0s autopkgtest [05:45:20]: starting date and time: 2025-11-03 05:45:20+0000 0s autopkgtest [05:45:20]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [05:45:20]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vpxkp56l/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:scipy --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scipy/1.16.3-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-3.secgroup --name adt-resolute-amd64-tombo-20251103-054520-juju-7f2275-prod-proposed-migration-environment-15-50063faf-e6c7-4f75-8118-626a8b5c8aff --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-tombo-20251103-054520-juju-7f2275-prod-proposed-migration-environment-15-50063faf-e6c7-4f75-8118-626a8b5c8aff from image adt/ubuntu-resolute-amd64-server-20251103.img (UUID 4bdb4dcd-ffc2-40ae-b789-f626dc1e5191)... 34s autopkgtest [05:45:54]: testbed dpkg architecture: amd64 34s autopkgtest [05:45:54]: testbed apt version: 3.1.11 34s autopkgtest [05:45:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 35s autopkgtest [05:45:55]: testbed release detected to be: None 35s autopkgtest [05:45:55]: updating testbed package index (apt update) 35s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 35s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 35s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 35s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 35s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [86.4 kB] 36s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 36s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1074 kB] 36s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [24.4 kB] 36s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [95.1 kB] 36s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [139 kB] 36s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3084 B] 36s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [64.6 kB] 36s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3744 B] 36s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 36s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [737 kB] 36s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [283 kB] 36s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [22.2 kB] 36s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [15.3 kB] 36s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [7180 B] 36s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [1312 B] 37s Fetched 2655 kB in 1s (2807 kB/s) 38s Reading package lists... 38s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 38s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 38s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 38s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 38s Reading package lists... 38s Reading package lists... 39s Building dependency tree... 39s Reading state information... 39s Calculating upgrade... 39s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 39s autopkgtest [05:45:59]: upgrading testbed (apt dist-upgrade and autopurge) 39s Reading package lists... 39s Building dependency tree... 39s Reading state information... 39s Calculating upgrade... 39s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 39s Reading package lists... 39s Building dependency tree... 39s Reading state information... 39s Solving dependencies... 40s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 42s autopkgtest [05:46:02]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 42s autopkgtest [05:46:02]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 45s Get:1 http://ftpmaster.internal/ubuntu resolute/universe tombo 1.5.1-7build3 (dsc) [2291 B] 45s Get:2 http://ftpmaster.internal/ubuntu resolute/universe tombo 1.5.1-7build3 (tar) [22.3 MB] 45s Get:3 http://ftpmaster.internal/ubuntu resolute/universe tombo 1.5.1-7build3 (diff) [9656 B] 45s gpgv: Signature made Tue Oct 21 17:53:35 2025 UTC 45s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 45s gpgv: Can't check signature: No public key 45s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7build3.dsc: no acceptable signature found 45s autopkgtest [05:46:05]: testing package tombo version 1.5.1-7build3 46s autopkgtest [05:46:06]: build not needed 47s autopkgtest [05:46:07]: test run-unit-test: preparing testbed 47s Reading package lists... 47s Building dependency tree... 47s Reading state information... 47s Solving dependencies... 47s The following NEW packages will be installed: 47s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 47s libhdf5-310 libhdf5-hl-310 libjs-jquery libjs-mathjax libjs-sphinxdoc 47s libjs-underscore liblapack3 liblzf1 libqhull-r8.0 libsz2 python3-decorator 47s python3-h5py python3-h5py-serial python3-mappy python3-numpy 47s python3-numpy-dev python3-packaging python3-scipy python3-tqdm 47s sphinx-rtd-theme-common tombo tombo-doc 47s 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded. 47s Need to get 66.5 MB of archives. 