basecalls and created within 176s [--corrected-group] containing re-squiggle results. 176s Default: ['BaseCalled_template'] 176s 176s Miscellaneous Arguments: 176s --quiet, -q Don't print status information. 176s --help, -h Print this help message and exit 176s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 176s [FAST5_BASEDIRS ...] --control-fast5-basedirs 176s CONTROL_FAST5_BASEDIRS 176s [CONTROL_FAST5_BASEDIRS ...] 176s [--overplot-threshold OVERPLOT_THRESHOLD] 176s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 176s [--num-regions NUM_REGIONS] 176s [--num-bases NUM_BASES] 176s [--pdf-filename PDF_FILENAME] 176s [--sequences-filename SEQUENCES_FILENAME] 176s [--corrected-group CORRECTED_GROUP] 176s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 176s [--quiet] [--help] 176s 176s Required Arguments: 176s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 176s Directories containing fast5 files. 176s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 176s Set of directories containing fast5 files for control 176s reads, containing only canonical nucleotides. 176s 176s Overplotting Arguments: 176s --overplot-threshold OVERPLOT_THRESHOLD 176s Coverage level to trigger alternative plot type 176s instead of raw signal. Default: 50 176s --overplot-type {Downsample,Boxplot,Quantile,Density} 176s Plot type for regions with higher coverage. Default: 176s Downsample 176s 176s Plotting Region Arguments: 176s --num-regions NUM_REGIONS 176s Number of regions to plot. Default: 10 176s --num-bases NUM_BASES 176s Number of bases to plot/output. Default: 21 176s 176s Output Arguments: 176s --pdf-filename PDF_FILENAME 176s PDF filename to store plot(s). Default: 176s tombo_results.max_difference.pdf 176s --sequences-filename SEQUENCES_FILENAME 176s File for sequences from selected regions. Sequences 176s will be stored in FASTA format. Default: None. 176s 176s FAST5 Data Arguments: 176s --corrected-group CORRECTED_GROUP 176s FAST5 group created by resquiggle command. Default: 176s RawGenomeCorrected_000 176s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 176s FAST5 subgroup(s) (under /Analyses/[--basecall- 176s group]/) containing basecalls and created within 176s [--corrected-group] containing re-squiggle results. 176s Default: ['BaseCalled_template'] 176s 176s Miscellaneous Arguments: 176s --quiet, -q Don't print status information. 176s --help, -h Print this help message and exit 176s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 176s [FAST5_BASEDIRS ...] --statistics-filename 176s STATISTICS_FILENAME 176s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 176s [--plot-standard-model] 176s [--plot-alternate-model {dcm,dam,6mA,5mC,CpG}] 176s [--overplot-threshold OVERPLOT_THRESHOLD] 176s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 176s [--num-regions NUM_REGIONS] 176s [--num-bases NUM_BASES] 176s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 176s [--pdf-filename PDF_FILENAME] 176s [--sequences-filename SEQUENCES_FILENAME] 176s [--corrected-group CORRECTED_GROUP] 176s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 176s [--quiet] [--help] 176s 176s Required Arguments: 176s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 176s Directories containing fast5 files. 176s --statistics-filename STATISTICS_FILENAME 176s File to save/load genomic base anchored statistics. 176s 176s Comparison Arguments: 176s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 176s Set of directories containing fast5 files for control 176s reads, containing only canonical nucleotides. 176s --plot-standard-model 176s Add default standard model distribution to the plot. 176s --plot-alternate-model {dcm,dam,6mA,5mC,CpG} 176s Add alternative model distribution to the plot. 176s 176s Overplotting Arguments: 176s --overplot-threshold OVERPLOT_THRESHOLD 176s Coverage level to trigger alternative plot type 176s instead of raw signal. Default: 50 176s --overplot-type {Downsample,Boxplot,Quantile,Density} 176s Plot type for regions with higher coverage. Default: 176s Downsample 176s 176s Plotting Region Arguments: 176s --num-regions NUM_REGIONS 176s Number of regions to plot. Default: 10 176s --num-bases NUM_BASES 176s Number of bases to plot/output. Default: 21 176s 176s Statistical