0s autopkgtest [18:04:51]: starting date and time: 2024-03-22 18:04:51+0000 0s autopkgtest [18:04:51]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [18:04:51]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tfqp7qyr/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:sphinx --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/7.2.6-6 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-4.secgroup --name adt-noble-s390x-tombo-20240322-180451-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 83s autopkgtest [18:06:14]: testbed dpkg architecture: s390x 84s autopkgtest [18:06:15]: testbed apt version: 2.7.12 84s autopkgtest [18:06:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 85s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 85s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 85s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [58.8 kB] 85s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [498 kB] 86s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3980 kB] 86s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [667 kB] 86s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 86s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 86s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 86s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4045 kB] 87s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 87s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [46.1 kB] 87s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 89s Fetched 9430 kB in 3s (3021 kB/s) 89s Reading package lists... 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s Calculating upgrade... 92s The following packages will be upgraded: 92s cloud-init debianutils fonts-ubuntu-console python3-markupsafe 92s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s Need to get 719 kB of archives. 92s After this operation, 11.3 kB disk space will be freed. 92s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.17 [90.1 kB] 93s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 93s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x python3-markupsafe s390x 2.1.5-1build1 [12.8 kB] 93s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x cloud-init all 24.1.2-0ubuntu1 [597 kB] 93s Preconfiguring packages ... 93s Fetched 719 kB in 1s (1215 kB/s) 93s (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 ... 52171 files and directories currently installed.) 93s Preparing to unpack .../debianutils_5.17_s390x.deb ... 93s Unpacking debianutils (5.17) over (5.16) ... 93s Setting up debianutils (5.17) ... 93s (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 ... 52171 files and directories currently installed.) 93s Preparing to unpack .../fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 93s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 93s Preparing to unpack .../python3-markupsafe_2.1.5-1build1_s390x.deb ... 93s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 93s Preparing to unpack .../cloud-init_24.1.2-0ubuntu1_all.deb ... 94s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 94s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 94s Setting up cloud-init (24.1.2-0ubuntu1) ... 95s Setting up python3-markupsafe (2.1.5-1build1) ... 95s Processing triggers for man-db (2.12.0-3) ... 96s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Unknown architecture, assuming PC-style ttyS0 97s sh: Attempting to set up Debian/Ubuntu apt sources automatically 97s sh: Distribution appears to be Ubuntu 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s eatmydata is already the newest version (131-1). 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s dbus is already the newest version (1.14.10-4ubuntu1). 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s rng-tools-debian is already the newest version (2.4). 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s The following packages will be REMOVED: 99s cloud-init* python3-configobj* python3-debconf* 99s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 99s After this operation, 3256 kB disk space will be freed. 99s (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 ... 52170 files and directories currently installed.) 99s Removing cloud-init (24.1.2-0ubuntu1) ... 100s Removing python3-configobj (5.0.8-3) ... 100s Removing python3-debconf (1.5.86) ... 100s Processing triggers for man-db (2.12.0-3) ... 100s (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 ... 51781 files and directories currently installed.) 100s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 101s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 101s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 101s invoke-rc.d: policy-rc.d denied execution of try-restart. 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s linux-generic is already the newest version (6.8.0-11.11+1). 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 102s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 102s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 104s Reading package lists... 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 104s Calculating upgrade... 104s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 104s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s autopkgtest [18:06:36]: rebooting testbed after setup commands that affected boot 129s autopkgtest [18:07:00]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 132s autopkgtest [18:07:03]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 137s Get:1 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (dsc) [2292 B] 137s Get:2 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (tar) [22.3 MB] 137s Get:3 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (diff) [7024 B] 138s gpgv: Signature made Sun Dec 17 19:23:46 2023 UTC 138s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 138s gpgv: issuer "tille@debian.org" 138s gpgv: Can't check signature: No public key 138s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6.dsc: no acceptable signature found 138s autopkgtest [18:07:09]: testing package tombo version 1.5.1-6 138s autopkgtest [18:07:09]: build not needed 150s autopkgtest [18:07:21]: test run-unit-test: preparing testbed 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Starting pkgProblemResolver with broken count: 0 157s Starting 2 pkgProblemResolver with broken count: 0 157s Done 157s The following additional packages will be installed: 157s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 157s libhdf5-103-1 libhdf5-hl-100 libjs-jquery libjs-mathjax libjs-sphinxdoc 157s libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 python3-decorator 157s python3-h5py python3-h5py-serial python3-mappy python3-numpy python3-scipy 157s python3-tqdm sphinx-rtd-theme-common tombo tombo-doc 157s Suggested packages: 157s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 157s gfortran python3-dev python3-pytest python-scipy-doc 157s Recommended packages: 157s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 157s python3-rpy2 157s The following NEW packages will be installed: 157s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 157s libblas3 libgfortran5 libhdf5-103-1 libhdf5-hl-100 libjs-jquery 157s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 157s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 157s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 157s tombo-doc 157s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 157s Need to get 67.5 MB/67.5 MB of archives. 157s After this operation, 242 MB of additional disk space will be used. 157s Get:1 /tmp/autopkgtest.6TbVqN/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [708 B] 157s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x fonts-lato all 2.015-1 [2781 kB] 160s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 160s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 161s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libaec0 s390x 1.1.2-1 [25.7 kB] 161s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 161s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 161s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libsz2 s390x 1.1.2-1 [5346 B] 161s Get:9 http://ftpmaster.internal/ubuntu noble/universe s390x libhdf5-103-1 s390x 1.10.10+repack-3ubuntu1 [1425 kB] 162s Get:10 http://ftpmaster.internal/ubuntu noble/universe s390x libhdf5-hl-100 s390x 1.10.10+repack-3ubuntu1 [57.5 kB] 162s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 162s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 162s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libjs-sphinxdoc all 7.2.6-4 [149 kB] 162s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 162s Get:15 http://ftpmaster.internal/ubuntu noble/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1 [28.4 kB] 162s Get:16 http://ftpmaster.internal/ubuntu noble/universe s390x liblzf1 s390x 3.6-4 [7020 B] 162s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 162s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x python3-numpy s390x 1:1.24.2-2 [5137 kB] 163s Get:19 http://ftpmaster.internal/ubuntu noble/universe s390x python3-h5py-serial s390x 3.10.0-1ubuntu1 [1535 kB] 163s Get:20 http://ftpmaster.internal/ubuntu noble/universe s390x python3-h5py all 3.10.0-1ubuntu1 [7970 B] 163s Get:21 http://ftpmaster.internal/ubuntu noble/universe s390x python3-mappy s390x 2.24+dfsg-3build2 [238 kB] 163s Get:22 http://ftpmaster.internal/ubuntu noble/universe s390x python3-tqdm all 4.64.1-2 [95.2 kB] 163s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] 164s Get:24 http://ftpmaster.internal/ubuntu noble/universe s390x python3-scipy s390x 1.11.4-6 [20.1 MB] 167s Get:25 http://ftpmaster.internal/ubuntu noble/universe s390x tombo s390x 1.5.1-6 [502 kB] 167s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 168s Get:27 http://ftpmaster.internal/ubuntu noble/universe s390x tombo-doc all 1.5.1-6 [21.7 MB] 178s Fetched 67.5 MB in 20s (3321 kB/s) 178s Selecting previously unselected package fonts-lato. 178s (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 ... 51726 files and directories currently installed.) 178s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 178s Unpacking fonts-lato (2.015-1) ... 178s Selecting previously unselected package fonts-font-awesome. 178s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 178s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 178s Selecting previously unselected package fonts-mathjax. 178s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 178s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 178s Selecting previously unselected package libaec0:s390x. 178s Preparing to unpack .../03-libaec0_1.1.2-1_s390x.deb ... 178s Unpacking libaec0:s390x (1.1.2-1) ... 178s Selecting previously unselected package libblas3:s390x. 178s Preparing to unpack .../04-libblas3_3.12.0-3_s390x.deb ... 178s Unpacking libblas3:s390x (3.12.0-3) ... 179s Selecting previously unselected package libgfortran5:s390x. 179s Preparing to unpack .../05-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 179s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 179s Selecting previously unselected package libsz2:s390x. 179s Preparing to unpack .../06-libsz2_1.1.2-1_s390x.deb ... 179s Unpacking libsz2:s390x (1.1.2-1) ... 179s Selecting previously unselected package libhdf5-103-1:s390x. 179s Preparing to unpack .../07-libhdf5-103-1_1.10.10+repack-3ubuntu1_s390x.deb ... 