47s After this operation, 246 MB of additional disk space will be used. 47s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-lato all 2.015-1 [2781 kB] 47s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 47s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 47s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-7ubuntu1 [939 kB] 47s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 47s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 48s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 48s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 48s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 libaec0 amd64 1.1.4-2 [22.9 kB] 48s Get:10 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsz2 amd64 1.1.4-2 [5516 B] 48s Get:11 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-310 amd64 1.14.5+repack-3build1 [1411 kB] 48s Get:12 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-3build1 [59.8 kB] 48s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 48s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 48s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 48s Get:16 http://ftpmaster.internal/ubuntu resolute/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 48s Get:17 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-7 [197 kB] 48s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 48s Get:19 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-h5py-serial amd64 3.13.0-1ubuntu1 [1184 kB] 48s Get:20 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-h5py all 3.13.0-1ubuntu1 [8230 B] 48s Get:21 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mappy amd64 2.27+dfsg-1build3 [187 kB] 48s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-packaging all 25.0-1 [52.8 kB] 48s Get:23 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-tqdm all 4.67.1-5 [92.1 kB] 48s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 48s Get:25 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 python3-scipy amd64 1.16.3-1 [18.8 MB] 48s Get:26 http://ftpmaster.internal/ubuntu resolute/universe amd64 tombo amd64 1.5.1-7build3 [510 kB] 48s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 49s Get:28 http://ftpmaster.internal/ubuntu resolute/universe amd64 tombo-doc all 1.5.1-7build3 [21.7 MB] 49s Fetched 66.5 MB in 2s (33.0 MB/s) 49s Selecting previously unselected package fonts-lato. 49s (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 ... 78551 files and directories currently installed.) 49s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 49s Unpacking fonts-lato (2.015-1) ... 49s Selecting previously unselected package python3-numpy-dev:amd64. 49s Preparing to unpack .../01-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 49s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 49s Selecting previously unselected package libblas3:amd64. 49s Preparing to unpack .../02-libblas3_3.12.1-6build1_amd64.deb ... 49s Unpacking libblas3:amd64 (3.12.1-6build1) ... 50s Selecting previously unselected package libgfortran5:amd64. 50s Preparing to unpack .../03-libgfortran5_15.2.0-7ubuntu1_amd64.deb ... 50s Unpacking libgfortran5:amd64 (15.2.0-7ubuntu1) ... 50s Selecting previously unselected package liblapack3:amd64. 50s Preparing to unpack .../04-liblapack3_3.12.1-6build1_amd64.deb ... 50s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 50s Selecting previously unselected package python3-numpy. 50s Preparing to unpack .../05-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 50s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 50s Selecting previously unselected package fonts-font-awesome. 50s Preparing to unpack .../06-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 50s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 50s Selecting previously unselected package fonts-mathjax. 50s Preparing to unpack .../07-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 50s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 50s Selecting previously unselected package libaec0:amd64. 50s Preparing to unpack .../08-libaec0_1.1.4-2_amd64.deb ... 50s Unpacking libaec0:amd64 (1.1.4-2) ... 50s Selecting previously unselected package libsz2:amd64. 50s Preparing to unpack .../09-libsz2_1.1.4-2_amd64.deb ... 50s Unpacking libsz2:amd64 (1.1.4-2) ... 50s Selecting previously unselected package libhdf5-310:amd64. 50s Preparing to unpack .../10-libhdf5-310_1.14.5+repack-3build1_amd64.deb ... 