Argument: 176s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 176s Dampen fraction modified estimates for low coverage 176s sites. Two parameters are unmodified and modified 176s pseudo read counts. This is equivalent to a beta prior 176s on the fraction estimate. Set to "0 0" to disable 176s dampened fraction estimation. Default: [2, 0] 176s 176s Output Arguments: 176s --pdf-filename PDF_FILENAME 176s PDF filename to store plot(s). Default: 176s tombo_results.significant_difference.pdf 176s --sequences-filename SEQUENCES_FILENAME 176s File for sequences from selected regions. Sequences 176s will be stored in FASTA format. Default: None. 176s 176s FAST5 Data Arguments: 176s --corrected-group CORRECTED_GROUP 176s FAST5 group created by resquiggle command. Default: 176s RawGenomeCorrected_000 176s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 176s FAST5 subgroup(s) (under /Analyses/[--basecall- 176s group]/) containing basecalls and created within 176s [--corrected-group] containing re-squiggle results. 176s Default: ['BaseCalled_template'] 176s 176s Miscellaneous Arguments: 176s --quiet, -q Don't print status information. 176s --help, -h Print this help message and exit 176s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 176s [FAST5_BASEDIRS ...] --motif MOTIF 176s --statistics-filename STATISTICS_FILENAME 176s --genome-fasta GENOME_FASTA 176s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 176s [--plot-standard-model] 176s [--plot-alternate-model {dam,6mA,CpG,5mC,dcm}] 176s [--overplot-threshold OVERPLOT_THRESHOLD] 176s [--num-regions NUM_REGIONS] 176s [--num-context NUM_CONTEXT] 176s [--num-statistics NUM_STATISTICS] 176s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 176s [--pdf-filename PDF_FILENAME] 176s [--corrected-group CORRECTED_GROUP] 176s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 176s [--quiet] [--help] 176s 176s Required Arguments: 176s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 176s Directories containing fast5 files. 176s --motif MOTIF Motif of interest at which to plot signal and 176s statsitics. Supports IUPAC single letter codes (use T 176s for RNA). 176s --statistics-filename STATISTICS_FILENAME 176s File to save/load genomic base anchored statistics. 176s --genome-fasta GENOME_FASTA 176s FASTA file used to re-squiggle. For faster sequence 176s access. 176s 176s Comparison Arguments: 176s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 176s Set of directories containing fast5 files for control 176s reads, containing only canonical nucleotides. 176s --plot-standard-model 176s Add default standard model distribution to the plot. 176s --plot-alternate-model {dam,6mA,CpG,5mC,dcm} 176s Add alternative model distribution to the plot. 176s 176s Overplotting Argument: 176s --overplot-threshold OVERPLOT_THRESHOLD 176s Coverage level to trigger alternative plot type 176s instead of raw signal. Default: 50 176s 176s Plotting Region Arguments: 176s --num-regions NUM_REGIONS 176s Number of regions to plot. Default: 3 176s --num-context NUM_CONTEXT 176s Number of context bases around motif. Default: 5 176s --num-statistics NUM_STATISTICS 176s Number of motif centered regions to include in 176s statistic distributions. Default: 200 176s 176s Statistical Argument: 176s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 176s Dampen fraction modified estimates for low coverage 176s sites. Two parameters are unmodified and modified 176s pseudo read counts. This is equivalent to a beta prior 176s on the fraction estimate. Set to "0 0" to disable 176s dampened fraction estimation. Default: [2, 0] 176s 176s Output Argument: 176s --pdf-filename PDF_FILENAME 176s PDF filename to store plot(s). Default: 176s tombo_results.motif_statistics.pdf 176s 176s FAST5 Data Arguments: 176s --corrected-group CORRECTED_GROUP 176s FAST5 group created by resquiggle command. Default: 176s RawGenomeCorrected_000 176s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 176s FAST5 subgroup(s) (under /Analyses/[--basecall- 176s group]/) containing basecalls and created within 176s [--corrected-group] containing re-squiggle results. 176s Default: ['BaseCalled_template'] 176s 176s Miscellaneous Arguments: 176s --quiet, -q Don't print status information. 