0s autopkgtest [19:35:41]: starting date and time: 2024-11-14 19:35:41+0000 0s autopkgtest [19:35:41]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [19:35:41]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.v3_e3hfh/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:numpy --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- lxd -r lxd-armhf-10.145.243.232 lxd-armhf-10.145.243.232:autopkgtest/ubuntu/plucky/armhf 53s autopkgtest [19:36:34]: testbed dpkg architecture: armhf 55s autopkgtest [19:36:36]: testbed apt version: 2.9.8 55s autopkgtest [19:36:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 63s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 63s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [937 kB] 63s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 63s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 63s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 63s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [110 kB] 63s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [674 kB] 63s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [4136 B] 63s Fetched 1926 kB in 1s (2199 kB/s) 64s Reading package lists... 80s tee: /proc/self/fd/2: Permission denied 102s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 102s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 102s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 102s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 104s Reading package lists... 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 105s Calculating upgrade... 105s The following packages will be upgraded: 105s libcap-ng0 pastebinit python3-systemd 105s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Need to get 72.8 kB of archives. 105s After this operation, 89.1 kB of additional disk space will be used. 105s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libcap-ng0 armhf 0.8.5-3build1 [13.8 kB] 106s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf pastebinit all 1.7.1-1 [14.9 kB] 106s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3-systemd armhf 235-1build5 [44.0 kB] 106s Fetched 72.8 kB in 0s (212 kB/s) 106s (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 ... 59560 files and directories currently installed.) 106s Preparing to unpack .../libcap-ng0_0.8.5-3build1_armhf.deb ... 106s Unpacking libcap-ng0:armhf (0.8.5-3build1) over (0.8.5-1) ... 106s Setting up libcap-ng0:armhf (0.8.5-3build1) ... 106s (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 ... 59560 files and directories currently installed.) 106s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 106s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 106s Preparing to unpack .../python3-systemd_235-1build5_armhf.deb ... 106s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 106s Setting up pastebinit (1.7.1-1) ... 106s Setting up python3-systemd (235-1build5) ... 107s Processing triggers for man-db (2.12.1-3) ... 107s Processing triggers for libc-bin (2.40-1ubuntu3) ... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s autopkgtest [19:37:32]: rebooting testbed after setup commands that affected boot 177s autopkgtest [19:38:38]: testbed running kernel: Linux 6.8.0-48-generic #48~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct 7 11:49:53 UTC 2 204s autopkgtest [19:39:05]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 218s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (dsc) [2291 B] 218s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (tar) [22.3 MB] 218s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (diff) [7100 B] 219s gpgv: Signature made Wed Apr 10 17:15:32 2024 UTC 219s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 219s gpgv: Can't check signature: No public key 219s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6build1.dsc: no acceptable signature found 219s autopkgtest [19:39:20]: testing package tombo version 1.5.1-6build1 221s autopkgtest [19:39:22]: build not needed 224s autopkgtest [19:39:25]: test run-unit-test: preparing testbed 233s Reading package lists... 234s Building dependency tree... 234s Reading state information... 234s Starting pkgProblemResolver with broken count: 0 234s Starting 2 pkgProblemResolver with broken count: 0 234s Done 235s The following additional packages will be installed: 235s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 235s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 235s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 235s python3-decorator python3-h5py python3-h5py-serial python3-mappy 235s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 235s tombo-doc 235s Suggested packages: 235s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 235s gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 235s Recommended packages: 235s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 235s python3-rpy2 235s The following NEW packages will be installed: 235s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 235s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 235s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 235s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 235s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 235s tombo-doc 235s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 235s Need to get 60.6 MB/60.6 MB of archives. 235s After this operation, 179 MB of additional disk space will be used. 235s Get:1 /tmp/autopkgtest.lDijx0/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [704 B] 235s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-lato all 2.015-1 [2781 kB] 236s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 236s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 236s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 236s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 236s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 236s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 236s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB] 236s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4ubuntu3 [55.9 kB] 236s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 236s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 236s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] 236s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 236s Get:15 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 236s Get:16 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 236s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 236s Get:18 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-numpy armhf 1:1.26.4+ds-11ubuntu1 [3975 kB] 236s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.11.0-5ubuntu1 [1061 kB] 236s Get:20 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.11.0-5ubuntu1 [7974 B] 236s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mappy armhf 2.27+dfsg-1 [172 kB] 236s Get:22 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-tqdm all 4.67.0-1 [91.6 kB] 236s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 236s Get:24 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5 [16.4 MB] 237s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf tombo armhf 1.5.1-6build1 [448 kB] 237s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 237s Get:27 http://ftpmaster.internal/ubuntu plucky/universe armhf tombo-doc all 1.5.1-6build1 [21.7 MB] 238s Fetched 60.6 MB in 2s (27.5 MB/s) 238s Selecting previously unselected package fonts-lato. 238s (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 ... 59565 files and directories currently installed.) 238s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 238s Unpacking fonts-lato (2.015-1) ... 238s Selecting previously unselected package fonts-font-awesome. 238s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 238s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 238s Selecting previously unselected package fonts-mathjax. 238s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 238s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 239s Selecting previously unselected package libaec0:armhf. 239s Preparing to unpack .../03-libaec0_1.1.3-1_armhf.deb ... 239s Unpacking libaec0:armhf (1.1.3-1) ... 239s Selecting previously unselected package libblas3:armhf. 239s Preparing to unpack .../04-libblas3_3.12.0-3build2_armhf.deb ... 239s Unpacking libblas3:armhf (3.12.0-3build2) ... 239s Selecting previously unselected package libgfortran5:armhf. 239s Preparing to unpack .../05-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 239s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 239s Selecting previously unselected package libsz2:armhf. 239s Preparing to unpack .../06-libsz2_1.1.3-1_armhf.deb ... 239s Unpacking libsz2:armhf (1.1.3-1) ... 239s Selecting previously unselected package libhdf5-103-1t64:armhf. 239s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ... 239s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 239s Selecting previously unselected package libhdf5-hl-100t64:armhf. 239s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_armhf.deb ... 239s Unpacking libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 239s Selecting previously unselected package libjs-jquery. 239s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 239s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 239s Selecting previously unselected package libjs-underscore. 239s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 239s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 239s Selecting previously unselected package libjs-sphinxdoc. 239s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-4_all.deb ... 239s Unpacking libjs-sphinxdoc (7.4.7-4) ... 239s Selecting previously unselected package liblapack3:armhf. 239s Preparing to unpack .../12-liblapack3_3.12.0-3build2_armhf.deb ... 239s Unpacking liblapack3:armhf (3.12.0-3build2) ... 239s Selecting previously unselected package liblbfgsb0:armhf. 239s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 239s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 239s Selecting previously unselected package liblzf1:armhf. 239s Preparing to unpack .../14-liblzf1_3.6-4_armhf.deb ... 239s Unpacking liblzf1:armhf (3.6-4) ... 239s Selecting previously unselected package python3-decorator. 239s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 239s Unpacking python3-decorator (5.1.1-5) ... 239s Selecting previously unselected package python3-numpy. 239s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-11ubuntu1_armhf.deb ... 239s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 239s Selecting previously unselected package python3-h5py-serial. 240s Preparing to unpack .../17-python3-h5py-serial_3.11.0-5ubuntu1_armhf.deb ... 240s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 240s Selecting previously unselected package python3-h5py. 240s Preparing to unpack .../18-python3-h5py_3.11.0-5ubuntu1_all.deb ... 240s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 240s Selecting previously unselected package python3-mappy. 240s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1_armhf.deb ... 240s Unpacking python3-mappy (2.27+dfsg-1) ... 