50s Unpacking libhdf5-310:amd64 (1.14.5+repack-3build1) ... 50s Selecting previously unselected package libhdf5-hl-310:amd64. 50s Preparing to unpack .../11-libhdf5-hl-310_1.14.5+repack-3build1_amd64.deb ... 50s Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-3build1) ... 50s Selecting previously unselected package libjs-jquery. 50s Preparing to unpack .../12-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 50s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 50s Selecting previously unselected package libjs-underscore. 50s Preparing to unpack .../13-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 50s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 50s Selecting previously unselected package libjs-sphinxdoc. 50s Preparing to unpack .../14-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 50s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 50s Selecting previously unselected package liblzf1:amd64. 50s Preparing to unpack .../15-liblzf1_3.6-4_amd64.deb ... 50s Unpacking liblzf1:amd64 (3.6-4) ... 50s Selecting previously unselected package libqhull-r8.0:amd64. 50s Preparing to unpack .../16-libqhull-r8.0_2020.2-7_amd64.deb ... 50s Unpacking libqhull-r8.0:amd64 (2020.2-7) ... 50s Selecting previously unselected package python3-decorator. 50s Preparing to unpack .../17-python3-decorator_5.2.1-2_all.deb ... 50s Unpacking python3-decorator (5.2.1-2) ... 50s Selecting previously unselected package python3-h5py-serial. 50s Preparing to unpack .../18-python3-h5py-serial_3.13.0-1ubuntu1_amd64.deb ... 50s Unpacking python3-h5py-serial (3.13.0-1ubuntu1) ... 50s Selecting previously unselected package python3-h5py. 50s Preparing to unpack .../19-python3-h5py_3.13.0-1ubuntu1_all.deb ... 50s Unpacking python3-h5py (3.13.0-1ubuntu1) ... 50s Selecting previously unselected package python3-mappy. 50s Preparing to unpack .../20-python3-mappy_2.27+dfsg-1build3_amd64.deb ... 50s Unpacking python3-mappy (2.27+dfsg-1build3) ... 50s Selecting previously unselected package python3-packaging. 50s Preparing to unpack .../21-python3-packaging_25.0-1_all.deb ... 50s Unpacking python3-packaging (25.0-1) ... 50s Selecting previously unselected package python3-tqdm. 50s Preparing to unpack .../22-python3-tqdm_4.67.1-5_all.deb ... 50s Unpacking python3-tqdm (4.67.1-5) ... 50s Selecting previously unselected package sphinx-rtd-theme-common. 50s Preparing to unpack .../23-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 50s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 50s Selecting previously unselected package python3-scipy. 50s Preparing to unpack .../24-python3-scipy_1.16.3-1_amd64.deb ... 50s Unpacking python3-scipy (1.16.3-1) ... 50s Selecting previously unselected package tombo. 50s Preparing to unpack .../25-tombo_1.5.1-7build3_amd64.deb ... 50s Unpacking tombo (1.5.1-7build3) ... 50s Selecting previously unselected package libjs-mathjax. 50s Preparing to unpack .../26-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 50s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 51s Selecting previously unselected package tombo-doc. 51s Preparing to unpack .../27-tombo-doc_1.5.1-7build3_all.deb ... 51s Unpacking tombo-doc (1.5.1-7build3) ... 51s Setting up fonts-lato (2.015-1) ... 51s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 51s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 51s Setting up python3-tqdm (4.67.1-5) ... 51s Setting up libqhull-r8.0:amd64 (2020.2-7) ... 51s Setting up python3-mappy (2.27+dfsg-1build3) ... 51s Setting up libaec0:amd64 (1.1.4-2) ... 51s Setting up python3-decorator (5.2.1-2) ... 51s Setting up libblas3:amd64 (3.12.1-6build1) ... 51s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 51s Setting up python3-packaging (25.0-1) ... 51s Setting up liblzf1:amd64 (3.6-4) ... 51s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 51s Setting up libgfortran5:amd64 (15.2.0-7ubuntu1) ... 51s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 51s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 51s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 51s Setting up libsz2:amd64 (1.1.4-2) ... 51s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 51s Setting up liblapack3:amd64 (3.12.1-6build1) ... 51s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 51s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 52s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 52s Setting up tombo-doc (1.5.1-7build3) ... 52s Setting up libhdf5-310:amd64 (1.14.5+repack-3build1) ... 52s Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3build1) ... 52s Setting up python3-scipy (1.16.3-1) ... 54s Setting up python3-h5py-serial (3.13.0-1ubuntu1) ... 