176s --help, -h Print this help message and exit 176s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 176s [GENOME_LOCATIONS ...] 176s --per-read-statistics-filename 176s PER_READ_STATISTICS_FILENAME 176s [--genome-fasta GENOME_FASTA] 176s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 176s [--num-reads NUM_READS] [--num-bases NUM_BASES] 176s [--box-center] [--pdf-filename PDF_FILENAME] 176s [--corrected-group CORRECTED_GROUP] 176s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 176s [--quiet] [--help] 176s 176s Required Arguments: 176s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 176s Genomic locations at which to plot signal. Format 176s locations as "chrm:position[:strand] 176s [chrm2:position2[:strand2] ...]" (strand not 176s applicable for all applications) 176s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 176s Binary file containing per-read statistics from 176s statistical testing. 176s 176s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 176s --genome-fasta GENOME_FASTA 176s FASTA file used to re-squiggle. For faster sequence 176s access. 176s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 176s Directories containing fast5 files. 176s 176s Plotting Region Arguments: 176s --num-reads NUM_READS 176s Number of reads to plot. Default: 100 176s --num-bases NUM_BASES 176s Number of bases to plot/output. Default: 51 176s --box-center Plot a box around the central base. 176s 176s Output Argument: 176s --pdf-filename PDF_FILENAME 176s PDF filename to store plot(s). Default: 176s tombo_results.per_read_stats.pdf 176s 176s FAST5 Data Arguments: 176s --corrected-group CORRECTED_GROUP 176s FAST5 group created by resquiggle command. Default: 176s RawGenomeCorrected_000 176s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 176s FAST5 subgroup(s) (under /Analyses/[--basecall- 176s group]/) containing basecalls and created within 176s [--corrected-group] containing re-squiggle results. 176s Default: ['BaseCalled_template'] 176s 176s Miscellaneous Arguments: 176s --quiet, -q Don't print status information. 176s --help, -h Print this help message and exit 177s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 177s [STATISTICS_FILENAMES ...] 177s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 177s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 177s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 177s [--genome-fasta GENOME_FASTA] 177s [--pdf-filename PDF_FILENAME] 177s [--statistics-per-block STATISTICS_PER_BLOCK] 177s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 177s [--quiet] [--help] 177s 177s Required Argument: 177s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 177s Files to load genomic base anchored statistics. 177s 177s Ground Truth Arguments (provide bed files or motifs): 177s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 177s Modification description and bed format files 177s containing single base locations of ground truth 177s modified sites. Bed files should contain 6 fields 177s including strand. Format descriptions as 177s "mod_name:locs.bed". Example: "CpG 177s bisulfite":bisulfite_locs.bed 177s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 177s Bed format files containing single base locations of 177s ground truth unmodified sites. Bed files should 177s contain 6 fields including strand. 177s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 177s Ground truth, motif centered, modified base 177s descriptions for computing ROC and PR curves. Each 177s statistics file is associated with a set of motif 177s descriptions. Format descriptions as: 177s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 177s mod_pos indicates the alternate-base within the motif 177s (1-based index). Example: CCWGG:2:"dcm 177s 5mC"::GATC:2:"dam 6mA" would assess the performance of 177s a single Tombo statistics file for identification of 177s E. coli dam and dcm methylation. 177s --genome-fasta GENOME_FASTA 177s FASTA file used to re-squiggle. For faster sequence 177s access. 