240s Selecting previously unselected package python3-tqdm. 240s Preparing to unpack .../20-python3-tqdm_4.67.0-1_all.deb ... 240s Unpacking python3-tqdm (4.67.0-1) ... 240s Selecting previously unselected package sphinx-rtd-theme-common. 240s Preparing to unpack .../21-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 240s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 240s Selecting previously unselected package python3-scipy. 240s Preparing to unpack .../22-python3-scipy_1.13.1-5_armhf.deb ... 240s Unpacking python3-scipy (1.13.1-5) ... 240s Selecting previously unselected package tombo. 240s Preparing to unpack .../23-tombo_1.5.1-6build1_armhf.deb ... 240s Unpacking tombo (1.5.1-6build1) ... 240s Selecting previously unselected package libjs-mathjax. 240s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 240s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 241s Selecting previously unselected package tombo-doc. 241s Preparing to unpack .../25-tombo-doc_1.5.1-6build1_all.deb ... 241s Unpacking tombo-doc (1.5.1-6build1) ... 241s Selecting previously unselected package autopkgtest-satdep. 241s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 241s Unpacking autopkgtest-satdep (0) ... 241s Setting up fonts-lato (2.015-1) ... 241s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 241s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 241s Setting up python3-tqdm (4.67.0-1) ... 242s Setting up python3-mappy (2.27+dfsg-1) ... 242s Setting up libaec0:armhf (1.1.3-1) ... 242s Setting up python3-decorator (5.1.1-5) ... 242s Setting up libblas3:armhf (3.12.0-3build2) ... 242s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 242s Setting up liblzf1:armhf (3.6-4) ... 242s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 242s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 242s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 242s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 242s Setting up libsz2:armhf (1.1.3-1) ... 242s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 242s Setting up liblapack3:armhf (3.12.0-3build2) ... 242s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 242s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 244s Setting up libjs-sphinxdoc (7.4.7-4) ... 244s Setting up tombo-doc (1.5.1-6build1) ... 244s Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 244s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 244s Setting up libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 244s Setting up python3-scipy (1.13.1-5) ... 248s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 248s Setting up python3-h5py (3.11.0-5ubuntu1) ... 249s Setting up tombo (1.5.1-6build1) ... 249s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 249s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 249s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 249s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 249s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 249s re.match('\+', fastq_rec[2]) is None): 249s Setting up autopkgtest-satdep (0) ... 249s Processing triggers for man-db (2.12.1-3) ... 249s Processing triggers for libc-bin (2.40-1ubuntu3) ... 265s (Reading database ... 66788 files and directories currently installed.) 265s Removing autopkgtest-satdep (0) ... 271s autopkgtest [19:40:12]: test run-unit-test: [----------------------- 273s ********* Testing help commands ********** 273s usage: tombo [-h] [-v] 273s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 273s ... 273s 273s ********** Tombo ********* 273s 273s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 273s 273s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 273s 273s Tombo command groups (additional help available within each command group): 273s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 273s preprocess Pre-process nanopore reads for Tombo processing. 273s filter Apply filter to Tombo index file for specified criterion. 273s detect_modifications Perform statistical testing to detect non-standard nucleotides. 273s text_output Output Tombo results in text files. 273s build_model Create canonical and alternative base Tombo models. 273s plot Save plots to visualize raw nanopore signal or testing results. 273s 273s options: 273s -h, --help show this help message and exit 273s -v, --version show Tombo version and exit. 273s usage: tombo resquiggle [--dna] [--rna] 273s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 273s [--q-score Q_SCORE] 273s [--signal-matching-score SIGNAL_MATCHING_SCORE] 273s [--processes PROCESSES] 273s [--corrected-group CORRECTED_GROUP] 273s [--basecall-group BASECALL_GROUP] 273s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 273s [--overwrite] 273s [--failed-reads-filename FAILED_READS_FILENAME] 273s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 273s [--print-advanced-arguments] [--quiet] [--help] 273s fast5s_basedir reference 273s 273s Required Arguments: 273s fast5s_basedir Directory containing fast5 files. All files ending in 273s "fast5" found recursively within this base directory 273s will be processed. 273s reference Reference genome/transcriptome FASTA file or minimap2 273s index (with "map-ont" preset) for mapping. 273s 273s Model Parameters: 273s --dna Explicitly select canonical DNA model. Default: 273s Automatically determine from FAST5s 273s --rna Explicitly select canonical RNA model. Default: 273s Automatically determine from FAST5s 273s 273s Read Filtering Argument: 273s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 273s Filter reads based on observations per base percentile 273s thresholds. Format thresholds as "percentile:thresh 273s [pctl2:thresh2 ...]". For example to filter reads with 273s 99th pctl > 200 obs/base or max > 5k obs/base use 273s "99:200 100:5000". 273s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 273s Default: 0.000000 273s --signal-matching-score SIGNAL_MATCHING_SCORE 273s Observed to expected signal matching score (higher 273s score indicates poor matching). Sample type defaults: 273s RNA : 2 || DNA : 1.1 273s 273s Multiprocessing Arguments: 273s --processes PROCESSES 273s Number of processes. Default: 1 273s 273s FAST5 Data Arguments: 273s --corrected-group CORRECTED_GROUP 273s FAST5 group created by resquiggle command. Default: 273s RawGenomeCorrected_000 273s --basecall-group BASECALL_GROUP 273s FAST5 group obtain original basecalls (under Analyses 273s group). Default: Basecall_1D_000 273s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 273s FAST5 subgroup(s) (under /Analyses/[--basecall- 273s group]/) containing basecalls and created within 273s [--corrected-group] containing re-squiggle results. 273s Default: ['BaseCalled_template'] 273s --overwrite Overwrite previous corrected group in FAST5 files. 273s Note: only effects --corrected-group or --new- 273s corrected-group. 273s 273s Input/Output Arguments: 273s --failed-reads-filename FAILED_READS_FILENAME 273s Output failed read filenames with assoicated error. 273s Default: Do not store failed reads. 273s --num-most-common-errors NUM_MOST_COMMON_ERRORS 273s Dynamically show this many most common errors so far 273s through run. Default: 0; Just show progress 273s 273s Advanced Arguments: 273s --print-advanced-arguments 273s Print advanced re-squiggle arguments and exit. 273s 273s Miscellaneous Arguments: 273s --quiet, -q Don't print status information. 273s --help, -h Print this help message and exit 273s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 273s --fastq-filenames 273s FASTQ_FILENAMES 273s [FASTQ_FILENAMES ...] 273s [--basecall-group BASECALL_GROUP] 273s [--basecall-subgroup BASECALL_SUBGROUP] 273s [--overwrite] 273s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 273s [--processes PROCESSES] 273s [--quiet] [--help] 273s 273s Required Arguments: 273s --fast5-basedir FAST5_BASEDIR 273s Directory containing fast5 files. 273s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 273s FASTQ filenames containing basecalls to be added to 273s raw FAST5 files. 273s 273s FAST5 Data Arguments: 273s --basecall-group BASECALL_GROUP 273s FAST5 group obtain original basecalls (under Analyses 273s group). Default: Basecall_1D_000 273s --basecall-subgroup BASECALL_SUBGROUP 273s FAST5 subgroup (under /Analyses/[--basecall-group]/) 273s under which to store basecalls from FASTQs. Default: 273s BaseCalled_template 273s --overwrite Overwrite previous corrected group in FAST5 files. 273s Note: only effects --corrected-group or --new- 273s corrected-group. 273s 273s Sequencing Summary Argument: 273s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 273s Sequencing summary filenames produced by albacore. 273s These can make annotation of raw FAST5 files with 273s FASTQ sequence much faster. 273s 273s Multiprocessing Argument: 273s --processes PROCESSES 273s Number of processes. Default: 1 273s 273s Miscellaneous Arguments: 273s --quiet, -q Don't print status information. 273s --help, -h Print this help message and exit 273s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 273s [FAST5_BASEDIRS ...] 273s [--corrected-group CORRECTED_GROUP] 273s [--quiet] [--help] 273s 273s Required Argument: 273s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 273s Directories containing fast5 files. 273s 273s FAST5 Data Argument: 273s --corrected-group CORRECTED_GROUP 273s FAST5 group created by resquiggle command. Default: 273s RawGenomeCorrected_000 273s 273s Miscellaneous Arguments: 273s --quiet, -q Don't print status information. 273s --help, -h Print this help message and exit 274s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 274s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 274s [--corrected-group CORRECTED_GROUP] [--quiet] 274s [--help] 274s 274s Required Argument: 274s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 274s Directories containing fast5 files. 274s 274s Read Filtering Argument: 274s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 274s Filter reads based on observations per base percentile 274s thresholds. Format thresholds as "percentile:thresh 274s [pctl2:thresh2 ...]". For example to filter reads with 274s 99th pctl > 200 obs/base or max > 5k obs/base use 274s "99:200 100:5000". 274s 274s FAST5 Data Argument: 274s --corrected-group CORRECTED_GROUP 274s FAST5 group created by resquiggle command. Default: 274s RawGenomeCorrected_000 274s 274s Miscellaneous Arguments: 274s --quiet, -q Don't print status information. 274s --help, -h Print this help message and exit 274s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 274s [FAST5_BASEDIRS ...] 274s [--percent-to-filter PERCENT_TO_FILTER] 274s [--corrected-group CORRECTED_GROUP] 274s [--quiet] [--help] 274s 274s Required Arguments: 274s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 274s Directories containing fast5 files. 274s 274s Read Filtering Argument: 274s --percent-to-filter PERCENT_TO_FILTER 274s Percentage of all reads to filter. Reads are randomly 274s selected weighted according to the approximate 274s coverage at the mapped genomic location. This can be 274s useful in modeling and testing. Default: 10.000000 274s 274s FAST5 Data Arguments: 274s --corrected-group CORRECTED_GROUP 274s FAST5 group created by resquiggle command. Default: 274s RawGenomeCorrected_000 274s 274s Miscellaneous Arguments: 274s --quiet, -q Don't print status information. 