54s Setting up python3-h5py (3.13.0-1ubuntu1) ... 54s Setting up tombo (1.5.1-7build3) ... 54s Processing triggers for man-db (2.13.1-1) ... 55s Processing triggers for libc-bin (2.42-0ubuntu3) ... 55s autopkgtest [05:46:15]: test run-unit-test: [----------------------- 56s ********* Testing help commands ********** 56s usage: tombo [-h] [-v] 56s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} ... 56s 56s ********** Tombo ********* 56s 56s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 56s 56s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 56s 56s Tombo command groups (additional help available within each command group): 56s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 56s preprocess Pre-process nanopore reads for Tombo processing. 56s filter Apply filter to Tombo index file for specified criterion. 56s detect_modifications Perform statistical testing to detect non-standard nucleotides. 56s text_output Output Tombo results in text files. 56s build_model Create canonical and alternative base Tombo models. 56s plot Save plots to visualize raw nanopore signal or testing results. 56s 56s options: 56s -h, --help show this help message and exit 56s -v, --version show Tombo version and exit. 56s usage: tombo resquiggle [--dna] [--rna] 56s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 56s [--q-score Q_SCORE] 56s [--signal-matching-score SIGNAL_MATCHING_SCORE] 56s [--processes PROCESSES] 56s [--corrected-group CORRECTED_GROUP] 56s [--basecall-group BASECALL_GROUP] 56s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 56s [--overwrite] 56s [--failed-reads-filename FAILED_READS_FILENAME] 56s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 56s [--print-advanced-arguments] [--quiet] [--help] 56s fast5s_basedir reference 56s 56s Required Arguments: 56s fast5s_basedir Directory containing fast5 files. All files ending in 56s "fast5" found recursively within this base directory 56s will be processed. 56s reference Reference genome/transcriptome FASTA file or minimap2 56s index (with "map-ont" preset) for mapping. 56s 56s Model Parameters: 56s --dna Explicitly select canonical DNA model. Default: 56s Automatically determine from FAST5s 56s --rna Explicitly select canonical RNA model. Default: 56s Automatically determine from FAST5s 56s 56s Read Filtering Argument: 56s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 56s Filter reads based on observations per base percentile 56s thresholds. Format thresholds as "percentile:thresh 56s [pctl2:thresh2 ...]". For example to filter reads with 56s 99th pctl > 200 obs/base or max > 5k obs/base use 56s "99:200 100:5000". 56s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 56s Default: 0.000000 56s --signal-matching-score SIGNAL_MATCHING_SCORE 56s Observed to expected signal matching score (higher 56s score indicates poor matching). Sample type defaults: 56s RNA : 2 || DNA : 1.1 56s 56s Multiprocessing Arguments: 56s --processes PROCESSES 56s Number of processes. Default: 1 56s 56s FAST5 Data Arguments: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s --basecall-group BASECALL_GROUP 56s FAST5 group obtain original basecalls (under Analyses 56s group). Default: Basecall_1D_000 56s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 56s FAST5 subgroup(s) (under /Analyses/[--basecall- 56s group]/) containing basecalls and created within 56s [--corrected-group] containing re-squiggle results. 56s Default: ['BaseCalled_template'] 56s --overwrite Overwrite previous corrected group in FAST5 files. 56s Note: only effects --corrected-group or --new- 56s corrected-group. 56s 56s Input/Output Arguments: 56s --failed-reads-filename FAILED_READS_FILENAME 56s Output failed read filenames with assoicated error. 56s Default: Do not store failed reads. 56s --num-most-common-errors NUM_MOST_COMMON_ERRORS 56s Dynamically show this many most common errors so far 56s through run. Default: 0; Just show progress 56s 56s Advanced Arguments: 56s --print-advanced-arguments 56s Print advanced re-squiggle arguments and exit. 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 56s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 56s [--basecall-group BASECALL_GROUP] 56s [--basecall-subgroup BASECALL_SUBGROUP] 56s [--overwrite] 56s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 56s [--processes PROCESSES] 56s [--quiet] [--help] 56s 56s Required Arguments: 56s --fast5-basedir FAST5_BASEDIR 56s Directory containing fast5 files. 56s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 56s FASTQ filenames containing basecalls to be added to 56s raw FAST5 files. 