179s Unpacking libhdf5-103-1:s390x (1.10.10+repack-3ubuntu1) ... 179s Selecting previously unselected package libhdf5-hl-100:s390x. 179s Preparing to unpack .../08-libhdf5-hl-100_1.10.10+repack-3ubuntu1_s390x.deb ... 179s Unpacking libhdf5-hl-100:s390x (1.10.10+repack-3ubuntu1) ... 179s Selecting previously unselected package libjs-jquery. 179s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 179s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 179s Selecting previously unselected package libjs-underscore. 179s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 179s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 179s Selecting previously unselected package libjs-sphinxdoc. 179s Preparing to unpack .../11-libjs-sphinxdoc_7.2.6-4_all.deb ... 179s Unpacking libjs-sphinxdoc (7.2.6-4) ... 179s Selecting previously unselected package liblapack3:s390x. 179s Preparing to unpack .../12-liblapack3_3.12.0-3_s390x.deb ... 179s Unpacking liblapack3:s390x (3.12.0-3) ... 179s Selecting previously unselected package liblbfgsb0:s390x. 179s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1_s390x.deb ... 179s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1) ... 179s Selecting previously unselected package liblzf1:s390x. 179s Preparing to unpack .../14-liblzf1_3.6-4_s390x.deb ... 179s Unpacking liblzf1:s390x (3.6-4) ... 179s Selecting previously unselected package python3-decorator. 179s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 179s Unpacking python3-decorator (5.1.1-5) ... 179s Selecting previously unselected package python3-numpy. 179s Preparing to unpack .../16-python3-numpy_1%3a1.24.2-2_s390x.deb ... 179s Unpacking python3-numpy (1:1.24.2-2) ... 179s Selecting previously unselected package python3-h5py-serial. 179s Preparing to unpack .../17-python3-h5py-serial_3.10.0-1ubuntu1_s390x.deb ... 179s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 179s Selecting previously unselected package python3-h5py. 179s Preparing to unpack .../18-python3-h5py_3.10.0-1ubuntu1_all.deb ... 179s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 179s Selecting previously unselected package python3-mappy. 179s Preparing to unpack .../19-python3-mappy_2.24+dfsg-3build2_s390x.deb ... 179s Unpacking python3-mappy (2.24+dfsg-3build2) ... 179s Selecting previously unselected package python3-tqdm. 179s Preparing to unpack .../20-python3-tqdm_4.64.1-2_all.deb ... 179s Unpacking python3-tqdm (4.64.1-2) ... 179s Selecting previously unselected package sphinx-rtd-theme-common. 179s Preparing to unpack .../21-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... 179s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 179s Selecting previously unselected package python3-scipy. 179s Preparing to unpack .../22-python3-scipy_1.11.4-6_s390x.deb ... 179s Unpacking python3-scipy (1.11.4-6) ... 180s Selecting previously unselected package tombo. 180s Preparing to unpack .../23-tombo_1.5.1-6_s390x.deb ... 180s Unpacking tombo (1.5.1-6) ... 180s Selecting previously unselected package libjs-mathjax. 180s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 180s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 181s Selecting previously unselected package tombo-doc. 181s Preparing to unpack .../25-tombo-doc_1.5.1-6_all.deb ... 181s Unpacking tombo-doc (1.5.1-6) ... 181s Selecting previously unselected package autopkgtest-satdep. 181s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 181s Unpacking autopkgtest-satdep (0) ... 181s Setting up fonts-lato (2.015-1) ... 181s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 181s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 181s Setting up python3-tqdm (4.64.1-2) ... 181s Setting up python3-mappy (2.24+dfsg-3build2) ... 181s Setting up libaec0:s390x (1.1.2-1) ... 181s Setting up python3-decorator (5.1.1-5) ... 182s Setting up libblas3:s390x (3.12.0-3) ... 182s update-alternatives: using /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 182s Setting up liblzf1:s390x (3.6-4) ... 182s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 182s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 182s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 182s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 182s Setting up libsz2:s390x (1.1.2-1) ... 182s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 182s Setting up liblapack3:s390x (3.12.0-3) ... 182s 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 182s Setting up python3-numpy (1:1.24.2-2) ... 183s Setting up libjs-sphinxdoc (7.2.6-4) ... 183s Setting up tombo-doc (1.5.1-6) ... 183s Setting up libhdf5-103-1:s390x (1.10.10+repack-3ubuntu1) ... 183s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1) ... 183s Setting up libhdf5-hl-100:s390x (1.10.10+repack-3ubuntu1) ... 183s Setting up 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[----------------------- 191s ********* Testing help commands ********** 191s usage: tombo [-h] [-v] 191s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 191s ... 191s 191s ********** Tombo ********* 191s 191s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 191s 191s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 191s 191s Tombo command groups (additional help available within each command group): 191s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 191s preprocess Pre-process nanopore reads for Tombo processing. 191s filter Apply filter to Tombo index file for specified criterion. 191s detect_modifications Perform statistical testing to detect non-standard nucleotides. 191s text_output Output Tombo results in text files. 191s build_model Create canonical and alternative base Tombo models. 191s plot Save plots to visualize raw nanopore signal or testing results. 191s 191s options: 191s -h, --help show this help message and exit 191s -v, --version show Tombo version and exit. 191s usage: tombo resquiggle [--dna] [--rna] 191s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 191s [--q-score Q_SCORE] 191s [--signal-matching-score SIGNAL_MATCHING_SCORE] 191s [--processes PROCESSES] 191s [--corrected-group CORRECTED_GROUP] 191s [--basecall-group BASECALL_GROUP] 191s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 191s [--overwrite] 191s [--failed-reads-filename FAILED_READS_FILENAME] 191s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 191s [--print-advanced-arguments] [--quiet] [--help] 191s fast5s_basedir reference 191s 191s Required Arguments: 191s fast5s_basedir Directory containing fast5 files. All files ending in 191s "fast5" found recursively within this base directory 191s will be processed. 191s reference Reference genome/transcriptome FASTA file or minimap2 191s index (with "map-ont" preset) for mapping. 191s 191s Model Parameters: 191s --dna Explicitly select canonical DNA model. Default: 191s Automatically determine from FAST5s 191s --rna Explicitly select canonical RNA model. Default: 191s Automatically determine from FAST5s 191s 191s Read Filtering Argument: 191s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 191s Filter reads based on observations per base percentile 191s thresholds. Format thresholds as "percentile:thresh 191s [pctl2:thresh2 ...]". For example to filter reads with 191s 99th pctl > 200 obs/base or max > 5k obs/base use 191s "99:200 100:5000". 191s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 191s Default: 0.000000 191s --signal-matching-score SIGNAL_MATCHING_SCORE 191s Observed to expected signal matching score (higher 191s score indicates poor matching). Sample type defaults: 191s RNA : 2 || DNA : 1.1 191s 191s Multiprocessing Arguments: 191s --processes PROCESSES 191s Number of processes. Default: 1 191s 191s FAST5 Data Arguments: 191s --corrected-group CORRECTED_GROUP 191s FAST5 group created by resquiggle command. Default: 191s RawGenomeCorrected_000 191s --basecall-group BASECALL_GROUP 191s FAST5 group obtain original basecalls (under Analyses 191s group). Default: Basecall_1D_000 191s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 191s FAST5 subgroup(s) (under /Analyses/[--basecall- 191s group]/) containing basecalls and created within 191s [--corrected-group] containing re-squiggle results. 191s Default: ['BaseCalled_template'] 191s --overwrite Overwrite previous corrected group in FAST5 files. 191s Note: only effects --corrected-group or --new- 191s corrected-group. 191s 191s Input/Output Arguments: 191s --failed-reads-filename FAILED_READS_FILENAME 191s Output failed read filenames with assoicated error. 191s Default: Do not store failed reads. 191s --num-most-common-errors NUM_MOST_COMMON_ERRORS 191s Dynamically show this many most common errors so far 191s through run. Default: 0; Just show progress 191s 191s Advanced Arguments: 191s --print-advanced-arguments 191s Print advanced re-squiggle arguments and exit. 191s 191s Miscellaneous Arguments: 191s --quiet, -q Don't print status information. 191s --help, -h Print this help message and exit 191s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 191s --fastq-filenames 191s FASTQ_FILENAMES 191s [FASTQ_FILENAMES ...] 191s [--basecall-group BASECALL_GROUP] 191s [--basecall-subgroup BASECALL_SUBGROUP] 191s [--overwrite] 191s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 191s [--processes PROCESSES] 191s [--quiet] [--help] 191s 191s Required Arguments: 191s --fast5-basedir FAST5_BASEDIR 191s Directory containing fast5 files. 191s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 191s FASTQ filenames containing basecalls to be added to 191s raw FAST5 files. 191s 191s FAST5 Data Arguments: 191s --basecall-group BASECALL_GROUP 191s FAST5 group obtain original basecalls (under Analyses 191s group). Default: Basecall_1D_000 191s --basecall-subgroup BASECALL_SUBGROUP 191s FAST5 subgroup (under /Analyses/[--basecall-group]/) 191s under which to store basecalls from FASTQs. Default: 191s BaseCalled_template 191s --overwrite Overwrite previous corrected group in FAST5 files. 191s Note: only effects --corrected-group or --new- 191s corrected-group. 191s 191s Sequencing Summary Argument: 191s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 191s Sequencing summary filenames produced by albacore. 191s These can make annotation of raw FAST5 files with 191s FASTQ sequence much faster. 191s 191s Multiprocessing Argument: 191s --processes PROCESSES 191s Number of processes. Default: 1 191s 191s Miscellaneous Arguments: 191s --quiet, -q Don't print status information. 191s --help, -h Print this help message and exit 191s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 191s [FAST5_BASEDIRS ...] 191s [--corrected-group CORRECTED_GROUP] 191s [--quiet] [--help] 191s 191s Required Argument: 191s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 191s Directories containing fast5 files. 191s 191s FAST5 Data Argument: 191s --corrected-group CORRECTED_GROUP 191s FAST5 group created by resquiggle command. Default: 191s RawGenomeCorrected_000 191s 191s Miscellaneous Arguments: 191s --quiet, -q Don't print status information. 191s --help, -h Print this help message and exit 191s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 191s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 191s [--corrected-group CORRECTED_GROUP] [--quiet] 191s [--help] 191s 191s Required Argument: 191s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 191s Directories containing fast5 files. 