274s --help, -h Print this help message and exit 274s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 274s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 274s [--corrected-group CORRECTED_GROUP] 274s [--basecall-group BASECALL_GROUP] [--quiet] 274s [--help] 274s 274s Required Arguments: 274s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 274s Directories containing fast5 files. 274s 274s Read Filtering Argument: 274s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 274s Default: 7.000000 274s 274s FAST5 Data Arguments: 274s --corrected-group CORRECTED_GROUP 274s FAST5 group created by resquiggle command. Default: 274s RawGenomeCorrected_000 274s --basecall-group BASECALL_GROUP 274s FAST5 group obtain original basecalls (under Analyses 274s group). Default: Basecall_1D_000 274s 274s Miscellaneous Arguments: 274s --quiet, -q Don't print status information. 274s --help, -h Print this help message and exit 274s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 274s [FAST5_BASEDIRS ...] 274s --signal-matching-score 274s SIGNAL_MATCHING_SCORE 274s [--corrected-group CORRECTED_GROUP] 274s [--quiet] [--help] 274s 274s Required Arguments: 274s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 274s Directories containing fast5 files. 274s --signal-matching-score SIGNAL_MATCHING_SCORE 274s Observed to expected signal matching score (higher 274s score indicates poor matching). Sample type defaults: 274s RNA : 2 || DNA : 1.1 274s 274s FAST5 Data Arguments: 274s --corrected-group CORRECTED_GROUP 274s FAST5 group created by resquiggle command. Default: 274s RawGenomeCorrected_000 274s 274s Miscellaneous Arguments: 274s --quiet, -q Don't print status information. 274s --help, -h Print this help message and exit 274s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 274s [FAST5_BASEDIRS ...] 274s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 274s [--include-partial-overlap] 274s [--corrected-group CORRECTED_GROUP] 274s [--quiet] [--help] 274s 274s Required Arguments: 274s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 274s Directories containing fast5 files. 274s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 274s Filter out reads not falling completely within include 274s regions. Omit start and end coordinates to include an 274s entire chromosome/sequence record. Format regions as 274s "chrm[:start-end] [chrm2[:start2-end2] ...]". 274s 274s Filter Argument: 274s --include-partial-overlap 274s Include reads that partially overlap the specified 274s region. Default: Only include reads completely 274s contained in a specified region 274s 274s FAST5 Data Argument: 274s --corrected-group CORRECTED_GROUP 274s FAST5 group created by resquiggle command. Default: 274s RawGenomeCorrected_000 274s 274s Miscellaneous Arguments: 274s --quiet, -q Don't print status information. 274s --help, -h Print this help message and exit 274s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 274s [FAST5_BASEDIRS ...] 274s --statistics-file-basename 274s STATISTICS_FILE_BASENAME [--dna] 274s [--rna] 274s [--fishers-method-context FISHERS_METHOD_CONTEXT] 274s [--minimum-test-reads MINIMUM_TEST_READS] 274s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 274s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 274s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 274s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 274s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 274s [--processes PROCESSES] 274s [--corrected-group CORRECTED_GROUP] 274s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 274s [--quiet] [--help] 274s 274s Required Argument: 274s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 274s Directories containing fast5 files. 274s --statistics-file-basename STATISTICS_FILE_BASENAME 274s File base name to save base by base statistics from 274s testing. Filenames will be [--statistics-file- 274s basename].[--alternate-bases]?.tombo.stats 274s 274s Comparison Model Arguments: 274s --dna Explicitly select canonical DNA model. Default: 274s Automatically determine from FAST5s 274s --rna Explicitly select canonical RNA model. Default: 274s Automatically determine from FAST5s 274s 274s Significance Test Arguments: 274s --fishers-method-context FISHERS_METHOD_CONTEXT 274s Number of context bases up and downstream over which 274s to compute Fisher's method combined p-values. Note: 274s Not applicable for alternative model likelihood ratio 274s tests. Default: 1. 274s --minimum-test-reads MINIMUM_TEST_READS 274s Number of reads required at a position to perform 274s significance testing or contribute to model 274s estimation. Default: 1 274s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 274s P-value threshold when computing fraction of 274s significant reads at each genomic position. If two 274s values are provided, statistics between these values 274s are not considered. Default thresholds: DNA:0.15-0.5 , 274s RNA:0.05-0.4 274s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 274s Dampen fraction modified estimates for low coverage 274s sites. Two parameters are unmodified and modified 274s pseudo read counts. This is equivalent to a beta prior 274s on the fraction estimate. Set to "0 0" to disable 274s dampened fraction estimation. Default: [2, 0] 274s 274s Output Argument: 274s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 274s Base for binary files containing per-read statistics 274s from statistical testing. Filenames will be [--per- 274s read-statistics-basename].[--alternate- 274s bases]?.tombo.per_read_stats 274s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 274s Number of the most significant sites to store for 274s faster access. If a longer list of most significant 274s sites is required the list must be re-computed from 274s all batches. Very large values can increase RAM usage. 274s Default: 100000 274s 274s Multiprocessing Arguments: 274s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 274s Size of regions over which to multiprocesses statistic 274s computation. For very deep samples a smaller value is 274s recommmended in order to control memory consumption. 274s Default: 10000 274s --processes PROCESSES 274s Number of processes. Default: 1 274s 274s FAST5 Data Arguments: 274s --corrected-group CORRECTED_GROUP 274s FAST5 group created by resquiggle command. Default: 274s RawGenomeCorrected_000 274s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 274s FAST5 subgroup(s) (under /Analyses/[--basecall- 274s group]/) containing basecalls and created within 274s [--corrected-group] containing re-squiggle results. 274s Default: ['BaseCalled_template'] 274s 274s Miscellaneous Arguments: 274s --quiet, -q Don't print status information. 274s --help, -h Print this help message and exit 274s usage: tombo detect_modifications alternative_model 274s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 274s [--statistics-file-basename STATISTICS_FILE_BASENAME] 274s [--alternate-bases {CpG,6mA,dam,dcm,5mC} [{CpG,6mA,dam,dcm,5mC} ...]] 274s [--print-available-models] 274s [--dna] [--rna] 274s [--minimum-test-reads MINIMUM_TEST_READS] 274s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 274s [--standard-log-likelihood-ratio] 274s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 274s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 274s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 274s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 274s [--processes PROCESSES] 274s [--corrected-group CORRECTED_GROUP] 274s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 274s [--quiet] [--help] 274s 274s Required Argument: 274s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 274s Directories containing fast5 files. 274s --statistics-file-basename STATISTICS_FILE_BASENAME 274s File base name to save base by base statistics from 274s testing. Filenames will be [--statistics-file- 274s basename].[--alternate-bases]?.tombo.stats 274s --alternate-bases {CpG,6mA,dam,dcm,5mC} [{CpG,6mA,dam,dcm,5mC} ...] 274s Default non-standard base model for testing (not 274s required if user created --alternate-model-filenames 274s is provided). 274s 274s Comparison Arguments: 274s --print-available-models 274s Print available alternative models and exit. 274s --dna Explicitly select canonical DNA model. Default: 274s Automatically determine from FAST5s 274s --rna Explicitly select canonical RNA model. Default: 274s Automatically determine from FAST5s 274s 274s Significance Test Arguments: 274s --minimum-test-reads MINIMUM_TEST_READS 274s Number of reads required at a position to perform 274s significance testing or contribute to model 274s estimation. Default: 1 274s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 274s Log likelihood ratio threshold when computing fraction 274s of significant reads at each genomic position. If two 274s values are provided, statistics between these values 274s are not considered. Default thresholds: DNA:-1.5-2.5 , 274s RNA:-2.5-2.5 274s --standard-log-likelihood-ratio 274s Use a standard log likelihood ratio (LLR) statistic. 274s Default is to use an outlier-robust LLR-like 274s statistic. Detail in full online documentation. 274s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 274s Dampen fraction modified estimates for low coverage 274s sites. Two parameters are unmodified and modified 274s pseudo read counts. This is equivalent to a beta prior 274s on the fraction estimate. Set to "0 0" to disable 274s dampened fraction estimation. Default: [2, 0] 274s 274s Output Argument: 274s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 274s Base for binary files containing per-read statistics 274s from statistical testing. Filenames will be [--per- 274s read-statistics-basename].[--alternate- 274s bases]?.tombo.per_read_stats 274s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 274s Number of the most significant sites to store for 274s faster access. If a longer list of most significant 274s sites is required the list must be re-computed from 274s all batches. Very large values can increase RAM usage. 274s Default: 100000 274s 274s Multiprocessing Arguments: 274s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 274s Size of regions over which to multiprocesses statistic 274s computation. For very deep samples a smaller value is 274s recommmended in order to control memory consumption. 274s Default: 10000 274s --processes PROCESSES 274s Number of processes. Default: 1 274s 274s FAST5 Data Arguments: 274s --corrected-group CORRECTED_GROUP 274s FAST5 group created by resquiggle command. Default: 274s RawGenomeCorrected_000 274s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 274s FAST5 subgroup(s) (under /Analyses/[--basecall- 274s group]/) containing basecalls and created within 274s [--corrected-group] containing re-squiggle results. 274s Default: ['BaseCalled_template'] 274s 274s Miscellaneous Arguments: 274s --quiet, -q Don't print status information. 