56s 56s FAST5 Data Arguments: 56s --basecall-group BASECALL_GROUP 56s FAST5 group obtain original basecalls (under Analyses 56s group). Default: Basecall_1D_000 56s --basecall-subgroup BASECALL_SUBGROUP 56s FAST5 subgroup (under /Analyses/[--basecall-group]/) 56s under which to store basecalls from FASTQs. Default: 56s BaseCalled_template 56s --overwrite Overwrite previous corrected group in FAST5 files. 56s Note: only effects --corrected-group or --new- 56s corrected-group. 56s 56s Sequencing Summary Argument: 56s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 56s Sequencing summary filenames produced by albacore. 56s These can make annotation of raw FAST5 files with 56s FASTQ sequence much faster. 56s 56s Multiprocessing Argument: 56s --processes PROCESSES 56s Number of processes. Default: 1 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo filter clear_filters 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s [--corrected-group CORRECTED_GROUP] 56s [--quiet] [--help] 56s 56s Required Argument: 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s Directories containing fast5 files. 56s 56s FAST5 Data Argument: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 56s [--corrected-group CORRECTED_GROUP] [--quiet] 56s [--help] 56s 56s Required Argument: 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s Directories containing fast5 files. 56s 56s Read Filtering Argument: 56s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 56s Filter reads based on observations per base percentile 56s thresholds. Format thresholds as "percentile:thresh 56s [pctl2:thresh2 ...]". For example to filter reads with 56s 99th pctl > 200 obs/base or max > 5k obs/base use 56s "99:200 100:5000". 56s 56s FAST5 Data Argument: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo filter level_coverage 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s [--percent-to-filter PERCENT_TO_FILTER] 56s [--corrected-group CORRECTED_GROUP] 56s [--quiet] [--help] 56s 56s Required Arguments: 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s Directories containing fast5 files. 56s 56s Read Filtering Argument: 56s --percent-to-filter PERCENT_TO_FILTER 56s Percentage of all reads to filter. Reads are randomly 56s selected weighted according to the approximate 56s coverage at the mapped genomic location. This can be 56s useful in modeling and testing. Default: 10.000000 56s 56s FAST5 Data Arguments: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo filter q_score 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s [--q-score Q_SCORE] 56s [--corrected-group CORRECTED_GROUP] 56s [--basecall-group BASECALL_GROUP] [--quiet] 56s [--help] 56s 56s Required Arguments: 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s Directories containing fast5 files. 56s 56s Read Filtering Argument: 56s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 56s Default: 7.000000 56s 56s FAST5 Data Arguments: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s --basecall-group BASECALL_GROUP 56s FAST5 group obtain original basecalls (under Analyses 56s group). Default: Basecall_1D_000 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo filter raw_signal_matching 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s --signal-matching-score SIGNAL_MATCHING_SCORE 56s [--corrected-group CORRECTED_GROUP] 56s [--quiet] [--help] 56s 56s Required Arguments: 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s Directories containing fast5 files. 56s --signal-matching-score SIGNAL_MATCHING_SCORE 56s Observed to expected signal matching score (higher 56s score indicates poor matching). Sample type defaults: 56s RNA : 2 || DNA : 1.1 56s 56s FAST5 Data Arguments: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo filter genome_locations 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 56s [--include-partial-overlap] 56s [--corrected-group CORRECTED_GROUP] 56s [--quiet] [--help] 56s 56s Required Arguments: 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s Directories containing fast5 files. 56s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 56s Filter out reads not falling completely within include 56s regions. Omit start and end coordinates to include an 56s entire chromosome/sequence record. Format regions as 56s "chrm[:start-end] [chrm2[:start2-end2] ...]". 