191s 191s Read Filtering Argument: 191s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 191s Filter reads based on observations per base percentile 191s thresholds. Format thresholds as "percentile:thresh 191s [pctl2:thresh2 ...]". For example to filter reads with 191s 99th pctl > 200 obs/base or max > 5k obs/base use 191s "99:200 100:5000". 191s 191s FAST5 Data Argument: 191s --corrected-group CORRECTED_GROUP 191s FAST5 group created by resquiggle command. Default: 191s RawGenomeCorrected_000 191s 191s Miscellaneous Arguments: 191s --quiet, -q Don't print status information. 191s --help, -h Print this help message and exit 191s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 191s [FAST5_BASEDIRS ...] 191s [--percent-to-filter PERCENT_TO_FILTER] 191s [--corrected-group CORRECTED_GROUP] 191s [--quiet] [--help] 191s 191s Required Arguments: 191s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 191s Directories containing fast5 files. 191s 191s Read Filtering Argument: 191s --percent-to-filter PERCENT_TO_FILTER 191s Percentage of all reads to filter. Reads are randomly 191s selected weighted according to the approximate 191s coverage at the mapped genomic location. This can be 191s useful in modeling and testing. Default: 10.000000 191s 191s FAST5 Data Arguments: 191s --corrected-group CORRECTED_GROUP 191s FAST5 group created by resquiggle command. Default: 191s RawGenomeCorrected_000 191s 191s Miscellaneous Arguments: 191s --quiet, -q Don't print status information. 191s --help, -h Print this help message and exit 191s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 191s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 191s [--corrected-group CORRECTED_GROUP] 191s [--basecall-group BASECALL_GROUP] [--quiet] 191s [--help] 191s 191s Required Arguments: 191s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 191s Directories containing fast5 files. 191s 191s Read Filtering Argument: 191s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 191s Default: 7.000000 191s 191s FAST5 Data Arguments: 191s --corrected-group CORRECTED_GROUP 191s FAST5 group created by resquiggle command. Default: 191s RawGenomeCorrected_000 191s --basecall-group BASECALL_GROUP 191s FAST5 group obtain original basecalls (under Analyses 191s group). Default: Basecall_1D_000 191s 191s Miscellaneous Arguments: 191s --quiet, -q Don't print status information. 191s --help, -h Print this help message and exit 191s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 191s [FAST5_BASEDIRS ...] 191s --signal-matching-score 191s SIGNAL_MATCHING_SCORE 191s [--corrected-group CORRECTED_GROUP] 191s [--quiet] [--help] 191s 191s Required Arguments: 191s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 191s Directories containing fast5 files. 191s --signal-matching-score SIGNAL_MATCHING_SCORE 191s Observed to expected signal matching score (higher 191s score indicates poor matching). Sample type defaults: 191s RNA : 2 || DNA : 1.1 191s 191s FAST5 Data Arguments: 191s --corrected-group CORRECTED_GROUP 191s FAST5 group created by resquiggle command. Default: 191s RawGenomeCorrected_000 191s 191s Miscellaneous Arguments: 191s --quiet, -q Don't print status information. 191s --help, -h Print this help message and exit 191s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 191s [FAST5_BASEDIRS ...] 191s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 191s [--include-partial-overlap] 191s [--corrected-group CORRECTED_GROUP] 191s [--quiet] [--help] 191s 191s Required Arguments: 191s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 191s Directories containing fast5 files. 191s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 191s Filter out reads not falling completely within include 191s regions. Omit start and end coordinates to include an 191s entire chromosome/sequence record. Format regions as 191s "chrm[:start-end] [chrm2[:start2-end2] ...]". 191s 191s Filter Argument: 191s --include-partial-overlap 191s Include reads that partially overlap the specified 191s region. Default: Only include reads completely 191s contained in a specified region 191s 191s FAST5 Data Argument: 191s --corrected-group CORRECTED_GROUP 191s FAST5 group created by resquiggle command. Default: 191s RawGenomeCorrected_000 191s 191s Miscellaneous Arguments: 191s --quiet, -q Don't print status information. 191s --help, -h Print this help message and exit 191s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 191s [FAST5_BASEDIRS ...] 191s --statistics-file-basename 191s STATISTICS_FILE_BASENAME [--dna] 191s [--rna] 191s [--fishers-method-context FISHERS_METHOD_CONTEXT] 191s [--minimum-test-reads MINIMUM_TEST_READS] 191s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 191s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 191s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 191s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 191s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 191s [--processes PROCESSES] 191s [--corrected-group CORRECTED_GROUP] 191s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 191s [--quiet] [--help] 191s 191s Required Argument: 191s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 191s Directories containing fast5 files. 191s --statistics-file-basename STATISTICS_FILE_BASENAME 191s File base name to save base by base statistics from 191s testing. Filenames will be [--statistics-file- 191s basename].[--alternate-bases]?.tombo.stats 191s 191s Comparison Model Arguments: 191s --dna Explicitly select canonical DNA model. Default: 191s Automatically determine from FAST5s 191s --rna Explicitly select canonical RNA model. Default: 191s Automatically determine from FAST5s 191s 191s Significance Test Arguments: 191s --fishers-method-context FISHERS_METHOD_CONTEXT 191s Number of context bases up and downstream over which 191s to compute Fisher's method combined p-values. Note: 191s Not applicable for alternative model likelihood ratio 191s tests. Default: 1. 191s --minimum-test-reads MINIMUM_TEST_READS 191s Number of reads required at a position to perform 191s significance testing or contribute to model 191s estimation. Default: 1 191s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 191s P-value threshold when computing fraction of 191s significant reads at each genomic position. If two 191s values are provided, statistics between these values 191s are not considered. Default thresholds: DNA:0.15-0.5 , 191s RNA:0.05-0.4 191s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 191s Dampen fraction modified estimates for low coverage 191s sites. Two parameters are unmodified and modified 191s pseudo read counts. This is equivalent to a beta prior 191s on the fraction estimate. Set to "0 0" to disable 191s dampened fraction estimation. Default: [2, 0] 191s 191s Output Argument: 191s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 191s Base for binary files containing per-read statistics 191s from statistical testing. Filenames will be [--per- 191s read-statistics-basename].[--alternate- 191s bases]?.tombo.per_read_stats 191s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 191s Number of the most significant sites to store for 191s faster access. If a longer list of most significant 191s sites is required the list must be re-computed from 191s all batches. Very large values can increase RAM usage. 191s Default: 100000 191s 191s Multiprocessing Arguments: 191s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 191s Size of regions over which to multiprocesses statistic 191s computation. For very deep samples a smaller value is 191s recommmended in order to control memory consumption. 191s Default: 10000 191s --processes PROCESSES 191s Number of processes. Default: 1 191s 191s FAST5 Data Arguments: 191s --corrected-group CORRECTED_GROUP 191s FAST5 group created by resquiggle command. Default: 191s RawGenomeCorrected_000 191s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 191s FAST5 subgroup(s) (under /Analyses/[--basecall- 191s group]/) containing basecalls and created within 191s [--corrected-group] containing re-squiggle results. 191s Default: ['BaseCalled_template'] 191s 191s Miscellaneous Arguments: 191s --quiet, -q Don't print status information. 191s --help, -h Print this help message and exit 191s usage: tombo detect_modifications alternative_model 191s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 191s [--statistics-file-basename STATISTICS_FILE_BASENAME] 191s [--alternate-bases {5mC,6mA,dcm,CpG,dam} [{5mC,6mA,dcm,CpG,dam} ...]] 191s [--print-available-models] 191s [--dna] [--rna] 191s [--minimum-test-reads MINIMUM_TEST_READS] 191s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 191s [--standard-log-likelihood-ratio] 191s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 191s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 191s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 191s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 191s [--processes PROCESSES] 191s [--corrected-group CORRECTED_GROUP] 191s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 191s [--quiet] [--help] 191s 191s Required Argument: 191s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 191s Directories containing fast5 files. 191s --statistics-file-basename STATISTICS_FILE_BASENAME 191s File base name to save base by base statistics from 191s testing. Filenames will be [--statistics-file- 191s basename].[--alternate-bases]?.tombo.stats 191s --alternate-bases {5mC,6mA,dcm,CpG,dam} [{5mC,6mA,dcm,CpG,dam} ...] 191s Default non-standard base model for testing (not 191s required if user created --alternate-model-filenames 191s is provided). 191s 191s Comparison Arguments: 191s --print-available-models 191s Print available alternative models and exit. 191s --dna Explicitly select canonical DNA model. Default: 191s Automatically determine from FAST5s 191s --rna Explicitly select canonical RNA model. Default: 191s Automatically determine from FAST5s 191s 191s Significance Test Arguments: 191s --minimum-test-reads MINIMUM_TEST_READS 191s Number of reads required at a position to perform 191s significance testing or contribute to model 191s estimation. Default: 1 191s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 191s Log likelihood ratio threshold when computing fraction 191s of significant reads at each genomic position. If two 191s values are provided, statistics between these values 191s are not considered. Default thresholds: DNA:-1.5-2.5 , 191s RNA:-2.5-2.5 191s --standard-log-likelihood-ratio 191s Use a standard log likelihood ratio (LLR) statistic. 191s Default is to use an outlier-robust LLR-like 191s statistic. Detail in full online documentation. 191s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 191s Dampen fraction modified estimates for low coverage 191s sites. Two parameters are unmodified and modified 191s pseudo read counts. This is equivalent to a beta prior 191s on the fraction estimate. Set to "0 0" to disable 191s dampened fraction estimation. Default: [2, 0] 191s 191s Output Argument: 191s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 191s Base for binary files containing per-read statistics 191s from statistical testing. Filenames will be [--per- 191s read-statistics-basename].[--alternate- 191s bases]?.tombo.per_read_stats 191s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 191s Number of the most significant sites to store for 191s faster access. If a longer list of most significant 191s sites is required the list must be re-computed from 191s all batches. Very large values can increase RAM usage. 