274s --help, -h Print this help message and exit 274s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 274s FAST5_BASEDIRS 274s [FAST5_BASEDIRS ...] 274s --statistics-file-basename 274s STATISTICS_FILE_BASENAME 274s --control-fast5-basedirs 274s CONTROL_FAST5_BASEDIRS 274s [CONTROL_FAST5_BASEDIRS ...] 274s [--sample-only-estimates] 274s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 274s [--dna] [--rna] 274s [--fishers-method-context FISHERS_METHOD_CONTEXT] 274s [--minimum-test-reads MINIMUM_TEST_READS] 274s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 274s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 274s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 274s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 274s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 274s [--processes PROCESSES] 274s [--corrected-group CORRECTED_GROUP] 274s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 274s [--quiet] [--help] 274s 274s Required Argument: 274s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 274s Directories containing fast5 files. 274s --statistics-file-basename STATISTICS_FILE_BASENAME 274s File base name to save base by base statistics from 274s testing. Filenames will be [--statistics-file- 274s basename].[--alternate-bases]?.tombo.stats 274s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 274s Set of directories containing fast5 files for control 274s reads, containing only canonical nucleotides. 274s 274s Model Prior Arguments: 274s --sample-only-estimates 274s Only use canonical sample to estimate expected signal 274s level and spread. Default: Use canonical model to 274s improve estimtates (esp. for low coverage regions) 274s using baysian posterior estimates. 274s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 274s Prior weights (one each for mean and spread) applied 274s to canonical base model for estimating posterior model 274s parameters for sample comparison. Default: [5, 40] 274s --dna Explicitly select canonical DNA model. Default: 274s Automatically determine from FAST5s 274s --rna Explicitly select canonical RNA model. Default: 274s Automatically determine from FAST5s 274s 274s Significance Test Arguments: 274s --fishers-method-context FISHERS_METHOD_CONTEXT 274s Number of context bases up and downstream over which 274s to compute Fisher's method combined p-values. Note: 274s Not applicable for alternative model likelihood ratio 274s tests. Default: 1. 274s --minimum-test-reads MINIMUM_TEST_READS 274s Number of reads required at a position to perform 274s significance testing or contribute to model 274s estimation. Default: 1 274s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 274s P-value threshold when computing fraction of 274s significant reads at each genomic position. If two 274s values are provided, statistics between these values 274s are not considered. Default thresholds: DNA:0.15-0.5 , 274s RNA:0.05-0.4 274s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 274s Dampen fraction modified estimates for low coverage 274s sites. Two parameters are unmodified and modified 274s pseudo read counts. This is equivalent to a beta prior 274s on the fraction estimate. Set to "0 0" to disable 274s dampened fraction estimation. Default: [2, 0] 274s 274s Output Argument: 274s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 274s Base for binary files containing per-read statistics 274s from statistical testing. Filenames will be [--per- 274s read-statistics-basename].[--alternate- 274s bases]?.tombo.per_read_stats 274s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 274s Number of the most significant sites to store for 274s faster access. If a longer list of most significant 274s sites is required the list must be re-computed from 274s all batches. Very large values can increase RAM usage. 274s Default: 100000 274s 274s Multiprocessing Arguments: 274s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 274s Size of regions over which to multiprocesses statistic 274s computation. For very deep samples a smaller value is 274s recommmended in order to control memory consumption. 274s Default: 10000 274s --processes PROCESSES 274s Number of processes. Default: 1 274s 274s FAST5 Data Arguments: 274s --corrected-group CORRECTED_GROUP 274s FAST5 group created by resquiggle command. Default: 274s RawGenomeCorrected_000 274s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 274s FAST5 subgroup(s) (under /Analyses/[--basecall- 274s group]/) containing basecalls and created within 274s [--corrected-group] containing re-squiggle results. 274s Default: ['BaseCalled_template'] 274s 274s Miscellaneous Arguments: 274s --quiet, -q Don't print status information. 274s --help, -h Print this help message and exit 275s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 275s FAST5_BASEDIRS 275s [FAST5_BASEDIRS ...] 275s --statistics-file-basename 275s STATISTICS_FILE_BASENAME 275s --alternate-fast5-basedirs 275s ALTERNATE_FAST5_BASEDIRS 275s [ALTERNATE_FAST5_BASEDIRS ...] 275s [--fishers-method-context FISHERS_METHOD_CONTEXT] 275s [--minimum-test-reads MINIMUM_TEST_READS] 275s [--statistic-type {ks,u,t}] 275s [--store-p-value] 275s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 275s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 275s [--processes PROCESSES] 275s [--corrected-group CORRECTED_GROUP] 275s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 275s [--quiet] [--help] 275s 275s Required Argument: 275s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 275s Directories containing fast5 files. 275s --statistics-file-basename STATISTICS_FILE_BASENAME 275s File base name to save base by base statistics from 275s testing. Filenames will be [--statistics-file- 275s basename].[--alternate-bases]?.tombo.stats 275s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 275s Set of directories containing fast5 files for 275s alternate set of reads. 275s 275s Significance Test Arguments: 275s --fishers-method-context FISHERS_METHOD_CONTEXT 275s Number of context bases up and downstream over which 275s to compute Fisher's method combined p-values. Note: 275s Not applicable for alternative model likelihood ratio 275s tests. Default: 1. 275s --minimum-test-reads MINIMUM_TEST_READS 275s Number of reads required at a position to perform 275s significance testing or contribute to model 275s estimation. Default: 50 275s --statistic-type {ks,u,t} 275s Type of statistical test to apply. Default: "ks" 275s --store-p-value Store p-value instead of effect-size statistic. 275s Statistics are D-statistic (KS-test), deviation from 275s even common language effect size (u-test), and Cohen's 275s D (t-test). 275s 275s Output Argument: 275s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 275s Number of the most significant sites to store for 275s faster access. If a longer list of most significant 275s sites is required the list must be re-computed from 275s all batches. Very large values can increase RAM usage. 275s Default: 100000 275s 275s Multiprocessing Arguments: 275s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 275s Size of regions over which to multiprocesses statistic 275s computation. For very deep samples a smaller value is 275s recommmended in order to control memory consumption. 275s Default: 10000 275s --processes PROCESSES 275s Number of processes. Default: 1 275s 275s FAST5 Data Arguments: 275s --corrected-group CORRECTED_GROUP 275s FAST5 group created by resquiggle command. Default: 275s RawGenomeCorrected_000 275s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 275s FAST5 subgroup(s) (under /Analyses/[--basecall- 275s group]/) containing basecalls and created within 275s [--corrected-group] containing re-squiggle results. 275s Default: ['BaseCalled_template'] 275s 275s Miscellaneous Arguments: 275s --quiet, -q Don't print status information. 275s --help, -h Print this help message and exit 275s usage: tombo detect_modifications aggregate_per_read_stats 275s --per-read-statistics-filename 275s PER_READ_STATISTICS_FILENAME 275s --statistics-filename 275s STATISTICS_FILENAME 275s --single-read-threshold 275s SINGLE_READ_THRESHOLD 275s [SINGLE_READ_THRESHOLD ...] 275s [--minimum-test-reads MINIMUM_TEST_READS] 275s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 275s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 275s [--processes PROCESSES] 275s [--corrected-group CORRECTED_GROUP] 275s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 275s [--quiet] [--help] 275s 275s Required Argument: 275s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 275s Binary file containing per-read statistics from 275s statistical testing. 275s --statistics-filename STATISTICS_FILENAME 275s File to save/load genomic base anchored statistics. 275s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 275s P-value or log likelihood ratio threshold when 275s computing fraction of significant reads at each 275s genomic position. If two values are provided, 275s statistics between these values are not considered. 275s 275s Significance Test Arguments: 275s --minimum-test-reads MINIMUM_TEST_READS 275s Number of reads required at a position to perform 275s significance testing or contribute to model 275s estimation. Default: 1 275s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 275s Dampen fraction modified estimates for low coverage 275s sites. Two parameters are unmodified and modified 275s pseudo read counts. This is equivalent to a beta prior 275s on the fraction estimate. Set to "0 0" to disable 275s dampened fraction estimation. Default: [2, 0] 275s 275s Output Argument: 275s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 275s Number of the most significant sites to store for 275s faster access. If a longer list of most significant 275s sites is required the list must be re-computed from 275s all batches. Very large values can increase RAM usage. 275s Default: 100000 275s 275s Multiprocessing Arguments: 275s --processes PROCESSES 275s Number of processes. Default: 1 275s 275s FAST5 Data Arguments: 275s --corrected-group CORRECTED_GROUP 275s FAST5 group created by resquiggle command. Default: 275s RawGenomeCorrected_000 275s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 275s FAST5 subgroup(s) (under /Analyses/[--basecall- 275s group]/) containing basecalls and created within 275s [--corrected-group] containing re-squiggle results. 275s Default: ['BaseCalled_template'] 275s 275s Miscellaneous Arguments: 275s --quiet, -q Don't print status information. 275s --help, -h Print this help message and exit 275s usage: tombo text_output browser_files 275s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 275s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 275s [--statistics-filename STATISTICS_FILENAME] 275s [--genome-fasta GENOME_FASTA] 275s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 275s [--browser-file-basename BROWSER_FILE_BASENAME] 275s [--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} ...]] 275s [--corrected-group CORRECTED_GROUP] 275s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 275s [--quiet] [--help] 275s 275s Data Arguments: 275s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 275s Directories containing fast5 files. 