56s 56s Filter Argument: 56s --include-partial-overlap 56s Include reads that partially overlap the specified 56s region. Default: Only include reads completely 56s contained in a specified region 56s 56s FAST5 Data Argument: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo detect_modifications de_novo 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s --statistics-file-basename STATISTICS_FILE_BASENAME 56s [--dna] [--rna] 56s [--fishers-method-context FISHERS_METHOD_CONTEXT] 56s [--minimum-test-reads MINIMUM_TEST_READS] 56s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 56s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 56s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 56s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 56s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 56s [--processes PROCESSES] 56s [--corrected-group CORRECTED_GROUP] 56s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 56s [--quiet] [--help] 56s 56s Required Argument: 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s Directories containing fast5 files. 56s --statistics-file-basename STATISTICS_FILE_BASENAME 56s File base name to save base by base statistics from 56s testing. Filenames will be [--statistics-file- 56s basename].[--alternate-bases]?.tombo.stats 56s 56s Comparison Model Arguments: 56s --dna Explicitly select canonical DNA model. Default: 56s Automatically determine from FAST5s 56s --rna Explicitly select canonical RNA model. Default: 56s Automatically determine from FAST5s 56s 56s Significance Test Arguments: 56s --fishers-method-context FISHERS_METHOD_CONTEXT 56s Number of context bases up and downstream over which 56s to compute Fisher's method combined p-values. Note: 56s Not applicable for alternative model likelihood ratio 56s tests. Default: 1. 56s --minimum-test-reads MINIMUM_TEST_READS 56s Number of reads required at a position to perform 56s significance testing or contribute to model 56s estimation. Default: 1 56s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 56s P-value threshold when computing fraction of 56s significant reads at each genomic position. If two 56s values are provided, statistics between these values 56s are not considered. Default thresholds: DNA:0.15-0.5 , 56s RNA:0.05-0.4 56s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 56s Dampen fraction modified estimates for low coverage 56s sites. Two parameters are unmodified and modified 56s pseudo read counts. This is equivalent to a beta prior 56s on the fraction estimate. Set to "0 0" to disable 56s dampened fraction estimation. Default: [2, 0] 56s 56s Output Argument: 56s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 56s Base for binary files containing per-read statistics 56s from statistical testing. Filenames will be [--per- 56s read-statistics-basename].[--alternate- 56s bases]?.tombo.per_read_stats 56s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 56s Number of the most significant sites to store for 56s faster access. If a longer list of most significant 56s sites is required the list must be re-computed from 56s all batches. Very large values can increase RAM usage. 56s Default: 100000 56s 56s Multiprocessing Arguments: 56s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 56s Size of regions over which to multiprocesses statistic 56s computation. For very deep samples a smaller value is 56s recommmended in order to control memory consumption. 56s Default: 10000 56s --processes PROCESSES 56s Number of processes. Default: 1 56s 56s FAST5 Data Arguments: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 56s FAST5 subgroup(s) (under /Analyses/[--basecall- 56s group]/) containing basecalls and created within 56s [--corrected-group] containing re-squiggle results. 56s Default: ['BaseCalled_template'] 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo detect_modifications alternative_model 56s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 56s [--statistics-file-basename STATISTICS_FILE_BASENAME] 56s [--alternate-bases {6mA,dcm,dam,5mC,CpG} [{6mA,dcm,dam,5mC,CpG} ...]] 56s [--print-available-models] 56s [--dna] [--rna] 56s [--minimum-test-reads MINIMUM_TEST_READS] 56s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 56s [--standard-log-likelihood-ratio] 56s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 56s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 56s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 56s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 56s [--processes PROCESSES] 56s [--corrected-group CORRECTED_GROUP] 56s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 56s [--quiet] [--help] 56s 56s Required Argument: 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s Directories containing fast5 files. 56s --statistics-file-basename STATISTICS_FILE_BASENAME 56s File base name to save base by base statistics from 56s testing. Filenames will be [--statistics-file- 56s basename].[--alternate-bases]?.tombo.stats 56s --alternate-bases {6mA,dcm,dam,5mC,CpG} [{6mA,dcm,dam,5mC,CpG} ...] 