191s Default: 100000 191s 191s Multiprocessing Arguments: 191s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 191s Size of regions over which to multiprocesses statistic 191s computation. For very deep samples a smaller value is 191s recommmended in order to control memory consumption. 191s Default: 10000 191s --processes PROCESSES 191s Number of processes. Default: 1 191s 191s FAST5 Data Arguments: 191s --corrected-group CORRECTED_GROUP 191s FAST5 group created by resquiggle command. Default: 191s RawGenomeCorrected_000 191s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 191s FAST5 subgroup(s) (under /Analyses/[--basecall- 191s group]/) containing basecalls and created within 191s [--corrected-group] containing re-squiggle results. 191s Default: ['BaseCalled_template'] 191s 191s Miscellaneous Arguments: 191s --quiet, -q Don't print status information. 191s --help, -h Print this help message and exit 191s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 191s FAST5_BASEDIRS 191s [FAST5_BASEDIRS ...] 191s --statistics-file-basename 191s STATISTICS_FILE_BASENAME 191s --control-fast5-basedirs 191s CONTROL_FAST5_BASEDIRS 191s [CONTROL_FAST5_BASEDIRS ...] 191s [--sample-only-estimates] 191s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 191s [--dna] [--rna] 191s [--fishers-method-context FISHERS_METHOD_CONTEXT] 191s [--minimum-test-reads MINIMUM_TEST_READS] 191s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 191s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 191s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 191s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 191s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 191s [--processes PROCESSES] 191s [--corrected-group CORRECTED_GROUP] 191s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 191s [--quiet] [--help] 191s 191s Required Argument: 191s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 191s Directories containing fast5 files. 191s --statistics-file-basename STATISTICS_FILE_BASENAME 191s File base name to save base by base statistics from 191s testing. Filenames will be [--statistics-file- 191s basename].[--alternate-bases]?.tombo.stats 191s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 191s Set of directories containing fast5 files for control 191s reads, containing only canonical nucleotides. 191s 191s Model Prior Arguments: 191s --sample-only-estimates 191s Only use canonical sample to estimate expected signal 191s level and spread. Default: Use canonical model to 191s improve estimtates (esp. for low coverage regions) 191s using baysian posterior estimates. 191s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 191s Prior weights (one each for mean and spread) applied 191s to canonical base model for estimating posterior model 191s parameters for sample comparison. Default: [5, 40] 191s --dna Explicitly select canonical DNA model. Default: 191s Automatically determine from FAST5s 191s --rna Explicitly select canonical RNA model. Default: 191s Automatically determine from FAST5s 191s 191s Significance Test Arguments: 191s --fishers-method-context FISHERS_METHOD_CONTEXT 191s Number of context bases up and downstream over which 191s to compute Fisher's method combined p-values. Note: 191s Not applicable for alternative model likelihood ratio 191s tests. Default: 1. 191s --minimum-test-reads MINIMUM_TEST_READS 191s Number of reads required at a position to perform 191s significance testing or contribute to model 191s estimation. Default: 1 191s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 191s P-value threshold when computing fraction of 191s significant reads at each genomic position. If two 191s values are provided, statistics between these values 191s are not considered. Default thresholds: DNA:0.15-0.5 , 191s RNA:0.05-0.4 191s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 191s Dampen fraction modified estimates for low coverage 191s sites. Two parameters are unmodified and modified 191s pseudo read counts. This is equivalent to a beta prior 191s on the fraction estimate. Set to "0 0" to disable 191s dampened fraction estimation. Default: [2, 0] 191s 191s Output Argument: 191s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 191s Base for binary files containing per-read statistics 191s from statistical testing. Filenames will be [--per- 191s read-statistics-basename].[--alternate- 191s bases]?.tombo.per_read_stats 191s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 191s Number of the most significant sites to store for 191s faster access. If a longer list of most significant 191s sites is required the list must be re-computed from 191s all batches. Very large values can increase RAM usage. 191s Default: 100000 191s 191s Multiprocessing Arguments: 191s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 191s Size of regions over which to multiprocesses statistic 191s computation. For very deep samples a smaller value is 191s recommmended in order to control memory consumption. 191s Default: 10000 191s --processes PROCESSES 191s Number of processes. Default: 1 191s 191s FAST5 Data Arguments: 191s --corrected-group CORRECTED_GROUP 191s FAST5 group created by resquiggle command. Default: 191s RawGenomeCorrected_000 191s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 191s FAST5 subgroup(s) (under /Analyses/[--basecall- 191s group]/) containing basecalls and created within 191s [--corrected-group] containing re-squiggle results. 191s Default: ['BaseCalled_template'] 191s 191s Miscellaneous Arguments: 191s --quiet, -q Don't print status information. 191s --help, -h Print this help message and exit 192s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 192s FAST5_BASEDIRS 192s [FAST5_BASEDIRS ...] 192s --statistics-file-basename 192s STATISTICS_FILE_BASENAME 192s --alternate-fast5-basedirs 192s ALTERNATE_FAST5_BASEDIRS 192s [ALTERNATE_FAST5_BASEDIRS ...] 192s [--fishers-method-context FISHERS_METHOD_CONTEXT] 192s [--minimum-test-reads MINIMUM_TEST_READS] 192s [--statistic-type {ks,u,t}] 192s [--store-p-value] 192s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 192s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 192s [--processes PROCESSES] 192s [--corrected-group CORRECTED_GROUP] 192s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 192s [--quiet] [--help] 192s 192s Required Argument: 192s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 192s Directories containing fast5 files. 192s --statistics-file-basename STATISTICS_FILE_BASENAME 192s File base name to save base by base statistics from 192s testing. Filenames will be [--statistics-file- 192s basename].[--alternate-bases]?.tombo.stats 192s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 192s Set of directories containing fast5 files for 192s alternate set of reads. 192s 192s Significance Test Arguments: 192s --fishers-method-context FISHERS_METHOD_CONTEXT 192s Number of context bases up and downstream over which 192s to compute Fisher's method combined p-values. Note: 192s Not applicable for alternative model likelihood ratio 192s tests. Default: 1. 192s --minimum-test-reads MINIMUM_TEST_READS 192s Number of reads required at a position to perform 192s significance testing or contribute to model 192s estimation. Default: 50 192s --statistic-type {ks,u,t} 192s Type of statistical test to apply. Default: "ks" 192s --store-p-value Store p-value instead of effect-size statistic. 192s Statistics are D-statistic (KS-test), deviation from 192s even common language effect size (u-test), and Cohen's 192s D (t-test). 192s 192s Output Argument: 192s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 192s Number of the most significant sites to store for 192s faster access. If a longer list of most significant 192s sites is required the list must be re-computed from 192s all batches. Very large values can increase RAM usage. 192s Default: 100000 192s 192s Multiprocessing Arguments: 192s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 192s Size of regions over which to multiprocesses statistic 192s computation. For very deep samples a smaller value is 192s recommmended in order to control memory consumption. 192s Default: 10000 192s --processes PROCESSES 192s Number of processes. Default: 1 192s 192s FAST5 Data Arguments: 192s --corrected-group CORRECTED_GROUP 192s FAST5 group created by resquiggle command. Default: 192s RawGenomeCorrected_000 192s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 192s FAST5 subgroup(s) (under /Analyses/[--basecall- 192s group]/) containing basecalls and created within 192s [--corrected-group] containing re-squiggle results. 192s Default: ['BaseCalled_template'] 192s 192s Miscellaneous Arguments: 192s --quiet, -q Don't print status information. 192s --help, -h Print this help message and exit 192s usage: tombo detect_modifications aggregate_per_read_stats 192s --per-read-statistics-filename 192s PER_READ_STATISTICS_FILENAME 192s --statistics-filename 192s STATISTICS_FILENAME 192s --single-read-threshold 192s SINGLE_READ_THRESHOLD 192s [SINGLE_READ_THRESHOLD ...] 192s [--minimum-test-reads MINIMUM_TEST_READS] 192s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 192s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 192s [--processes PROCESSES] 192s [--corrected-group CORRECTED_GROUP] 192s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 192s [--quiet] [--help] 192s 192s Required Argument: 192s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 192s Binary file containing per-read statistics from 192s statistical testing. 192s --statistics-filename STATISTICS_FILENAME 192s File to save/load genomic base anchored statistics. 192s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 192s P-value or log likelihood ratio threshold when 192s computing fraction of significant reads at each 192s genomic position. If two values are provided, 192s statistics between these values are not considered. 192s 192s Significance Test Arguments: 192s --minimum-test-reads MINIMUM_TEST_READS 192s Number of reads required at a position to perform 192s significance testing or contribute to model 192s estimation. Default: 1 192s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 192s Dampen fraction modified estimates for low coverage 192s sites. Two parameters are unmodified and modified 192s pseudo read counts. This is equivalent to a beta prior 192s on the fraction estimate. Set to "0 0" to disable 192s dampened fraction estimation. Default: [2, 0] 192s 192s Output Argument: 192s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 192s Number of the most significant sites to store for 192s faster access. If a longer list of most significant 192s sites is required the list must be re-computed from 192s all batches. Very large values can increase RAM usage. 192s Default: 100000 192s 192s Multiprocessing Arguments: 192s --processes PROCESSES 192s Number of processes. Default: 1 192s 192s FAST5 Data Arguments: 192s --corrected-group CORRECTED_GROUP 192s FAST5 group created by resquiggle command. Default: 192s RawGenomeCorrected_000 192s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 192s FAST5 subgroup(s) (under /Analyses/[--basecall- 192s group]/) containing basecalls and created within 192s [--corrected-group] containing re-squiggle results. 