177s 177s Output Arguments: 177s --pdf-filename PDF_FILENAME 177s PDF filename to store plot(s). Default: 177s tombo_results.roc.pdf 177s 177s Down-sampling Arguments: 177s --statistics-per-block STATISTICS_PER_BLOCK 177s Number of randomly selected per-read, per-base 177s statistics to extract from each genomic block for 177s plotting. Default: Include all stats 177s --total-statistics-limit TOTAL_STATISTICS_LIMIT 177s Total per-read statistics to be extracted for 177s plotting. Avoids memory overflow for large runs. 177s Default: 5000000 177s 177s Miscellaneous Arguments: 177s --quiet, -q Don't print status information. 177s --help, -h Print this help message and exit 177s usage: tombo plot per_read_roc --per-read-statistics-filenames 177s PER_READ_STATISTICS_FILENAMES 177s [PER_READ_STATISTICS_FILENAMES ...] 177s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 177s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 177s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 177s [--genome-fasta GENOME_FASTA] 177s [--statistics-per-block STATISTICS_PER_BLOCK] 177s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 177s [--pdf-filename PDF_FILENAME] [--quiet] 177s [--help] 177s 177s Required Argument: 177s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 177s Binary files containing per-read statistics from 177s statistical testing. 177s 177s Ground Truth Arguments (provide bed files or motifs): 177s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 177s Modification description and bed format files 177s containing single base locations of ground truth 177s modified sites. Bed files should contain 6 fields 177s including strand. Format descriptions as 177s "mod_name:locs.bed". Example: "CpG 177s bisulfite":bisulfite_locs.bed 177s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 177s Bed format files containing single base locations of 177s ground truth unmodified sites. Bed files should 177s contain 6 fields including strand. 177s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 177s Ground truth, motif centered, modified base 177s descriptions for computing ROC and PR curves. Each 177s statistics file is associated with a set of motif 177s descriptions. Format descriptions as: 177s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 177s mod_pos indicates the alternate-base within the motif 177s (1-based index). Example: CCWGG:2:"dcm 177s 5mC"::GATC:2:"dam 6mA" would assess the performance of 177s a single Tombo statistics file for identification of 177s E. coli dam and dcm methylation. 177s --genome-fasta GENOME_FASTA 177s FASTA file used to re-squiggle. For faster sequence 177s access. 177s 177s Down-sampling Arguments: 177s --statistics-per-block STATISTICS_PER_BLOCK 177s Number of randomly selected per-read, per-base 177s statistics to extract from each genomic block for 177s plotting. Default: 100000 177s --total-statistics-limit TOTAL_STATISTICS_LIMIT 177s Total per-read statistics to be extracted for 177s plotting. Avoids memory overflow for large runs. 177s Default: 5000000 177s 177s Output Arguments: 177s --pdf-filename PDF_FILENAME 177s PDF filename to store plot(s). Default: 177s tombo_results.per_reads_roc.pdf 177s 177s Miscellaneous Arguments: 177s --quiet, -q Don't print status information. 177s --help, -h Print this help message and exit 177s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 177s [--upstream-bases {0,1,2,3,4}] 177s [--downstream-bases {0,1,2,3,4}] [--read-mean] 177s [--num-kmer-threshold NUM_KMER_THRESHOLD] 177s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 177s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 177s [--corrected-group CORRECTED_GROUP] 177s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 177s [--quiet] [--help] 177s 177s Required Argument: 177s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 177s Directories containing fast5 files. 177s 177s Data Processing Arguments: 177s --upstream-bases {0,1,2,3,4} 177s Upstream bases in k-mer. Default: 1 177s --downstream-bases {0,1,2,3,4} 177s Downstream bases in k-mer. Default: 2 177s --read-mean Plot k-mer means across whole reads as opposed to 177s individual k-mer event levels. 