275s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 275s Set of directories containing fast5 files for control 275s reads, containing only canonical nucleotides. 275s --statistics-filename STATISTICS_FILENAME 275s File to save/load genomic base anchored statistics. 275s 275s Statistic Motif Filter Arguments: 275s --genome-fasta GENOME_FASTA 275s FASTA file used to re-squiggle. For faster sequence 275s access. 275s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 275s Ground truth, motif centered, modified base 275s descriptions for output filtering. Format descriptions 275s as: "motif:mod_pos:name". The mod_pos indicates the 275s modified base within the motif (1-based index). 275s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 275s output for identification of E. coli dam and dcm 275s methylation. 275s 275s Output Arguments: 275s --browser-file-basename BROWSER_FILE_BASENAME 275s Basename for output browser files. Two files (plus and 275s minus strand) will be produced for each --file-types 275s supplied. Filenames formatted as "[browser-file- 275s basename].[file- 275s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 275s Default: tombo_results 275s --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} ...] 275s Data types of genome browser files to produce. 275s Produced coverage files are in bedGraph format, while 275s all other file types will be in wiggle format 275s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 275s Default: "coverage" 275s 275s FAST5 Data Arguments: 275s --corrected-group CORRECTED_GROUP 275s FAST5 group created by resquiggle command. Default: 275s RawGenomeCorrected_000 275s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 275s FAST5 subgroup(s) (under /Analyses/[--basecall- 275s group]/) containing basecalls and created within 275s [--corrected-group] containing re-squiggle results. 275s Default: ['BaseCalled_template'] 275s 275s Miscellaneous Arguments: 275s --quiet, -q Don't print status information. 275s --help, -h Print this help message and exit 275s usage: tombo text_output signif_sequence_context --statistics-filename 275s STATISTICS_FILENAME 275s [--genome-fasta GENOME_FASTA] 275s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 275s [--num-regions NUM_REGIONS] 275s [--num-bases NUM_BASES] 275s [--sequences-filename SEQUENCES_FILENAME] 275s [--corrected-group CORRECTED_GROUP] 275s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 275s [--quiet] [--help] 275s 275s Required Argument: 275s --statistics-filename STATISTICS_FILENAME 275s File to save/load genomic base anchored statistics. 275s 275s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 275s --genome-fasta GENOME_FASTA 275s FASTA file used to re-squiggle. For faster sequence 275s access. 275s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 275s Directories containing fast5 files. 275s 275s Region Selection Arguments: 275s --num-regions NUM_REGIONS 275s Number of regions to plot. Default: 100 275s --num-bases NUM_BASES 275s Number of bases to plot/output. Default: 15 275s 275s Output Arguments: 275s --sequences-filename SEQUENCES_FILENAME 275s File for sequences from selected regions. Sequences 275s will be stored in FASTA format. Default: 275s tombo_results.significant_regions.fasta. 275s 275s FAST5 Data Arguments: 275s --corrected-group CORRECTED_GROUP 275s FAST5 group created by resquiggle command. Default: 275s RawGenomeCorrected_000 275s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 275s FAST5 subgroup(s) (under /Analyses/[--basecall- 275s group]/) containing basecalls and created within 275s [--corrected-group] containing re-squiggle results. 275s Default: ['BaseCalled_template'] 275s 275s Miscellaneous Arguments: 275s --quiet, -q Don't print status information. 275s --help, -h Print this help message and exit 275s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 275s [FAST5_BASEDIRS ...] 275s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 275s [--plot-standard-model] 275s [--plot-alternate-model {6mA,dam,CpG,5mC,dcm}] 275s [--overplot-threshold OVERPLOT_THRESHOLD] 275s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 275s [--num-regions NUM_REGIONS] 275s [--num-bases NUM_BASES] 275s [--pdf-filename PDF_FILENAME] 275s [--corrected-group CORRECTED_GROUP] 275s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 275s [--quiet] [--help] 275s 275s Required Argument: 275s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 275s Directories containing fast5 files. 275s 275s Comparison Arguments: 275s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 275s Set of directories containing fast5 files for control 275s reads, containing only canonical nucleotides. 275s --plot-standard-model 275s Add default standard model distribution to the plot. 275s --plot-alternate-model {6mA,dam,CpG,5mC,dcm} 275s Add alternative model distribution to the plot. 275s 275s Overplotting Arguments: 275s --overplot-threshold OVERPLOT_THRESHOLD 275s Coverage level to trigger alternative plot type 275s instead of raw signal. Default: 50 275s --overplot-type {Downsample,Boxplot,Quantile,Density} 275s Plot type for regions with higher coverage. Default: 275s Downsample 275s 275s Plotting Region Arguments: 275s --num-regions NUM_REGIONS 275s Number of regions to plot. Default: 10 275s --num-bases NUM_BASES 275s Number of bases to plot/output. Default: 21 275s 275s Output Argument: 275s --pdf-filename PDF_FILENAME 275s PDF filename to store plot(s). Default: 275s tombo_results.max_coverage.pdf 275s 275s FAST5 Data Arguments: 275s --corrected-group CORRECTED_GROUP 275s FAST5 group created by resquiggle command. Default: 275s RawGenomeCorrected_000 275s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 275s FAST5 subgroup(s) (under /Analyses/[--basecall- 275s group]/) containing basecalls and created within 275s [--corrected-group] containing re-squiggle results. 275s Default: ['BaseCalled_template'] 275s 275s Miscellaneous Arguments: 275s --quiet, -q Don't print status information. 275s --help, -h Print this help message and exit 275s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 275s [FAST5_BASEDIRS ...] --genome-locations 275s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 275s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 275s [--plot-standard-model] 275s [--plot-alternate-model {CpG,5mC,6mA,dam,dcm}] 275s [--overplot-threshold OVERPLOT_THRESHOLD] 275s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 275s [--num-bases NUM_BASES] 275s [--pdf-filename PDF_FILENAME] 275s [--corrected-group CORRECTED_GROUP] 275s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 275s [--quiet] [--help] 275s 275s Required Arguments: 275s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 275s Directories containing fast5 files. 275s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 275s Genomic locations at which to plot signal. Format 275s locations as "chrm:position[:strand] 275s [chrm2:position2[:strand2] ...]" (strand not 275s applicable for all applications) 275s 275s Comparison Arguments: 275s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 275s Set of directories containing fast5 files for control 275s reads, containing only canonical nucleotides. 275s --plot-standard-model 275s Add default standard model distribution to the plot. 275s --plot-alternate-model {CpG,5mC,6mA,dam,dcm} 275s Add alternative model distribution to the plot. 275s 275s Overplotting Arguments: 275s --overplot-threshold OVERPLOT_THRESHOLD 275s Coverage level to trigger alternative plot type 275s instead of raw signal. Default: 50 275s --overplot-type {Downsample,Boxplot,Quantile,Density} 275s Plot type for regions with higher coverage. Default: 275s Downsample 275s 275s Plotting Region Argument: 275s --num-bases NUM_BASES 275s Number of bases to plot/output. Default: 21 275s 275s Output Argument: 275s --pdf-filename PDF_FILENAME 275s PDF filename to store plot(s). Default: 275s tombo_results.genome_locations.pdf 275s 275s FAST5 Data Arguments: 275s --corrected-group CORRECTED_GROUP 275s FAST5 group created by resquiggle command. Default: 275s RawGenomeCorrected_000 275s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 275s FAST5 subgroup(s) (under /Analyses/[--basecall- 275s group]/) containing basecalls and created within 275s [--corrected-group] containing re-squiggle results. 275s Default: ['BaseCalled_template'] 275s 275s Miscellaneous Arguments: 275s --quiet, -q Don't print status information. 275s --help, -h Print this help message and exit 275s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 275s [FAST5_BASEDIRS ...] --motif MOTIF 275s --genome-fasta GENOME_FASTA 275s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 275s [--plot-standard-model] 275s [--plot-alternate-model {CpG,6mA,dam,5mC,dcm}] 275s [--overplot-threshold OVERPLOT_THRESHOLD] 275s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 275s [--num-regions NUM_REGIONS] 275s [--num-bases NUM_BASES] [--deepest-coverage] 275s [--pdf-filename PDF_FILENAME] 275s [--corrected-group CORRECTED_GROUP] 275s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 275s [--quiet] [--help] 275s 275s Required Arguments: 275s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 275s Directories containing fast5 files. 275s --motif MOTIF Motif of interest at which to plot signal and 275s statsitics. Supports IUPAC single letter codes (use T 275s for RNA). 275s --genome-fasta GENOME_FASTA 275s FASTA file used to re-squiggle. For faster sequence 275s access. 275s 275s Comparison Arguments: 275s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 275s Set of directories containing fast5 files for control 275s reads, containing only canonical nucleotides. 275s --plot-standard-model 275s Add default standard model distribution to the plot. 275s --plot-alternate-model {CpG,6mA,dam,5mC,dcm} 275s Add alternative model distribution to the plot. 275s 275s Overplotting Arguments: 275s --overplot-threshold OVERPLOT_THRESHOLD 275s Coverage level to trigger alternative plot type 275s instead of raw signal. Default: 50 275s --overplot-type {Downsample,Boxplot,Quantile,Density} 275s Plot type for regions with higher coverage. Default: 275s Downsample 275s 275s Plotting Region Arguments: 275s --num-regions NUM_REGIONS 275s Number of regions to plot. Default: 10 275s --num-bases NUM_BASES 275s Number of bases to plot/output. Default: 21 275s --deepest-coverage Plot the deepest coverage regions. 275s 275s Output Argument: 275s --pdf-filename PDF_FILENAME 275s PDF filename to store plot(s). Default: 275s tombo_results.motif_centered.pdf 275s 275s FAST5 Data Arguments: 275s --corrected-group CORRECTED_GROUP 275s FAST5 group created by resquiggle command. Default: 275s RawGenomeCorrected_000 275s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 275s FAST5 subgroup(s) (under /Analyses/[--basecall- 275s group]/) containing basecalls and created within 275s [--corrected-group] containing re-squiggle results. 275s Default: ['BaseCalled_template'] 275s 275s Miscellaneous Arguments: 275s --quiet, -q Don't print status information. 