192s Default: ['BaseCalled_template'] 192s 192s Miscellaneous Arguments: 192s --quiet, -q Don't print status information. 192s --help, -h Print this help message and exit 192s usage: tombo text_output browser_files 192s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 192s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 192s [--statistics-filename STATISTICS_FILENAME] 192s [--genome-fasta GENOME_FASTA] 192s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 192s [--browser-file-basename BROWSER_FILE_BASENAME] 192s [--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} ...]] 192s [--corrected-group CORRECTED_GROUP] 192s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 192s [--quiet] [--help] 192s 192s Data Arguments: 192s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 192s Directories containing fast5 files. 192s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 192s Set of directories containing fast5 files for control 192s reads, containing only canonical nucleotides. 192s --statistics-filename STATISTICS_FILENAME 192s File to save/load genomic base anchored statistics. 192s 192s Statistic Motif Filter Arguments: 192s --genome-fasta GENOME_FASTA 192s FASTA file used to re-squiggle. For faster sequence 192s access. 192s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 192s Ground truth, motif centered, modified base 192s descriptions for output filtering. Format descriptions 192s as: "motif:mod_pos:name". The mod_pos indicates the 192s modified base within the motif (1-based index). 192s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 192s output for identification of E. coli dam and dcm 192s methylation. 192s 192s Output Arguments: 192s --browser-file-basename BROWSER_FILE_BASENAME 192s Basename for output browser files. Two files (plus and 192s minus strand) will be produced for each --file-types 192s supplied. Filenames formatted as "[browser-file- 192s basename].[file- 192s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 192s Default: tombo_results 192s --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} ...] 192s Data types of genome browser files to produce. 192s Produced coverage files are in bedGraph format, while 192s all other file types will be in wiggle format 192s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 192s Default: "coverage" 192s 192s FAST5 Data Arguments: 192s --corrected-group CORRECTED_GROUP 192s FAST5 group created by resquiggle command. Default: 192s RawGenomeCorrected_000 192s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 192s FAST5 subgroup(s) (under /Analyses/[--basecall- 192s group]/) containing basecalls and created within 192s [--corrected-group] containing re-squiggle results. 192s Default: ['BaseCalled_template'] 192s 192s Miscellaneous Arguments: 192s --quiet, -q Don't print status information. 192s --help, -h Print this help message and exit 192s usage: tombo text_output signif_sequence_context --statistics-filename 192s STATISTICS_FILENAME 192s [--genome-fasta GENOME_FASTA] 192s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 192s [--num-regions NUM_REGIONS] 192s [--num-bases NUM_BASES] 192s [--sequences-filename SEQUENCES_FILENAME] 192s [--corrected-group CORRECTED_GROUP] 192s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 192s [--quiet] [--help] 192s 192s Required Argument: 192s --statistics-filename STATISTICS_FILENAME 192s File to save/load genomic base anchored statistics. 192s 192s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 192s --genome-fasta GENOME_FASTA 192s FASTA file used to re-squiggle. For faster sequence 192s access. 192s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 192s Directories containing fast5 files. 192s 192s Region Selection Arguments: 192s --num-regions NUM_REGIONS 192s Number of regions to plot. Default: 100 192s --num-bases NUM_BASES 192s Number of bases to plot/output. Default: 15 192s 192s Output Arguments: 192s --sequences-filename SEQUENCES_FILENAME 192s File for sequences from selected regions. Sequences 192s will be stored in FASTA format. Default: 192s tombo_results.significant_regions.fasta. 192s 192s FAST5 Data Arguments: 192s --corrected-group CORRECTED_GROUP 192s FAST5 group created by resquiggle command. Default: 192s RawGenomeCorrected_000 192s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 192s FAST5 subgroup(s) (under /Analyses/[--basecall- 192s group]/) containing basecalls and created within 192s [--corrected-group] containing re-squiggle results. 192s Default: ['BaseCalled_template'] 192s 192s Miscellaneous Arguments: 192s --quiet, -q Don't print status information. 192s --help, -h Print this help message and exit 192s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 192s [FAST5_BASEDIRS ...] 192s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 192s [--plot-standard-model] 192s [--plot-alternate-model {CpG,dam,5mC,6mA,dcm}] 192s [--overplot-threshold OVERPLOT_THRESHOLD] 192s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 192s [--num-regions NUM_REGIONS] 192s [--num-bases NUM_BASES] 192s [--pdf-filename PDF_FILENAME] 192s [--corrected-group CORRECTED_GROUP] 192s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 192s [--quiet] [--help] 192s 192s Required Argument: 192s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 192s Directories containing fast5 files. 192s 192s Comparison Arguments: 192s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 192s Set of directories containing fast5 files for control 192s reads, containing only canonical nucleotides. 192s --plot-standard-model 192s Add default standard model distribution to the plot. 192s --plot-alternate-model {CpG,dam,5mC,6mA,dcm} 192s Add alternative model distribution to the plot. 192s 192s Overplotting Arguments: 192s --overplot-threshold OVERPLOT_THRESHOLD 192s Coverage level to trigger alternative plot type 192s instead of raw signal. Default: 50 192s --overplot-type {Downsample,Boxplot,Quantile,Density} 192s Plot type for regions with higher coverage. Default: 192s Downsample 192s 192s Plotting Region Arguments: 192s --num-regions NUM_REGIONS 192s Number of regions to plot. Default: 10 192s --num-bases NUM_BASES 192s Number of bases to plot/output. Default: 21 192s 192s Output Argument: 192s --pdf-filename PDF_FILENAME 192s PDF filename to store plot(s). Default: 192s tombo_results.max_coverage.pdf 192s 192s FAST5 Data Arguments: 192s --corrected-group CORRECTED_GROUP 192s FAST5 group created by resquiggle command. Default: 192s RawGenomeCorrected_000 192s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 192s FAST5 subgroup(s) (under /Analyses/[--basecall- 192s group]/) containing basecalls and created within 192s [--corrected-group] containing re-squiggle results. 192s Default: ['BaseCalled_template'] 192s 192s Miscellaneous Arguments: 192s --quiet, -q Don't print status information. 192s --help, -h Print this help message and exit 192s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 192s [FAST5_BASEDIRS ...] --genome-locations 192s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 192s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 192s [--plot-standard-model] 192s [--plot-alternate-model {dcm,5mC,CpG,dam,6mA}] 192s [--overplot-threshold OVERPLOT_THRESHOLD] 192s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 192s [--num-bases NUM_BASES] 192s [--pdf-filename PDF_FILENAME] 192s [--corrected-group CORRECTED_GROUP] 192s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 192s [--quiet] [--help] 192s 192s Required Arguments: 192s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 192s Directories containing fast5 files. 192s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 192s Genomic locations at which to plot signal. Format 192s locations as "chrm:position[:strand] 192s [chrm2:position2[:strand2] ...]" (strand not 192s applicable for all applications) 192s 192s Comparison Arguments: 192s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 192s Set of directories containing fast5 files for control 192s reads, containing only canonical nucleotides. 192s --plot-standard-model 192s Add default standard model distribution to the plot. 192s --plot-alternate-model {dcm,5mC,CpG,dam,6mA} 192s Add alternative model distribution to the plot. 192s 192s Overplotting Arguments: 192s --overplot-threshold OVERPLOT_THRESHOLD 192s Coverage level to trigger alternative plot type 192s instead of raw signal. Default: 50 192s --overplot-type {Downsample,Boxplot,Quantile,Density} 192s Plot type for regions with higher coverage. Default: 192s Downsample 192s 192s Plotting Region Argument: 192s --num-bases NUM_BASES 192s Number of bases to plot/output. Default: 21 192s 192s Output Argument: 192s --pdf-filename PDF_FILENAME 192s PDF filename to store plot(s). Default: 192s tombo_results.genome_locations.pdf 192s 192s FAST5 Data Arguments: 192s --corrected-group CORRECTED_GROUP 192s FAST5 group created by resquiggle command. Default: 192s RawGenomeCorrected_000 192s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 192s FAST5 subgroup(s) (under /Analyses/[--basecall- 192s group]/) containing basecalls and created within 192s [--corrected-group] containing re-squiggle results. 192s Default: ['BaseCalled_template'] 192s 192s Miscellaneous Arguments: 192s --quiet, -q Don't print status information. 192s --help, -h Print this help message and exit 192s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 192s [FAST5_BASEDIRS ...] --motif MOTIF 192s --genome-fasta GENOME_FASTA 192s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 192s [--plot-standard-model] 192s [--plot-alternate-model {dcm,6mA,5mC,CpG,dam}] 192s [--overplot-threshold OVERPLOT_THRESHOLD] 192s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 192s [--num-regions NUM_REGIONS] 192s [--num-bases NUM_BASES] [--deepest-coverage] 192s [--pdf-filename PDF_FILENAME] 192s [--corrected-group CORRECTED_GROUP] 192s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 192s [--quiet] [--help] 192s 192s Required Arguments: 192s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 192s Directories containing fast5 files. 192s --motif MOTIF Motif of interest at which to plot signal and 192s statsitics. Supports IUPAC single letter codes (use T 192s for RNA). 192s --genome-fasta GENOME_FASTA 192s FASTA file used to re-squiggle. For faster sequence 192s access. 192s 192s Comparison Arguments: 192s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 192s Set of directories containing fast5 files for control 192s reads, containing only canonical nucleotides. 192s --plot-standard-model 192s Add default standard model distribution to the plot. 192s --plot-alternate-model {dcm,6mA,5mC,CpG,dam} 192s Add alternative model distribution to the plot. 192s 192s Overplotting Arguments: 192s --overplot-threshold OVERPLOT_THRESHOLD 192s Coverage level to trigger alternative plot type 192s instead of raw signal. Default: 50 192s --overplot-type {Downsample,Boxplot,Quantile,Density} 192s Plot type for regions with higher coverage. Default: 192s Downsample 192s 192s Plotting Region Arguments: 192s --num-regions NUM_REGIONS 192s Number of regions to plot. Default: 10 192s --num-bases NUM_BASES 192s Number of bases to plot/output. Default: 21 192s --deepest-coverage Plot the deepest coverage regions. 