177s --num-kmer-threshold NUM_KMER_THRESHOLD 177s Observations of each k-mer required to include a read 177s in read level averages. Default: 1 177s 177s Plotting Region Arguments: 177s --num-reads NUM_READS 177s Number of reads to plot. Default: 100 177s 177s Output Arguments: 177s --pdf-filename PDF_FILENAME 177s PDF filename to store plot(s). Default: 177s tombo_results.kmer_distribution.pdf 177s --r-data-filename R_DATA_FILENAME 177s Filename to save R data structure. Default: Don't save 177s --dont-plot Don't plot result. Useful to produce only R data file. 177s 177s FAST5 Data Arguments: 177s --corrected-group CORRECTED_GROUP 177s FAST5 group created by resquiggle command. Default: 177s RawGenomeCorrected_000 177s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 177s FAST5 subgroup(s) (under /Analyses/[--basecall- 177s group]/) containing basecalls and created within 177s [--corrected-group] containing re-squiggle results. 177s Default: ['BaseCalled_template'] 177s 177s Miscellaneous Arguments: 177s --quiet, -q Don't print status information. 177s --help, -h Print this help message and exit 177s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 177s [FAST5_BASEDIRS ...] 177s --control-fast5-basedirs 177s CONTROL_FAST5_BASEDIRS 177s [CONTROL_FAST5_BASEDIRS ...] 177s --statistics-filename 177s STATISTICS_FILENAME 177s [--genome-fasta GENOME_FASTA] 177s [--processes PROCESSES] 177s [--num-regions NUM_REGIONS] 177s [--num-bases NUM_BASES] 177s [--slide-span SLIDE_SPAN] 177s [--pdf-filename PDF_FILENAME] 177s [--r-data-filename R_DATA_FILENAME] 177s [--corrected-group CORRECTED_GROUP] 177s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 177s [--quiet] [--help] 177s 177s Required Arguments: 177s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 177s Directories containing fast5 files. 177s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 177s Set of directories containing fast5 files for control 177s reads, containing only canonical nucleotides. 177s --statistics-filename STATISTICS_FILENAME 177s File to save/load genomic base anchored statistics. 177s 177s FASTA Sequence Argument: 177s --genome-fasta GENOME_FASTA 177s FASTA file used to re-squiggle. For faster sequence 177s access. 177s 177s Multiprocessing Argument: 177s --processes PROCESSES 177s Number of processes. Default: 1 177s 177s Plotting Region Arguments: 177s --num-regions NUM_REGIONS 177s Number of regions to plot. Default: 10 177s --num-bases NUM_BASES 177s Number of bases to plot/output. Default: 21 177s --slide-span SLIDE_SPAN 177s Number of bases offset over which to search when 177s computing distances for signal cluster plotting. 177s Default: 0 (exact position) 177s 177s Output Arguments: 177s --pdf-filename PDF_FILENAME 177s PDF filename to store plot(s). Default: 177s tombo_results.signal_clusters.pdf 177s --r-data-filename R_DATA_FILENAME 177s Filename to save R data structure. Default: Don't save 177s 177s FAST5 Data Arguments: 177s --corrected-group CORRECTED_GROUP 177s FAST5 group created by resquiggle command. Default: 177s RawGenomeCorrected_000 177s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 177s FAST5 subgroup(s) (under /Analyses/[--basecall- 177s group]/) containing basecalls and created within 177s [--corrected-group] containing re-squiggle results. 177s Default: ['BaseCalled_template'] 177s 177s Miscellaneous Arguments: 177s --quiet, -q Don't print status information. 177s --help, -h Print this help message and exit 177s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 177s 177s Required Arguments: 177s fast5s_basedir Directory containing fast5 files. All files ending in 177s "fast5" found recursively within this base directory will be 177s processed. 177s 177s Miscellaneous Arguments: 177s --quiet, -q Don't print status information. 177s --help, -h Print this help message and exit 177s usage: tombo build_model event_resquiggle 177s [--minimap2-executable MINIMAP2_EXECUTABLE] 177s [--minimap2-index MINIMAP2_INDEX] 177s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 177s [--graphmap-executable GRAPHMAP_EXECUTABLE] 177s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 177s [--normalization-type {median,pA,pA_raw,none}] 177s [--pore-model-filename PORE_MODEL_FILENAME] 177s [--outlier-threshold OUTLIER_THRESHOLD] 177s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 177s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 177s [--timeout TIMEOUT] 177s [--cpts-limit CPTS_LIMIT] 177s [--skip-index] [--overwrite] 177s [--failed-reads-filename FAILED_READS_FILENAME] 177s [--include-event-stdev] 177s [--corrected-group CORRECTED_GROUP] 177s [--basecall-group BASECALL_GROUP] 177s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 177s [--processes PROCESSES] 177s [--align-processes ALIGN_PROCESSES] 177s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 177s [--resquiggle-processes RESQUIGGLE_PROCESSES] 177s [--quiet] [--help] 177s fast5s_basedir reference_fasta 177s 177s Required Arguments: 177s fast5s_basedir Directory containing fast5 files. All files ending in 177s "fast5" found recursively within this base directory 177s will be processed. 