275s --help, -h Print this help message and exit 275s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 275s [FAST5_BASEDIRS ...] --control-fast5-basedirs 275s CONTROL_FAST5_BASEDIRS 275s [CONTROL_FAST5_BASEDIRS ...] 275s [--overplot-threshold OVERPLOT_THRESHOLD] 275s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 275s [--num-regions NUM_REGIONS] 275s [--num-bases NUM_BASES] 275s [--pdf-filename PDF_FILENAME] 275s [--sequences-filename SEQUENCES_FILENAME] 275s [--corrected-group CORRECTED_GROUP] 275s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 275s [--quiet] [--help] 275s 275s Required Arguments: 275s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 275s Directories containing fast5 files. 275s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 275s Set of directories containing fast5 files for control 275s reads, containing only canonical nucleotides. 275s 275s Overplotting Arguments: 275s --overplot-threshold OVERPLOT_THRESHOLD 275s Coverage level to trigger alternative plot type 275s instead of raw signal. Default: 50 275s --overplot-type {Downsample,Boxplot,Quantile,Density} 275s Plot type for regions with higher coverage. Default: 275s Downsample 275s 275s Plotting Region Arguments: 275s --num-regions NUM_REGIONS 275s Number of regions to plot. Default: 10 275s --num-bases NUM_BASES 275s Number of bases to plot/output. Default: 21 275s 275s Output Arguments: 275s --pdf-filename PDF_FILENAME 275s PDF filename to store plot(s). Default: 275s tombo_results.max_difference.pdf 275s --sequences-filename SEQUENCES_FILENAME 275s File for sequences from selected regions. Sequences 275s will be stored in FASTA format. Default: None. 275s 275s FAST5 Data Arguments: 275s --corrected-group CORRECTED_GROUP 275s FAST5 group created by resquiggle command. Default: 275s RawGenomeCorrected_000 275s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 275s FAST5 subgroup(s) (under /Analyses/[--basecall- 275s group]/) containing basecalls and created within 275s [--corrected-group] containing re-squiggle results. 275s Default: ['BaseCalled_template'] 275s 275s Miscellaneous Arguments: 275s --quiet, -q Don't print status information. 275s --help, -h Print this help message and exit 275s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 275s [FAST5_BASEDIRS ...] --statistics-filename 275s STATISTICS_FILENAME 275s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 275s [--plot-standard-model] 275s [--plot-alternate-model {dam,6mA,CpG,5mC,dcm}] 275s [--overplot-threshold OVERPLOT_THRESHOLD] 275s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 275s [--num-regions NUM_REGIONS] 275s [--num-bases NUM_BASES] 275s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 275s [--pdf-filename PDF_FILENAME] 275s [--sequences-filename SEQUENCES_FILENAME] 275s [--corrected-group CORRECTED_GROUP] 275s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 275s [--quiet] [--help] 275s 275s Required Arguments: 275s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 275s Directories containing fast5 files. 275s --statistics-filename STATISTICS_FILENAME 275s File to save/load genomic base anchored statistics. 275s 275s Comparison Arguments: 275s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 275s Set of directories containing fast5 files for control 275s reads, containing only canonical nucleotides. 275s --plot-standard-model 275s Add default standard model distribution to the plot. 275s --plot-alternate-model {dam,6mA,CpG,5mC,dcm} 275s Add alternative model distribution to the plot. 275s 275s Overplotting Arguments: 275s --overplot-threshold OVERPLOT_THRESHOLD 275s Coverage level to trigger alternative plot type 275s instead of raw signal. Default: 50 275s --overplot-type {Downsample,Boxplot,Quantile,Density} 275s Plot type for regions with higher coverage. Default: 275s Downsample 275s 275s Plotting Region Arguments: 275s --num-regions NUM_REGIONS 275s Number of regions to plot. Default: 10 275s --num-bases NUM_BASES 275s Number of bases to plot/output. Default: 21 275s 275s Statistical Argument: 275s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 275s Dampen fraction modified estimates for low coverage 275s sites. Two parameters are unmodified and modified 275s pseudo read counts. This is equivalent to a beta prior 275s on the fraction estimate. Set to "0 0" to disable 275s dampened fraction estimation. Default: [2, 0] 275s 275s Output Arguments: 275s --pdf-filename PDF_FILENAME 275s PDF filename to store plot(s). Default: 275s tombo_results.significant_difference.pdf 275s --sequences-filename SEQUENCES_FILENAME 275s File for sequences from selected regions. Sequences 275s will be stored in FASTA format. Default: None. 275s 275s FAST5 Data Arguments: 275s --corrected-group CORRECTED_GROUP 275s FAST5 group created by resquiggle command. Default: 275s RawGenomeCorrected_000 275s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 275s FAST5 subgroup(s) (under /Analyses/[--basecall- 275s group]/) containing basecalls and created within 275s [--corrected-group] containing re-squiggle results. 275s Default: ['BaseCalled_template'] 275s 275s Miscellaneous Arguments: 275s --quiet, -q Don't print status information. 275s --help, -h Print this help message and exit 276s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 276s [FAST5_BASEDIRS ...] --motif MOTIF 276s --statistics-filename STATISTICS_FILENAME 276s --genome-fasta GENOME_FASTA 276s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 276s [--plot-standard-model] 276s [--plot-alternate-model {CpG,dam,5mC,6mA,dcm}] 276s [--overplot-threshold OVERPLOT_THRESHOLD] 276s [--num-regions NUM_REGIONS] 276s [--num-context NUM_CONTEXT] 276s [--num-statistics NUM_STATISTICS] 276s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 276s [--pdf-filename PDF_FILENAME] 276s [--corrected-group CORRECTED_GROUP] 276s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 276s [--quiet] [--help] 276s 276s Required Arguments: 276s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 276s Directories containing fast5 files. 276s --motif MOTIF Motif of interest at which to plot signal and 276s statsitics. Supports IUPAC single letter codes (use T 276s for RNA). 276s --statistics-filename STATISTICS_FILENAME 276s File to save/load genomic base anchored statistics. 276s --genome-fasta GENOME_FASTA 276s FASTA file used to re-squiggle. For faster sequence 276s access. 276s 276s Comparison Arguments: 276s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 276s Set of directories containing fast5 files for control 276s reads, containing only canonical nucleotides. 276s --plot-standard-model 276s Add default standard model distribution to the plot. 276s --plot-alternate-model {CpG,dam,5mC,6mA,dcm} 276s Add alternative model distribution to the plot. 276s 276s Overplotting Argument: 276s --overplot-threshold OVERPLOT_THRESHOLD 276s Coverage level to trigger alternative plot type 276s instead of raw signal. Default: 50 276s 276s Plotting Region Arguments: 276s --num-regions NUM_REGIONS 276s Number of regions to plot. Default: 3 276s --num-context NUM_CONTEXT 276s Number of context bases around motif. Default: 5 276s --num-statistics NUM_STATISTICS 276s Number of motif centered regions to include in 276s statistic distributions. Default: 200 276s 276s Statistical Argument: 276s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 276s Dampen fraction modified estimates for low coverage 276s sites. Two parameters are unmodified and modified 276s pseudo read counts. This is equivalent to a beta prior 276s on the fraction estimate. Set to "0 0" to disable 276s dampened fraction estimation. Default: [2, 0] 276s 276s Output Argument: 276s --pdf-filename PDF_FILENAME 276s PDF filename to store plot(s). Default: 276s tombo_results.motif_statistics.pdf 276s 276s FAST5 Data Arguments: 276s --corrected-group CORRECTED_GROUP 276s FAST5 group created by resquiggle command. Default: 276s RawGenomeCorrected_000 276s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 276s FAST5 subgroup(s) (under /Analyses/[--basecall- 276s group]/) containing basecalls and created within 276s [--corrected-group] containing re-squiggle results. 276s Default: ['BaseCalled_template'] 276s 276s Miscellaneous Arguments: 276s --quiet, -q Don't print status information. 276s --help, -h Print this help message and exit 276s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 276s [GENOME_LOCATIONS ...] 276s --per-read-statistics-filename 276s PER_READ_STATISTICS_FILENAME 276s [--genome-fasta GENOME_FASTA] 276s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 276s [--num-reads NUM_READS] [--num-bases NUM_BASES] 276s [--box-center] [--pdf-filename PDF_FILENAME] 276s [--corrected-group CORRECTED_GROUP] 276s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 276s [--quiet] [--help] 276s 276s Required Arguments: 276s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 276s Genomic locations at which to plot signal. Format 276s locations as "chrm:position[:strand] 276s [chrm2:position2[:strand2] ...]" (strand not 276s applicable for all applications) 276s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 276s Binary file containing per-read statistics from 276s statistical testing. 276s 276s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 276s --genome-fasta GENOME_FASTA 276s FASTA file used to re-squiggle. For faster sequence 276s access. 276s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 276s Directories containing fast5 files. 276s 276s Plotting Region Arguments: 276s --num-reads NUM_READS 276s Number of reads to plot. Default: 100 276s --num-bases NUM_BASES 276s Number of bases to plot/output. Default: 51 276s --box-center Plot a box around the central base. 276s 276s Output Argument: 276s --pdf-filename PDF_FILENAME 276s PDF filename to store plot(s). Default: 276s tombo_results.per_read_stats.pdf 276s 276s FAST5 Data Arguments: 276s --corrected-group CORRECTED_GROUP 276s FAST5 group created by resquiggle command. Default: 276s RawGenomeCorrected_000 276s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 276s FAST5 subgroup(s) (under /Analyses/[--basecall- 276s group]/) containing basecalls and created within 276s [--corrected-group] containing re-squiggle results. 276s Default: ['BaseCalled_template'] 276s 276s Miscellaneous Arguments: 276s --quiet, -q Don't print status information. 276s --help, -h Print this help message and exit 276s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 276s [STATISTICS_FILENAMES ...] 276s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 276s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 276s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 276s [--genome-fasta GENOME_FASTA] 276s [--pdf-filename PDF_FILENAME] 276s [--statistics-per-block STATISTICS_PER_BLOCK] 276s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 276s [--quiet] [--help] 276s 276s Required Argument: 276s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 276s Files to load genomic base anchored statistics. 