192s 192s Output Argument: 192s --pdf-filename PDF_FILENAME 192s PDF filename to store plot(s). Default: 192s tombo_results.motif_centered.pdf 192s 192s FAST5 Data Arguments: 192s --corrected-group CORRECTED_GROUP 192s FAST5 group created by resquiggle command. Default: 192s RawGenomeCorrected_000 192s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 192s FAST5 subgroup(s) (under /Analyses/[--basecall- 192s group]/) containing basecalls and created within 192s [--corrected-group] containing re-squiggle results. 192s Default: ['BaseCalled_template'] 192s 192s Miscellaneous Arguments: 192s --quiet, -q Don't print status information. 192s --help, -h Print this help message and exit 192s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 192s [FAST5_BASEDIRS ...] --control-fast5-basedirs 192s CONTROL_FAST5_BASEDIRS 192s [CONTROL_FAST5_BASEDIRS ...] 192s [--overplot-threshold OVERPLOT_THRESHOLD] 192s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 192s [--num-regions NUM_REGIONS] 192s [--num-bases NUM_BASES] 192s [--pdf-filename PDF_FILENAME] 192s [--sequences-filename SEQUENCES_FILENAME] 192s [--corrected-group CORRECTED_GROUP] 192s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 192s [--quiet] [--help] 192s 192s Required Arguments: 192s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 192s Directories containing fast5 files. 192s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 192s Set of directories containing fast5 files for control 192s reads, containing only canonical nucleotides. 192s 192s Overplotting Arguments: 192s --overplot-threshold OVERPLOT_THRESHOLD 192s Coverage level to trigger alternative plot type 192s instead of raw signal. Default: 50 192s --overplot-type {Downsample,Boxplot,Quantile,Density} 192s Plot type for regions with higher coverage. Default: 192s Downsample 192s 192s Plotting Region Arguments: 192s --num-regions NUM_REGIONS 192s Number of regions to plot. Default: 10 192s --num-bases NUM_BASES 192s Number of bases to plot/output. Default: 21 192s 192s Output Arguments: 192s --pdf-filename PDF_FILENAME 192s PDF filename to store plot(s). Default: 192s tombo_results.max_difference.pdf 192s --sequences-filename SEQUENCES_FILENAME 192s File for sequences from selected regions. Sequences 192s will be stored in FASTA format. Default: None. 192s 192s FAST5 Data Arguments: 192s --corrected-group CORRECTED_GROUP 192s FAST5 group created by resquiggle command. Default: 192s RawGenomeCorrected_000 192s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 192s FAST5 subgroup(s) (under /Analyses/[--basecall- 192s group]/) containing basecalls and created within 192s [--corrected-group] containing re-squiggle results. 192s Default: ['BaseCalled_template'] 192s 192s Miscellaneous Arguments: 192s --quiet, -q Don't print status information. 192s --help, -h Print this help message and exit 192s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 192s [FAST5_BASEDIRS ...] --statistics-filename 192s STATISTICS_FILENAME 192s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 192s [--plot-standard-model] 192s [--plot-alternate-model {dam,5mC,dcm,6mA,CpG}] 192s [--overplot-threshold OVERPLOT_THRESHOLD] 192s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 192s [--num-regions NUM_REGIONS] 192s [--num-bases NUM_BASES] 192s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 192s [--pdf-filename PDF_FILENAME] 192s [--sequences-filename SEQUENCES_FILENAME] 192s [--corrected-group CORRECTED_GROUP] 192s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 192s [--quiet] [--help] 192s 192s Required Arguments: 192s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 192s Directories containing fast5 files. 192s --statistics-filename STATISTICS_FILENAME 192s File to save/load genomic base anchored statistics. 192s 192s Comparison Arguments: 192s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 192s Set of directories containing fast5 files for control 192s reads, containing only canonical nucleotides. 192s --plot-standard-model 192s Add default standard model distribution to the plot. 192s --plot-alternate-model {dam,5mC,dcm,6mA,CpG} 192s Add alternative model distribution to the plot. 192s 192s Overplotting Arguments: 192s --overplot-threshold OVERPLOT_THRESHOLD 192s Coverage level to trigger alternative plot type 192s instead of raw signal. Default: 50 192s --overplot-type {Downsample,Boxplot,Quantile,Density} 192s Plot type for regions with higher coverage. Default: 192s Downsample 192s 192s Plotting Region Arguments: 192s --num-regions NUM_REGIONS 192s Number of regions to plot. Default: 10 192s --num-bases NUM_BASES 192s Number of bases to plot/output. Default: 21 192s 192s Statistical Argument: 192s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 192s Dampen fraction modified estimates for low coverage 192s sites. Two parameters are unmodified and modified 192s pseudo read counts. This is equivalent to a beta prior 192s on the fraction estimate. Set to "0 0" to disable 192s dampened fraction estimation. Default: [2, 0] 192s 192s Output Arguments: 192s --pdf-filename PDF_FILENAME 192s PDF filename to store plot(s). Default: 192s tombo_results.significant_difference.pdf 192s --sequences-filename SEQUENCES_FILENAME 192s File for sequences from selected regions. Sequences 192s will be stored in FASTA format. Default: None. 192s 192s FAST5 Data Arguments: 192s --corrected-group CORRECTED_GROUP 192s FAST5 group created by resquiggle command. Default: 192s RawGenomeCorrected_000 192s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 192s FAST5 subgroup(s) (under /Analyses/[--basecall- 192s group]/) containing basecalls and created within 192s [--corrected-group] containing re-squiggle results. 192s Default: ['BaseCalled_template'] 192s 192s Miscellaneous Arguments: 192s --quiet, -q Don't print status information. 192s --help, -h Print this help message and exit 192s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 192s [FAST5_BASEDIRS ...] --motif MOTIF 192s --statistics-filename STATISTICS_FILENAME 192s --genome-fasta GENOME_FASTA 192s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 192s [--plot-standard-model] 192s [--plot-alternate-model {5mC,dam,6mA,dcm,CpG}] 192s [--overplot-threshold OVERPLOT_THRESHOLD] 192s [--num-regions NUM_REGIONS] 192s [--num-context NUM_CONTEXT] 192s [--num-statistics NUM_STATISTICS] 192s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 192s [--pdf-filename PDF_FILENAME] 192s [--corrected-group CORRECTED_GROUP] 192s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 192s [--quiet] [--help] 192s 192s Required Arguments: 192s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 192s Directories containing fast5 files. 192s --motif MOTIF Motif of interest at which to plot signal and 192s statsitics. Supports IUPAC single letter codes (use T 192s for RNA). 192s --statistics-filename STATISTICS_FILENAME 192s File to save/load genomic base anchored statistics. 192s --genome-fasta GENOME_FASTA 192s FASTA file used to re-squiggle. For faster sequence 192s access. 192s 192s Comparison Arguments: 192s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 192s Set of directories containing fast5 files for control 192s reads, containing only canonical nucleotides. 192s --plot-standard-model 192s Add default standard model distribution to the plot. 192s --plot-alternate-model {5mC,dam,6mA,dcm,CpG} 192s Add alternative model distribution to the plot. 192s 192s Overplotting Argument: 192s --overplot-threshold OVERPLOT_THRESHOLD 192s Coverage level to trigger alternative plot type 192s instead of raw signal. Default: 50 192s 192s Plotting Region Arguments: 192s --num-regions NUM_REGIONS 192s Number of regions to plot. Default: 3 192s --num-context NUM_CONTEXT 192s Number of context bases around motif. Default: 5 192s --num-statistics NUM_STATISTICS 192s Number of motif centered regions to include in 192s statistic distributions. Default: 200 192s 192s Statistical Argument: 192s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 192s Dampen fraction modified estimates for low coverage 192s sites. Two parameters are unmodified and modified 192s pseudo read counts. This is equivalent to a beta prior 192s on the fraction estimate. Set to "0 0" to disable 192s dampened fraction estimation. Default: [2, 0] 192s 192s Output Argument: 192s --pdf-filename PDF_FILENAME 192s PDF filename to store plot(s). Default: 192s tombo_results.motif_statistics.pdf 192s 192s FAST5 Data Arguments: 192s --corrected-group CORRECTED_GROUP 192s FAST5 group created by resquiggle command. Default: 192s RawGenomeCorrected_000 192s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 192s FAST5 subgroup(s) (under /Analyses/[--basecall- 192s group]/) containing basecalls and created within 192s [--corrected-group] containing re-squiggle results. 192s Default: ['BaseCalled_template'] 192s 192s Miscellaneous Arguments: 192s --quiet, -q Don't print status information. 192s --help, -h Print this help message and exit 192s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 192s [GENOME_LOCATIONS ...] 192s --per-read-statistics-filename 192s PER_READ_STATISTICS_FILENAME 192s [--genome-fasta GENOME_FASTA] 192s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 192s [--num-reads NUM_READS] [--num-bases NUM_BASES] 192s [--box-center] [--pdf-filename PDF_FILENAME] 192s [--corrected-group CORRECTED_GROUP] 192s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 192s [--quiet] [--help] 192s 192s Required Arguments: 192s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 192s Genomic locations at which to plot signal. Format 192s locations as "chrm:position[:strand] 192s [chrm2:position2[:strand2] ...]" (strand not 192s applicable for all applications) 192s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 192s Binary file containing per-read statistics from 192s statistical testing. 192s 192s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 192s --genome-fasta GENOME_FASTA 192s FASTA file used to re-squiggle. For faster sequence 192s access. 192s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 192s Directories containing fast5 files. 192s 192s Plotting Region Arguments: 192s --num-reads NUM_READS 192s Number of reads to plot. Default: 100 192s --num-bases NUM_BASES 192s Number of bases to plot/output. Default: 51 192s --box-center Plot a box around the central base. 192s 192s Output Argument: 192s --pdf-filename PDF_FILENAME 192s PDF filename to store plot(s). Default: 192s tombo_results.per_read_stats.pdf 192s 192s FAST5 Data Arguments: 192s --corrected-group CORRECTED_GROUP 192s FAST5 group created by resquiggle command. Default: 192s RawGenomeCorrected_000 192s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 192s FAST5 subgroup(s) (under /Analyses/[--basecall- 192s group]/) containing basecalls and created within 192s [--corrected-group] containing re-squiggle results. 192s Default: ['BaseCalled_template'] 192s 192s Miscellaneous Arguments: 192s --quiet, -q Don't print status information. 192s --help, -h Print this help message and exit 192s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 192s [STATISTICS_FILENAMES ...] 192s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 192s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 192s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 192s [--genome-fasta GENOME_FASTA] 192s [--pdf-filename PDF_FILENAME] 192s [--statistics-per-block STATISTICS_PER_BLOCK] 192s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 192s [--quiet] [--help] 192s 192s Required Argument: 192s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 192s Files to load genomic base anchored statistics. 