177s reference_fasta Reference genome/transcriptome FASTA file for mapping. 177s 177s Mapper Arguments (One mapper is required): 177s --minimap2-executable MINIMAP2_EXECUTABLE 177s Path to minimap2 executable. 177s --minimap2-index MINIMAP2_INDEX 177s Path to minimap2 index (with map-ont preset) file 177s corresponding to the [genome_fasta] provided. 177s --bwa-mem-executable BWA_MEM_EXECUTABLE 177s Path to bwa-mem executable. 177s --graphmap-executable GRAPHMAP_EXECUTABLE 177s Path to graphmap executable. 177s --alignment-batch-size ALIGNMENT_BATCH_SIZE 177s Number of reads included in each alignment call. Note: 177s A new system mapping call is made for each batch 177s (including loading of the genome), so it is advised to 177s use larger values for larger genomes. Default: 1000 177s 177s Signal Processing Arguments: 177s --normalization-type {median,pA,pA_raw,none} 177s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 177s as in the ONT events (using offset, range and 177s digitization), "pA": k-mer-based correction for pA 177s drift as in nanopolish (requires [--pore-model- 177s filename]), "median": median and MAD from raw signal. 177s Default: median 177s --pore-model-filename PORE_MODEL_FILENAME 177s File containing kmer model parameters (level_mean and 177s level_stdv) used in order to compute kmer-based 177s corrected pA values. E.g. https://github.com/jts/nanop 177s olish/blob/master/etc/r9- 177s models/template_median68pA.5mers.model 177s --outlier-threshold OUTLIER_THRESHOLD 177s Windosrize the signal at this number of scale values. 177s Negative value disables outlier clipping. Default: 177s 5.000000 177s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 177s Specify the 2 parameters for segmentation 1) running 177s neighboring windows width 2) minimum raw observations 177s per genomic base. Sample type defaults: RNA : 12 6 || 177s DNA : 5 3 177s 177s Read Filtering Arguments: 177s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 177s Filter reads based on observations per base percentile 177s thresholds. Format thresholds as "percentile:thresh 177s [pctl2:thresh2 ...]". For example to filter reads with 177s 99th pctl > 200 obs/base or max > 5k obs/base use 177s "99:200 100:5000". 177s --timeout TIMEOUT Timeout in seconds for processing a single read. 177s Default: No timeout. 177s --cpts-limit CPTS_LIMIT 177s Maximum number of changepoints to find within a single 177s indel group. Default: No limit. 177s 177s Input/Output Arguments: 177s --skip-index Skip creation of tombo index. This drastically slows 177s downstream tombo commands. Default stores tombo index 177s named ".[--fast5-basedir].[--corrected- 177s group].tombo.index" to be loaded automatically for 177s downstream commands. 177s --overwrite Overwrite previous corrected group in FAST5 files. 177s Note: only effects --corrected-group or --new- 177s corrected-group. 177s --failed-reads-filename FAILED_READS_FILENAME 177s Output failed read filenames with assoicated error. 177s Default: Do not store failed reads. 177s --include-event-stdev 177s Include corrected event standard deviation in output 177s FAST5 data. 177s 177s FAST5 Data Arguments: 177s --corrected-group CORRECTED_GROUP 177s FAST5 group created by resquiggle command. Default: 177s RawGenomeCorrected_000 177s --basecall-group BASECALL_GROUP 177s FAST5 group obtain original basecalls (under Analyses 177s group). Default: Basecall_1D_000 177s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 177s FAST5 subgroup(s) (under /Analyses/[--basecall- 177s group]/) containing basecalls and created within 177s [--corrected-group] containing re-squiggle results. 