276s 276s Ground Truth Arguments (provide bed files or motifs): 276s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 276s Modification description and bed format files 276s containing single base locations of ground truth 276s modified sites. Bed files should contain 6 fields 276s including strand. Format descriptions as 276s "mod_name:locs.bed". Example: "CpG 276s bisulfite":bisulfite_locs.bed 276s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 276s Bed format files containing single base locations of 276s ground truth unmodified sites. Bed files should 276s contain 6 fields including strand. 276s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 276s Ground truth, motif centered, modified base 276s descriptions for computing ROC and PR curves. Each 276s statistics file is associated with a set of motif 276s descriptions. Format descriptions as: 276s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 276s mod_pos indicates the alternate-base within the motif 276s (1-based index). Example: CCWGG:2:"dcm 276s 5mC"::GATC:2:"dam 6mA" would assess the performance of 276s a single Tombo statistics file for identification of 276s E. coli dam and dcm methylation. 276s --genome-fasta GENOME_FASTA 276s FASTA file used to re-squiggle. For faster sequence 276s access. 276s 276s Output Arguments: 276s --pdf-filename PDF_FILENAME 276s PDF filename to store plot(s). Default: 276s tombo_results.roc.pdf 276s 276s Down-sampling Arguments: 276s --statistics-per-block STATISTICS_PER_BLOCK 276s Number of randomly selected per-read, per-base 276s statistics to extract from each genomic block for 276s plotting. Default: Include all stats 276s --total-statistics-limit TOTAL_STATISTICS_LIMIT 276s Total per-read statistics to be extracted for 276s plotting. Avoids memory overflow for large runs. 276s Default: 5000000 276s 276s Miscellaneous Arguments: 276s --quiet, -q Don't print status information. 276s --help, -h Print this help message and exit 276s usage: tombo plot per_read_roc --per-read-statistics-filenames 276s PER_READ_STATISTICS_FILENAMES 276s [PER_READ_STATISTICS_FILENAMES ...] 276s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 276s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 276s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 276s [--genome-fasta GENOME_FASTA] 276s [--statistics-per-block STATISTICS_PER_BLOCK] 276s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 276s [--pdf-filename PDF_FILENAME] [--quiet] 276s [--help] 276s 276s Required Argument: 276s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 276s Binary files containing per-read statistics from 276s statistical testing. 276s 276s Ground Truth Arguments (provide bed files or motifs): 276s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 276s Modification description and bed format files 276s containing single base locations of ground truth 276s modified sites. Bed files should contain 6 fields 276s including strand. Format descriptions as 276s "mod_name:locs.bed". Example: "CpG 276s bisulfite":bisulfite_locs.bed 276s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 276s Bed format files containing single base locations of 276s ground truth unmodified sites. Bed files should 276s contain 6 fields including strand. 276s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 276s Ground truth, motif centered, modified base 276s descriptions for computing ROC and PR curves. Each 276s statistics file is associated with a set of motif 276s descriptions. Format descriptions as: 276s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 276s mod_pos indicates the alternate-base within the motif 276s (1-based index). Example: CCWGG:2:"dcm 276s 5mC"::GATC:2:"dam 6mA" would assess the performance of 276s a single Tombo statistics file for identification of 276s E. coli dam and dcm methylation. 276s --genome-fasta GENOME_FASTA 276s FASTA file used to re-squiggle. For faster sequence 276s access. 276s 276s Down-sampling Arguments: 276s --statistics-per-block STATISTICS_PER_BLOCK 276s Number of randomly selected per-read, per-base 276s statistics to extract from each genomic block for 276s plotting. Default: 100000 276s --total-statistics-limit TOTAL_STATISTICS_LIMIT 276s Total per-read statistics to be extracted for 276s plotting. Avoids memory overflow for large runs. 276s Default: 5000000 276s 276s Output Arguments: 276s --pdf-filename PDF_FILENAME 276s PDF filename to store plot(s). Default: 276s tombo_results.per_reads_roc.pdf 276s 276s Miscellaneous Arguments: 276s --quiet, -q Don't print status information. 276s --help, -h Print this help message and exit 276s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 276s [--upstream-bases {0,1,2,3,4}] 276s [--downstream-bases {0,1,2,3,4}] [--read-mean] 276s [--num-kmer-threshold NUM_KMER_THRESHOLD] 276s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 276s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 276s [--corrected-group CORRECTED_GROUP] 276s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 276s [--quiet] [--help] 276s 276s Required Argument: 276s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 276s Directories containing fast5 files. 276s 276s Data Processing Arguments: 276s --upstream-bases {0,1,2,3,4} 276s Upstream bases in k-mer. Default: 1 276s --downstream-bases {0,1,2,3,4} 276s Downstream bases in k-mer. Default: 2 276s --read-mean Plot k-mer means across whole reads as opposed to 276s individual k-mer event levels. 276s --num-kmer-threshold NUM_KMER_THRESHOLD 276s Observations of each k-mer required to include a read 276s in read level averages. Default: 1 276s 276s Plotting Region Arguments: 276s --num-reads NUM_READS 276s Number of reads to plot. Default: 100 276s 276s Output Arguments: 276s --pdf-filename PDF_FILENAME 276s PDF filename to store plot(s). Default: 276s tombo_results.kmer_distribution.pdf 276s --r-data-filename R_DATA_FILENAME 276s Filename to save R data structure. Default: Don't save 276s --dont-plot Don't plot result. Useful to produce only R data file. 276s 276s FAST5 Data Arguments: 276s --corrected-group CORRECTED_GROUP 276s FAST5 group created by resquiggle command. Default: 276s RawGenomeCorrected_000 276s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 276s FAST5 subgroup(s) (under /Analyses/[--basecall- 276s group]/) containing basecalls and created within 276s [--corrected-group] containing re-squiggle results. 276s Default: ['BaseCalled_template'] 276s 276s Miscellaneous Arguments: 276s --quiet, -q Don't print status information. 276s --help, -h Print this help message and exit 276s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 276s [FAST5_BASEDIRS ...] 276s --control-fast5-basedirs 276s CONTROL_FAST5_BASEDIRS 276s [CONTROL_FAST5_BASEDIRS ...] 276s --statistics-filename 276s STATISTICS_FILENAME 276s [--genome-fasta GENOME_FASTA] 276s [--processes PROCESSES] 276s [--num-regions NUM_REGIONS] 276s [--num-bases NUM_BASES] 276s [--slide-span SLIDE_SPAN] 276s [--pdf-filename PDF_FILENAME] 276s [--r-data-filename R_DATA_FILENAME] 276s [--corrected-group CORRECTED_GROUP] 276s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 276s [--quiet] [--help] 276s 276s Required Arguments: 276s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 276s Directories containing fast5 files. 276s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 276s Set of directories containing fast5 files for control 276s reads, containing only canonical nucleotides. 276s --statistics-filename STATISTICS_FILENAME 276s File to save/load genomic base anchored statistics. 276s 276s FASTA Sequence Argument: 276s --genome-fasta GENOME_FASTA 276s FASTA file used to re-squiggle. For faster sequence 276s access. 276s 276s Multiprocessing Argument: 276s --processes PROCESSES 276s Number of processes. Default: 1 276s 276s Plotting Region Arguments: 276s --num-regions NUM_REGIONS 276s Number of regions to plot. Default: 10 276s --num-bases NUM_BASES 276s Number of bases to plot/output. Default: 21 276s --slide-span SLIDE_SPAN 276s Number of bases offset over which to search when 276s computing distances for signal cluster plotting. 276s Default: 0 (exact position) 276s 276s Output Arguments: 276s --pdf-filename PDF_FILENAME 276s PDF filename to store plot(s). Default: 276s tombo_results.signal_clusters.pdf 276s --r-data-filename R_DATA_FILENAME 276s Filename to save R data structure. Default: Don't save 276s 276s FAST5 Data Arguments: 276s --corrected-group CORRECTED_GROUP 276s FAST5 group created by resquiggle command. Default: 276s RawGenomeCorrected_000 276s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 276s FAST5 subgroup(s) (under /Analyses/[--basecall- 276s group]/) containing basecalls and created within 276s [--corrected-group] containing re-squiggle results. 276s Default: ['BaseCalled_template'] 276s 276s Miscellaneous Arguments: 276s --quiet, -q Don't print status information. 276s --help, -h Print this help message and exit 276s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 276s 276s Required Arguments: 276s fast5s_basedir Directory containing fast5 files. All files ending in 276s "fast5" found recursively within this base directory will be 276s processed. 276s 276s Miscellaneous Arguments: 276s --quiet, -q Don't print status information. 276s --help, -h Print this help message and exit 276s usage: tombo build_model event_resquiggle 276s [--minimap2-executable MINIMAP2_EXECUTABLE] 276s [--minimap2-index MINIMAP2_INDEX] 276s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 276s [--graphmap-executable GRAPHMAP_EXECUTABLE] 276s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 276s [--normalization-type {median,pA,pA_raw,none}] 276s [--pore-model-filename PORE_MODEL_FILENAME] 276s [--outlier-threshold OUTLIER_THRESHOLD] 276s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 276s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 276s [--timeout TIMEOUT] 276s [--cpts-limit CPTS_LIMIT] 276s [--skip-index] [--overwrite] 276s [--failed-reads-filename FAILED_READS_FILENAME] 276s [--include-event-stdev] 276s [--corrected-group CORRECTED_GROUP] 276s [--basecall-group BASECALL_GROUP] 276s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 276s [--processes PROCESSES] 276s [--align-processes ALIGN_PROCESSES] 276s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 276s [--resquiggle-processes RESQUIGGLE_PROCESSES] 276s [--quiet] [--help] 276s fast5s_basedir reference_fasta 276s 276s Required Arguments: 276s fast5s_basedir Directory containing fast5 files. All files ending in 276s "fast5" found recursively within this base directory 276s will be processed. 276s reference_fasta Reference genome/transcriptome FASTA file for mapping. 276s 276s Mapper Arguments (One mapper is required): 276s --minimap2-executable MINIMAP2_EXECUTABLE 276s Path to minimap2 executable. 276s --minimap2-index MINIMAP2_INDEX 276s Path to minimap2 index (with map-ont preset) file 276s corresponding to the [genome_fasta] provided. 276s --bwa-mem-executable BWA_MEM_EXECUTABLE 276s Path to bwa-mem executable. 276s --graphmap-executable GRAPHMAP_EXECUTABLE 276s Path to graphmap executable. 