192s 192s Ground Truth Arguments (provide bed files or motifs): 192s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 192s Modification description and bed format files 192s containing single base locations of ground truth 192s modified sites. Bed files should contain 6 fields 192s including strand. Format descriptions as 192s "mod_name:locs.bed". Example: "CpG 192s bisulfite":bisulfite_locs.bed 192s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 192s Bed format files containing single base locations of 192s ground truth unmodified sites. Bed files should 192s contain 6 fields including strand. 192s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 192s Ground truth, motif centered, modified base 192s descriptions for computing ROC and PR curves. Each 192s statistics file is associated with a set of motif 192s descriptions. Format descriptions as: 192s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 192s mod_pos indicates the alternate-base within the motif 192s (1-based index). Example: CCWGG:2:"dcm 192s 5mC"::GATC:2:"dam 6mA" would assess the performance of 192s a single Tombo statistics file for identification of 192s E. coli dam and dcm methylation. 192s --genome-fasta GENOME_FASTA 192s FASTA file used to re-squiggle. For faster sequence 192s access. 192s 192s Output Arguments: 192s --pdf-filename PDF_FILENAME 192s PDF filename to store plot(s). Default: 192s tombo_results.roc.pdf 192s 192s Down-sampling Arguments: 192s --statistics-per-block STATISTICS_PER_BLOCK 192s Number of randomly selected per-read, per-base 192s statistics to extract from each genomic block for 192s plotting. Default: Include all stats 192s --total-statistics-limit TOTAL_STATISTICS_LIMIT 192s Total per-read statistics to be extracted for 192s plotting. Avoids memory overflow for large runs. 192s Default: 5000000 192s 192s Miscellaneous Arguments: 192s --quiet, -q Don't print status information. 192s --help, -h Print this help message and exit 192s usage: tombo plot per_read_roc --per-read-statistics-filenames 192s PER_READ_STATISTICS_FILENAMES 192s [PER_READ_STATISTICS_FILENAMES ...] 192s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 192s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 192s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 192s [--genome-fasta GENOME_FASTA] 192s [--statistics-per-block STATISTICS_PER_BLOCK] 192s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 192s [--pdf-filename PDF_FILENAME] [--quiet] 192s [--help] 192s 192s Required Argument: 192s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 192s Binary files containing per-read statistics from 192s statistical testing. 192s 192s Ground Truth Arguments (provide bed files or motifs): 192s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 192s Modification description and bed format files 192s containing single base locations of ground truth 192s modified sites. Bed files should contain 6 fields 192s including strand. Format descriptions as 192s "mod_name:locs.bed". Example: "CpG 192s bisulfite":bisulfite_locs.bed 192s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 192s Bed format files containing single base locations of 192s ground truth unmodified sites. Bed files should 192s contain 6 fields including strand. 192s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 192s Ground truth, motif centered, modified base 192s descriptions for computing ROC and PR curves. Each 192s statistics file is associated with a set of motif 192s descriptions. Format descriptions as: 192s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 192s mod_pos indicates the alternate-base within the motif 192s (1-based index). Example: CCWGG:2:"dcm 192s 5mC"::GATC:2:"dam 6mA" would assess the performance of 192s a single Tombo statistics file for identification of 192s E. coli dam and dcm methylation. 192s --genome-fasta GENOME_FASTA 192s FASTA file used to re-squiggle. For faster sequence 192s access. 192s 192s Down-sampling Arguments: 192s --statistics-per-block STATISTICS_PER_BLOCK 192s Number of randomly selected per-read, per-base 192s statistics to extract from each genomic block for 192s plotting. Default: 100000 192s --total-statistics-limit TOTAL_STATISTICS_LIMIT 192s Total per-read statistics to be extracted for 192s plotting. Avoids memory overflow for large runs. 192s Default: 5000000 192s 192s Output Arguments: 192s --pdf-filename PDF_FILENAME 192s PDF filename to store plot(s). Default: 192s tombo_results.per_reads_roc.pdf 192s 192s Miscellaneous Arguments: 192s --quiet, -q Don't print status information. 192s --help, -h Print this help message and exit 193s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 193s [--upstream-bases {0,1,2,3,4}] 193s [--downstream-bases {0,1,2,3,4}] [--read-mean] 193s [--num-kmer-threshold NUM_KMER_THRESHOLD] 193s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 193s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 193s [--corrected-group CORRECTED_GROUP] 193s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 193s [--quiet] [--help] 193s 193s Required Argument: 193s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 193s Directories containing fast5 files. 193s 193s Data Processing Arguments: 193s --upstream-bases {0,1,2,3,4} 193s Upstream bases in k-mer. Default: 1 193s --downstream-bases {0,1,2,3,4} 193s Downstream bases in k-mer. Default: 2 193s --read-mean Plot k-mer means across whole reads as opposed to 193s individual k-mer event levels. 193s --num-kmer-threshold NUM_KMER_THRESHOLD 193s Observations of each k-mer required to include a read 193s in read level averages. Default: 1 193s 193s Plotting Region Arguments: 193s --num-reads NUM_READS 193s Number of reads to plot. Default: 100 193s 193s Output Arguments: 193s --pdf-filename PDF_FILENAME 193s PDF filename to store plot(s). Default: 193s tombo_results.kmer_distribution.pdf 193s --r-data-filename R_DATA_FILENAME 193s Filename to save R data structure. Default: Don't save 193s --dont-plot Don't plot result. Useful to produce only R data file. 193s 193s FAST5 Data Arguments: 193s --corrected-group CORRECTED_GROUP 193s FAST5 group created by resquiggle command. Default: 193s RawGenomeCorrected_000 193s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 193s FAST5 subgroup(s) (under /Analyses/[--basecall- 193s group]/) containing basecalls and created within 193s [--corrected-group] containing re-squiggle results. 193s Default: ['BaseCalled_template'] 193s 193s Miscellaneous Arguments: 193s --quiet, -q Don't print status information. 193s --help, -h Print this help message and exit 193s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 193s [FAST5_BASEDIRS ...] 193s --control-fast5-basedirs 193s CONTROL_FAST5_BASEDIRS 193s [CONTROL_FAST5_BASEDIRS ...] 193s --statistics-filename 193s STATISTICS_FILENAME 193s [--genome-fasta GENOME_FASTA] 193s [--processes PROCESSES] 193s [--num-regions NUM_REGIONS] 193s [--num-bases NUM_BASES] 193s [--slide-span SLIDE_SPAN] 193s [--pdf-filename PDF_FILENAME] 193s [--r-data-filename R_DATA_FILENAME] 193s [--corrected-group CORRECTED_GROUP] 193s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 193s [--quiet] [--help] 193s 193s Required Arguments: 193s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 193s Directories containing fast5 files. 193s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 193s Set of directories containing fast5 files for control 193s reads, containing only canonical nucleotides. 193s --statistics-filename STATISTICS_FILENAME 193s File to save/load genomic base anchored statistics. 193s 193s FASTA Sequence Argument: 193s --genome-fasta GENOME_FASTA 193s FASTA file used to re-squiggle. For faster sequence 193s access. 193s 193s Multiprocessing Argument: 193s --processes PROCESSES 193s Number of processes. Default: 1 193s 193s Plotting Region Arguments: 193s --num-regions NUM_REGIONS 193s Number of regions to plot. Default: 10 193s --num-bases NUM_BASES 193s Number of bases to plot/output. Default: 21 193s --slide-span SLIDE_SPAN 193s Number of bases offset over which to search when 193s computing distances for signal cluster plotting. 193s Default: 0 (exact position) 193s 193s Output Arguments: 193s --pdf-filename PDF_FILENAME 193s PDF filename to store plot(s). Default: 193s tombo_results.signal_clusters.pdf 193s --r-data-filename R_DATA_FILENAME 193s Filename to save R data structure. Default: Don't save 193s 193s FAST5 Data Arguments: 193s --corrected-group CORRECTED_GROUP 193s FAST5 group created by resquiggle command. Default: 193s RawGenomeCorrected_000 193s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 193s FAST5 subgroup(s) (under /Analyses/[--basecall- 193s group]/) containing basecalls and created within 193s [--corrected-group] containing re-squiggle results. 193s Default: ['BaseCalled_template'] 193s 193s Miscellaneous Arguments: 193s --quiet, -q Don't print status information. 193s --help, -h Print this help message and exit 193s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 193s 193s Required Arguments: 193s fast5s_basedir Directory containing fast5 files. All files ending in 193s "fast5" found recursively within this base directory will be 193s processed. 193s 193s Miscellaneous Arguments: 193s --quiet, -q Don't print status information. 193s --help, -h Print this help message and exit 193s usage: tombo build_model event_resquiggle 193s [--minimap2-executable MINIMAP2_EXECUTABLE] 193s [--minimap2-index MINIMAP2_INDEX] 193s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 193s [--graphmap-executable GRAPHMAP_EXECUTABLE] 193s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 193s [--normalization-type {median,pA,pA_raw,none}] 193s [--pore-model-filename PORE_MODEL_FILENAME] 193s [--outlier-threshold OUTLIER_THRESHOLD] 193s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 193s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 193s [--timeout TIMEOUT] 193s [--cpts-limit CPTS_LIMIT] 193s [--skip-index] [--overwrite] 193s [--failed-reads-filename FAILED_READS_FILENAME] 193s [--include-event-stdev] 193s [--corrected-group CORRECTED_GROUP] 193s [--basecall-group BASECALL_GROUP] 193s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 193s [--processes PROCESSES] 193s [--align-processes ALIGN_PROCESSES] 193s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 193s [--resquiggle-processes RESQUIGGLE_PROCESSES] 193s [--quiet] [--help] 193s fast5s_basedir reference_fasta 193s 193s Required Arguments: 193s fast5s_basedir Directory containing fast5 files. All files ending in 193s "fast5" found recursively within this base directory 193s will be processed. 193s reference_fasta Reference genome/transcriptome FASTA file for mapping. 193s 193s Mapper Arguments (One mapper is required): 193s --minimap2-executable MINIMAP2_EXECUTABLE 193s Path to minimap2 executable. 193s --minimap2-index MINIMAP2_INDEX 193s Path to minimap2 index (with map-ont preset) file 193s corresponding to the [genome_fasta] provided. 193s --bwa-mem-executable BWA_MEM_EXECUTABLE 193s Path to bwa-mem executable. 193s --graphmap-executable GRAPHMAP_EXECUTABLE 193s Path to graphmap executable. 