177s Default: ['BaseCalled_template'] 177s 177s Multiprocessing Arguments: 177s --processes PROCESSES 177s Number of processes. Default: 2 177s --align-processes ALIGN_PROCESSES 177s Number of processes to use for parsing and aligning 177s original basecalls. Each process will independently 177s load the genome into memory, so use caution with 177s larger genomes (e.g. human). Default: 1 177s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 177s Number of threads to use for aligner system call. 177s Default: [--processes] / (2 * [--align-processes)] 177s --resquiggle-processes RESQUIGGLE_PROCESSES 177s Number of processes to use for resquiggle algorithm. 177s Default: [--processes] / 2 177s 177s Miscellaneous Arguments: 177s --quiet, -q Don't print status information. 177s --help, -h Print this help message and exit 177s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 177s [FAST5_BASEDIRS ...] 177s --tombo-model-filename 177s TOMBO_MODEL_FILENAME 177s [--estimate-mean] 177s [--kmer-specific-sd] 177s [--upstream-bases {0,1,2,3,4}] 177s [--downstream-bases {0,1,2,3,4}] 177s [--minimum-test-reads MINIMUM_TEST_READS] 177s [--coverage-threshold COVERAGE_THRESHOLD] 177s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 177s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 177s [--processes PROCESSES] 177s [--corrected-group CORRECTED_GROUP] 177s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 177s [--quiet] [--help] 177s 177s Required Arguments: 177s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 177s Directories containing fast5 files. 177s --tombo-model-filename TOMBO_MODEL_FILENAME 177s Filename to save Tombo model. 177s 177s Modeling Arguments: 177s --estimate-mean Use the mean instead of median for model level 177s estimation. Note: This can cause poor fits due to 177s outliers 177s --kmer-specific-sd Estimate standard deviation for each k-mers 177s individually. 177s --upstream-bases {0,1,2,3,4} 177s Upstream bases in k-mer. Default: 1 177s --downstream-bases {0,1,2,3,4} 177s Downstream bases in k-mer. Default: 2 177s 177s Filtering Arguments: 177s --minimum-test-reads MINIMUM_TEST_READS 177s Number of reads required at a position to perform 177s significance testing or contribute to model 177s estimation. Default: 10 177s --coverage-threshold COVERAGE_THRESHOLD 177s Maximum mean coverage per region when estimating k-mer 177s model (limits compute time for deep samples). Default: 177s 100 177s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 177s Number of each k-mer observations required in order to 177s produce a reference (genomic locations for standard 177s reference and per-read for alternative reference). 177s Default: 5 177s 177s Multiprocessing Arguments: 177s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 177s Size of regions over which to multiprocesses statistic 177s computation. For very deep samples a smaller value is 177s recommmended in order to control memory consumption. 177s Default: 10000 177s --processes PROCESSES 177s Number of processes. Default: 1 177s 177s FAST5 Data Arguments: 177s --corrected-group CORRECTED_GROUP 177s FAST5 group created by resquiggle command. Default: 177s RawGenomeCorrected_000 177s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 177s FAST5 subgroup(s) (under /Analyses/[--basecall- 177s group]/) containing basecalls and created within 177s [--corrected-group] containing re-squiggle results. 177s Default: ['BaseCalled_template'] 177s 177s Miscellaneous Arguments: 177s --quiet, -q Don't print status information. 177s --help, -h Print this help message and exit 177s usage: tombo build_model estimate_alt_reference --alternate-model-filename 177s ALTERNATE_MODEL_FILENAME 177s --alternate-model-name 177s ALTERNATE_MODEL_NAME 177s --alternate-model-base 177s {A,C,G,T} 177s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 177s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 177s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 177s [--control-density-filename CONTROL_DENSITY_FILENAME] 177s [--dna] [--rna] 177s [--tombo-model-filename TOMBO_MODEL_FILENAME] 177s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 177s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 177s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 177s [--save-density-basename SAVE_DENSITY_BASENAME] 177s [--processes PROCESSES] 177s [--corrected-group CORRECTED_GROUP] 177s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 177s [--quiet] [--help] 177s 177s Required Arguments: 177s --alternate-model-filename ALTERNATE_MODEL_FILENAME 177s Tombo model for alternative likelihood ratio 177s significance testing. 