276s --alignment-batch-size ALIGNMENT_BATCH_SIZE 276s Number of reads included in each alignment call. Note: 276s A new system mapping call is made for each batch 276s (including loading of the genome), so it is advised to 276s use larger values for larger genomes. Default: 1000 276s 276s Signal Processing Arguments: 276s --normalization-type {median,pA,pA_raw,none} 276s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 276s as in the ONT events (using offset, range and 276s digitization), "pA": k-mer-based correction for pA 276s drift as in nanopolish (requires [--pore-model- 276s filename]), "median": median and MAD from raw signal. 276s Default: median 276s --pore-model-filename PORE_MODEL_FILENAME 276s File containing kmer model parameters (level_mean and 276s level_stdv) used in order to compute kmer-based 276s corrected pA values. E.g. https://github.com/jts/nanop 276s olish/blob/master/etc/r9- 276s models/template_median68pA.5mers.model 276s --outlier-threshold OUTLIER_THRESHOLD 276s Windosrize the signal at this number of scale values. 276s Negative value disables outlier clipping. Default: 276s 5.000000 276s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 276s Specify the 2 parameters for segmentation 1) running 276s neighboring windows width 2) minimum raw observations 276s per genomic base. Sample type defaults: RNA : 12 6 || 276s DNA : 5 3 276s 276s Read Filtering Arguments: 276s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 276s Filter reads based on observations per base percentile 276s thresholds. Format thresholds as "percentile:thresh 276s [pctl2:thresh2 ...]". For example to filter reads with 276s 99th pctl > 200 obs/base or max > 5k obs/base use 276s "99:200 100:5000". 276s --timeout TIMEOUT Timeout in seconds for processing a single read. 276s Default: No timeout. 276s --cpts-limit CPTS_LIMIT 276s Maximum number of changepoints to find within a single 276s indel group. Default: No limit. 276s 276s Input/Output Arguments: 276s --skip-index Skip creation of tombo index. This drastically slows 276s downstream tombo commands. Default stores tombo index 276s named ".[--fast5-basedir].[--corrected- 276s group].tombo.index" to be loaded automatically for 276s downstream commands. 276s --overwrite Overwrite previous corrected group in FAST5 files. 276s Note: only effects --corrected-group or --new- 276s corrected-group. 276s --failed-reads-filename FAILED_READS_FILENAME 276s Output failed read filenames with assoicated error. 276s Default: Do not store failed reads. 276s --include-event-stdev 276s Include corrected event standard deviation in output 276s FAST5 data. 276s 276s FAST5 Data Arguments: 276s --corrected-group CORRECTED_GROUP 276s FAST5 group created by resquiggle command. Default: 276s RawGenomeCorrected_000 276s --basecall-group BASECALL_GROUP 276s FAST5 group obtain original basecalls (under Analyses 276s group). Default: Basecall_1D_000 276s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 276s FAST5 subgroup(s) (under /Analyses/[--basecall- 276s group]/) containing basecalls and created within 276s [--corrected-group] containing re-squiggle results. 276s Default: ['BaseCalled_template'] 276s 276s Multiprocessing Arguments: 276s --processes PROCESSES 276s Number of processes. Default: 2 276s --align-processes ALIGN_PROCESSES 276s Number of processes to use for parsing and aligning 276s original basecalls. Each process will independently 276s load the genome into memory, so use caution with 276s larger genomes (e.g. human). Default: 1 276s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 276s Number of threads to use for aligner system call. 276s Default: [--processes] / (2 * [--align-processes)] 276s --resquiggle-processes RESQUIGGLE_PROCESSES 276s Number of processes to use for resquiggle algorithm. 276s Default: [--processes] / 2 276s 276s Miscellaneous Arguments: 276s --quiet, -q Don't print status information. 276s --help, -h Print this help message and exit 276s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 276s [FAST5_BASEDIRS ...] 276s --tombo-model-filename 276s TOMBO_MODEL_FILENAME 276s [--estimate-mean] 276s [--kmer-specific-sd] 276s [--upstream-bases {0,1,2,3,4}] 276s [--downstream-bases {0,1,2,3,4}] 276s [--minimum-test-reads MINIMUM_TEST_READS] 276s [--coverage-threshold COVERAGE_THRESHOLD] 276s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 276s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 276s [--processes PROCESSES] 276s [--corrected-group CORRECTED_GROUP] 276s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 276s [--quiet] [--help] 276s 276s Required Arguments: 276s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 276s Directories containing fast5 files. 276s --tombo-model-filename TOMBO_MODEL_FILENAME 276s Filename to save Tombo model. 276s 276s Modeling Arguments: 276s --estimate-mean Use the mean instead of median for model level 276s estimation. Note: This can cause poor fits due to 276s outliers 276s --kmer-specific-sd Estimate standard deviation for each k-mers 276s individually. 276s --upstream-bases {0,1,2,3,4} 276s Upstream bases in k-mer. Default: 1 276s --downstream-bases {0,1,2,3,4} 276s Downstream bases in k-mer. Default: 2 276s 276s Filtering Arguments: 276s --minimum-test-reads MINIMUM_TEST_READS 276s Number of reads required at a position to perform 276s significance testing or contribute to model 276s estimation. Default: 10 276s --coverage-threshold COVERAGE_THRESHOLD 276s Maximum mean coverage per region when estimating k-mer 276s model (limits compute time for deep samples). Default: 276s 100 276s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 276s Number of each k-mer observations required in order to 276s produce a reference (genomic locations for standard 276s reference and per-read for alternative reference). 276s Default: 5 276s 276s Multiprocessing Arguments: 276s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 276s Size of regions over which to multiprocesses statistic 276s computation. For very deep samples a smaller value is 276s recommmended in order to control memory consumption. 276s Default: 10000 276s --processes PROCESSES 276s Number of processes. Default: 1 276s 276s FAST5 Data Arguments: 276s --corrected-group CORRECTED_GROUP 276s FAST5 group created by resquiggle command. Default: 276s RawGenomeCorrected_000 276s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 276s FAST5 subgroup(s) (under /Analyses/[--basecall- 276s group]/) containing basecalls and created within 276s [--corrected-group] containing re-squiggle results. 276s Default: ['BaseCalled_template'] 276s 276s Miscellaneous Arguments: 276s --quiet, -q Don't print status information. 276s --help, -h Print this help message and exit 277s usage: tombo build_model estimate_alt_reference --alternate-model-filename 277s ALTERNATE_MODEL_FILENAME 277s --alternate-model-name 277s ALTERNATE_MODEL_NAME 277s --alternate-model-base 277s {A,C,G,T} 277s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 277s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 277s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 277s [--control-density-filename CONTROL_DENSITY_FILENAME] 277s [--dna] [--rna] 277s [--tombo-model-filename TOMBO_MODEL_FILENAME] 277s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 277s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 277s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 277s [--save-density-basename SAVE_DENSITY_BASENAME] 277s [--processes PROCESSES] 277s [--corrected-group CORRECTED_GROUP] 277s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 277s [--quiet] [--help] 277s 277s Required Arguments: 277s --alternate-model-filename ALTERNATE_MODEL_FILENAME 277s Tombo model for alternative likelihood ratio 277s significance testing. 277s --alternate-model-name ALTERNATE_MODEL_NAME 277s A short name to associate with this alternate model 277s (e.g. 5mC, 6mA, etc.). This text will be included in 277s output filenames when this model is used for testing. 277s --alternate-model-base {A,C,G,T} 277s Non-standard base is an alternative to this base. 277s 277s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 277s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 277s Directories containing fast5 files. 277s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 277s Set of directories containing fast5 files for control 277s reads, containing only canonical nucleotides. 277s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 277s File containing k-mer level kernel density estimates 277s for the alternative sample saved using --save-density- 277s basename. 277s --control-density-filename CONTROL_DENSITY_FILENAME 277s File containing k-mer level kernel density estimates 277s for the control sample saved using --save-density- 277s basename. 277s 277s Standard Model Arguments: 277s --dna Explicitly select canonical DNA model. Default: 277s Automatically determine from FAST5s 277s --rna Explicitly select canonical RNA model. Default: 277s Automatically determine from FAST5s 277s --tombo-model-filename TOMBO_MODEL_FILENAME 277s Tombo model filename. If no file is provided, the 277s default DNA or RNA Tombo model will be used. 277s 277s Model Fitting Arguments: 277s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 277s When esitmating the alternative base incorporation 277s rate, this percent of k-mers are assumed to have 277s significantly shifted signal so the alternative 277s distribution minimally overlaps the standard base 277s distribution. Default: 5.000000 277s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 277s Bandwidth applied when performing Gaussian kernal 277s density esitmation on standard and alternative base 277s signal distributions. Default: 0.050000 277s 277s Filtering Argument: 277s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 277s Number of each k-mer observations required in order to 277s produce a reference (genomic locations for standard 277s reference and per-read for alternative reference). 277s Default: 1000 277s 277s Output Argument: 277s --save-density-basename SAVE_DENSITY_BASENAME 277s Basename to save alternative model estimation density 277s estimation information. See scripts/debug_est_alt.R 277s for info use example. Default: Don't save. 277s 277s Multiprocessing Arguments: 277s --processes PROCESSES 277s Number of processes. Default: 1 277s 277s FAST5 Data Arguments: 277s --corrected-group CORRECTED_GROUP 277s FAST5 group created by resquiggle command. Default: 277s RawGenomeCorrected_000 277s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 277s FAST5 subgroup(s) (under /Analyses/[--basecall- 277s group]/) containing basecalls and created within 277s [--corrected-group] containing re-squiggle results. 277s Default: ['BaseCalled_template'] 277s 277s Miscellaneous Arguments: 277s --quiet, -q Don't print status information. 277s --help, -h Print this help message and exit 277s This test only tests the help system 277s There is an extensive test in 277s 277s tombo/tests/shell_tests.sh 277s 277s but this requires to download larger data 277s sets which is not done for the moment. 277s autopkgtest [19:40:18]: test run-unit-test: -----------------------] 281s autopkgtest [19:40:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 281s run-unit-test PASS 285s autopkgtest [19:40:26]: @@@@@@@@@@@@@@@@@@@@ summary 285s run-unit-test PASS