193s --alignment-batch-size ALIGNMENT_BATCH_SIZE 193s Number of reads included in each alignment call. Note: 193s A new system mapping call is made for each batch 193s (including loading of the genome), so it is advised to 193s use larger values for larger genomes. Default: 1000 193s 193s Signal Processing Arguments: 193s --normalization-type {median,pA,pA_raw,none} 193s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 193s as in the ONT events (using offset, range and 193s digitization), "pA": k-mer-based correction for pA 193s drift as in nanopolish (requires [--pore-model- 193s filename]), "median": median and MAD from raw signal. 193s Default: median 193s --pore-model-filename PORE_MODEL_FILENAME 193s File containing kmer model parameters (level_mean and 193s level_stdv) used in order to compute kmer-based 193s corrected pA values. E.g. https://github.com/jts/nanop 193s olish/blob/master/etc/r9- 193s models/template_median68pA.5mers.model 193s --outlier-threshold OUTLIER_THRESHOLD 193s Windosrize the signal at this number of scale values. 193s Negative value disables outlier clipping. Default: 193s 5.000000 193s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 193s Specify the 2 parameters for segmentation 1) running 193s neighboring windows width 2) minimum raw observations 193s per genomic base. Sample type defaults: RNA : 12 6 || 193s DNA : 5 3 193s 193s Read Filtering Arguments: 193s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 193s Filter reads based on observations per base percentile 193s thresholds. Format thresholds as "percentile:thresh 193s [pctl2:thresh2 ...]". For example to filter reads with 193s 99th pctl > 200 obs/base or max > 5k obs/base use 193s "99:200 100:5000". 193s --timeout TIMEOUT Timeout in seconds for processing a single read. 193s Default: No timeout. 193s --cpts-limit CPTS_LIMIT 193s Maximum number of changepoints to find within a single 193s indel group. Default: No limit. 193s 193s Input/Output Arguments: 193s --skip-index Skip creation of tombo index. This drastically slows 193s downstream tombo commands. Default stores tombo index 193s named ".[--fast5-basedir].[--corrected- 193s group].tombo.index" to be loaded automatically for 193s downstream commands. 193s --overwrite Overwrite previous corrected group in FAST5 files. 193s Note: only effects --corrected-group or --new- 193s corrected-group. 193s --failed-reads-filename FAILED_READS_FILENAME 193s Output failed read filenames with assoicated error. 193s Default: Do not store failed reads. 193s --include-event-stdev 193s Include corrected event standard deviation in output 193s FAST5 data. 193s 193s FAST5 Data Arguments: 193s --corrected-group CORRECTED_GROUP 193s FAST5 group created by resquiggle command. Default: 193s RawGenomeCorrected_000 193s --basecall-group BASECALL_GROUP 193s FAST5 group obtain original basecalls (under Analyses 193s group). Default: Basecall_1D_000 193s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 193s FAST5 subgroup(s) (under /Analyses/[--basecall- 193s group]/) containing basecalls and created within 193s [--corrected-group] containing re-squiggle results. 193s Default: ['BaseCalled_template'] 193s 193s Multiprocessing Arguments: 193s --processes PROCESSES 193s Number of processes. Default: 2 193s --align-processes ALIGN_PROCESSES 193s Number of processes to use for parsing and aligning 193s original basecalls. Each process will independently 193s load the genome into memory, so use caution with 193s larger genomes (e.g. human). Default: 1 193s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 193s Number of threads to use for aligner system call. 193s Default: [--processes] / (2 * [--align-processes)] 193s --resquiggle-processes RESQUIGGLE_PROCESSES 193s Number of processes to use for resquiggle algorithm. 193s Default: [--processes] / 2 193s 193s Miscellaneous Arguments: 193s --quiet, -q Don't print status information. 193s --help, -h Print this help message and exit 193s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 193s [FAST5_BASEDIRS ...] 193s --tombo-model-filename 193s TOMBO_MODEL_FILENAME 193s [--estimate-mean] 193s [--kmer-specific-sd] 193s [--upstream-bases {0,1,2,3,4}] 193s [--downstream-bases {0,1,2,3,4}] 193s [--minimum-test-reads MINIMUM_TEST_READS] 193s [--coverage-threshold COVERAGE_THRESHOLD] 193s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 193s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 193s [--processes PROCESSES] 193s [--corrected-group CORRECTED_GROUP] 193s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 193s [--quiet] [--help] 193s 193s Required Arguments: 193s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 193s Directories containing fast5 files. 193s --tombo-model-filename TOMBO_MODEL_FILENAME 193s Filename to save Tombo model. 193s 193s Modeling Arguments: 193s --estimate-mean Use the mean instead of median for model level 193s estimation. Note: This can cause poor fits due to 193s outliers 193s --kmer-specific-sd Estimate standard deviation for each k-mers 193s individually. 193s --upstream-bases {0,1,2,3,4} 193s Upstream bases in k-mer. Default: 1 193s --downstream-bases {0,1,2,3,4} 193s Downstream bases in k-mer. Default: 2 193s 193s Filtering Arguments: 193s --minimum-test-reads MINIMUM_TEST_READS 193s Number of reads required at a position to perform 193s significance testing or contribute to model 193s estimation. Default: 10 193s --coverage-threshold COVERAGE_THRESHOLD 193s Maximum mean coverage per region when estimating k-mer 193s model (limits compute time for deep samples). Default: 193s 100 193s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 193s Number of each k-mer observations required in order to 193s produce a reference (genomic locations for standard 193s reference and per-read for alternative reference). 193s Default: 5 193s 193s Multiprocessing Arguments: 193s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 193s Size of regions over which to multiprocesses statistic 193s computation. For very deep samples a smaller value is 193s recommmended in order to control memory consumption. 193s Default: 10000 193s --processes PROCESSES 193s Number of processes. Default: 1 193s 193s FAST5 Data Arguments: 193s --corrected-group CORRECTED_GROUP 193s FAST5 group created by resquiggle command. Default: 193s RawGenomeCorrected_000 193s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 193s FAST5 subgroup(s) (under /Analyses/[--basecall- 193s group]/) containing basecalls and created within 193s [--corrected-group] containing re-squiggle results. 193s Default: ['BaseCalled_template'] 193s 193s Miscellaneous Arguments: 193s --quiet, -q Don't print status information. 193s --help, -h Print this help message and exit 193s usage: tombo build_model estimate_alt_reference --alternate-model-filename 193s ALTERNATE_MODEL_FILENAME 193s --alternate-model-name 193s ALTERNATE_MODEL_NAME 193s --alternate-model-base 193s {A,C,G,T} 193s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 193s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 193s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 193s [--control-density-filename CONTROL_DENSITY_FILENAME] 193s [--dna] [--rna] 193s [--tombo-model-filename TOMBO_MODEL_FILENAME] 193s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 193s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 193s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 193s [--save-density-basename SAVE_DENSITY_BASENAME] 193s [--processes PROCESSES] 193s [--corrected-group CORRECTED_GROUP] 193s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 193s [--quiet] [--help] 193s 193s Required Arguments: 193s --alternate-model-filename ALTERNATE_MODEL_FILENAME 193s Tombo model for alternative likelihood ratio 193s significance testing. 193s --alternate-model-name ALTERNATE_MODEL_NAME 193s A short name to associate with this alternate model 193s (e.g. 5mC, 6mA, etc.). This text will be included in 193s output filenames when this model is used for testing. 193s --alternate-model-base {A,C,G,T} 193s Non-standard base is an alternative to this base. 193s 193s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 193s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 193s Directories containing fast5 files. 193s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 193s Set of directories containing fast5 files for control 193s reads, containing only canonical nucleotides. 193s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 193s File containing k-mer level kernel density estimates 193s for the alternative sample saved using --save-density- 193s basename. 193s --control-density-filename CONTROL_DENSITY_FILENAME 193s File containing k-mer level kernel density estimates 193s for the control sample saved using --save-density- 193s basename. 193s 193s Standard Model Arguments: 193s --dna Explicitly select canonical DNA model. Default: 193s Automatically determine from FAST5s 193s --rna Explicitly select canonical RNA model. Default: 193s Automatically determine from FAST5s 193s --tombo-model-filename TOMBO_MODEL_FILENAME 193s Tombo model filename. If no file is provided, the 193s default DNA or RNA Tombo model will be used. 193s 193s Model Fitting Arguments: 193s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 193s When esitmating the alternative base incorporation 193s rate, this percent of k-mers are assumed to have 193s significantly shifted signal so the alternative 193s distribution minimally overlaps the standard base 193s distribution. Default: 5.000000 193s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 193s Bandwidth applied when performing Gaussian kernal 193s density esitmation on standard and alternative base 193s signal distributions. Default: 0.050000 193s 193s Filtering Argument: 193s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 193s Number of each k-mer observations required in order to 193s produce a reference (genomic locations for standard 193s reference and per-read for alternative reference). 193s Default: 1000 193s 193s Output Argument: 193s --save-density-basename SAVE_DENSITY_BASENAME 193s Basename to save alternative model estimation density 193s estimation information. See scripts/debug_est_alt.R 193s for info use example. Default: Don't save. 193s 193s Multiprocessing Arguments: 193s --processes PROCESSES 193s Number of processes. Default: 1 193s 193s FAST5 Data Arguments: 193s --corrected-group CORRECTED_GROUP 193s FAST5 group created by resquiggle command. Default: 193s RawGenomeCorrected_000 193s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 193s FAST5 subgroup(s) (under /Analyses/[--basecall- 193s group]/) containing basecalls and created within 193s [--corrected-group] containing re-squiggle results. 193s Default: ['BaseCalled_template'] 193s 193s Miscellaneous Arguments: 193s --quiet, -q Don't print status information. 193s --help, -h Print this help message and exit 193s This test only tests the help system 193s There is an extensive test in 193s 193s tombo/tests/shell_tests.sh 193s 193s but this requires to download larger data 193s sets which is not done for the moment. 193s autopkgtest [18:08:04]: test run-unit-test: -----------------------] 194s run-unit-test PASS 194s autopkgtest [18:08:05]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 194s autopkgtest [18:08:05]: @@@@@@@@@@@@@@@@@@@@ summary 194s run-unit-test PASS 207s Creating nova instance adt-noble-s390x-tombo-20240322-180451-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240321.img (UUID f7ee8f0f-480f-4014-94f0-3be2a19e259d)...