177s --alternate-model-name ALTERNATE_MODEL_NAME 177s A short name to associate with this alternate model 177s (e.g. 5mC, 6mA, etc.). This text will be included in 177s output filenames when this model is used for testing. 177s --alternate-model-base {A,C,G,T} 177s Non-standard base is an alternative to this base. 177s 177s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 177s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 177s Directories containing fast5 files. 177s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 177s Set of directories containing fast5 files for control 177s reads, containing only canonical nucleotides. 177s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 177s File containing k-mer level kernel density estimates 177s for the alternative sample saved using --save-density- 177s basename. 177s --control-density-filename CONTROL_DENSITY_FILENAME 177s File containing k-mer level kernel density estimates 177s for the control sample saved using --save-density- 177s basename. 177s 177s Standard Model Arguments: 177s --dna Explicitly select canonical DNA model. Default: 177s Automatically determine from FAST5s 177s --rna Explicitly select canonical RNA model. Default: 177s Automatically determine from FAST5s 177s --tombo-model-filename TOMBO_MODEL_FILENAME 177s Tombo model filename. If no file is provided, the 177s default DNA or RNA Tombo model will be used. 177s 177s Model Fitting Arguments: 177s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 177s When esitmating the alternative base incorporation 177s rate, this percent of k-mers are assumed to have 177s significantly shifted signal so the alternative 177s distribution minimally overlaps the standard base 177s distribution. Default: 5.000000 177s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 177s Bandwidth applied when performing Gaussian kernal 177s density esitmation on standard and alternative base 177s signal distributions. Default: 0.050000 177s 177s Filtering Argument: 177s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 177s Number of each k-mer observations required in order to 177s produce a reference (genomic locations for standard 177s reference and per-read for alternative reference). 177s Default: 1000 177s 177s Output Argument: 177s --save-density-basename SAVE_DENSITY_BASENAME 177s Basename to save alternative model estimation density 177s estimation information. See scripts/debug_est_alt.R 177s for info use example. Default: Don't save. 177s 177s Multiprocessing Arguments: 177s --processes PROCESSES 177s Number of processes. Default: 1 177s 177s FAST5 Data Arguments: 177s --corrected-group CORRECTED_GROUP 177s FAST5 group created by resquiggle command. Default: 177s RawGenomeCorrected_000 177s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 177s FAST5 subgroup(s) (under /Analyses/[--basecall- 177s group]/) containing basecalls and created within 177s [--corrected-group] containing re-squiggle results. 177s Default: ['BaseCalled_template'] 177s 177s Miscellaneous Arguments: 177s --quiet, -q Don't print status information. 177s --help, -h Print this help message and exit 177s This test only tests the help system 177s There is an extensive test in 177s 177s tombo/tests/shell_tests.sh 177s 177s but this requires to download larger data 177s sets which is not done for the moment. 177s autopkgtest [10:02:18]: test run-unit-test: -----------------------] 178s autopkgtest [10:02:19]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 178s run-unit-test PASS 178s autopkgtest [10:02:19]: @@@@@@@@@@@@@@@@@@@@ summary 178s run-unit-test PASS 190s nova [W] Using flock in prodstack6-s390x 190s Creating nova instance adt-plucky-s390x-tombo-20241030-095920-juju-7f2275-prod-proposed-migration-environment-15-bf6178d7-47b9-4a88-86ed-4c05ce562492 from image adt/ubuntu-plucky-s390x-server-20241029.img (UUID f65adb75-f507-40e2-9b64-4d84ffb9df90)...