56s Default non-standard base model for testing (not 56s required if user created --alternate-model-filenames 56s is provided). 56s 56s Comparison Arguments: 56s --print-available-models 56s Print available alternative models and exit. 56s --dna Explicitly select canonical DNA model. Default: 56s Automatically determine from FAST5s 56s --rna Explicitly select canonical RNA model. Default: 56s Automatically determine from FAST5s 56s 56s Significance Test Arguments: 56s --minimum-test-reads MINIMUM_TEST_READS 56s Number of reads required at a position to perform 56s significance testing or contribute to model 56s estimation. Default: 1 56s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 56s Log likelihood ratio threshold when computing fraction 56s of significant reads at each genomic position. If two 56s values are provided, statistics between these values 56s are not considered. Default thresholds: DNA:-1.5-2.5 , 56s RNA:-2.5-2.5 56s --standard-log-likelihood-ratio 56s Use a standard log likelihood ratio (LLR) statistic. 56s Default is to use an outlier-robust LLR-like 56s statistic. Detail in full online documentation. 56s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 56s Dampen fraction modified estimates for low coverage 56s sites. Two parameters are unmodified and modified 56s pseudo read counts. This is equivalent to a beta prior 56s on the fraction estimate. Set to "0 0" to disable 56s dampened fraction estimation. Default: [2, 0] 56s 56s Output Argument: 56s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 56s Base for binary files containing per-read statistics 56s from statistical testing. Filenames will be [--per- 56s read-statistics-basename].[--alternate- 56s bases]?.tombo.per_read_stats 56s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 56s Number of the most significant sites to store for 56s faster access. If a longer list of most significant 56s sites is required the list must be re-computed from 56s all batches. Very large values can increase RAM usage. 56s Default: 100000 56s 56s Multiprocessing Arguments: 56s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 56s Size of regions over which to multiprocesses statistic 56s computation. For very deep samples a smaller value is 56s recommmended in order to control memory consumption. 56s Default: 10000 56s --processes PROCESSES 56s Number of processes. Default: 1 56s 56s FAST5 Data Arguments: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 56s FAST5 subgroup(s) (under /Analyses/[--basecall- 56s group]/) containing basecalls and created within 56s [--corrected-group] containing re-squiggle results. 56s Default: ['BaseCalled_template'] 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo detect_modifications model_sample_compare 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s --statistics-file-basename STATISTICS_FILE_BASENAME 56s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 56s [--sample-only-estimates] 56s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 56s [--dna] [--rna] 56s [--fishers-method-context FISHERS_METHOD_CONTEXT] 56s [--minimum-test-reads MINIMUM_TEST_READS] 56s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 56s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 56s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 56s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 56s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 56s [--processes PROCESSES] 56s [--corrected-group CORRECTED_GROUP] 56s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 56s [--quiet] [--help] 56s 56s Required Argument: 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s Directories containing fast5 files. 56s --statistics-file-basename STATISTICS_FILE_BASENAME 56s File base name to save base by base statistics from 56s testing. Filenames will be [--statistics-file- 56s basename].[--alternate-bases]?.tombo.stats 56s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 56s Set of directories containing fast5 files for control 56s reads, containing only canonical nucleotides. 56s 56s Model Prior Arguments: 56s --sample-only-estimates 56s Only use canonical sample to estimate expected signal 56s level and spread. Default: Use canonical model to 56s improve estimtates (esp. for low coverage regions) 56s using baysian posterior estimates. 56s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 56s Prior weights (one each for mean and spread) applied 56s to canonical base model for estimating posterior model 56s parameters for sample comparison. Default: [5, 40] 56s --dna Explicitly select canonical DNA model. Default: 56s Automatically determine from FAST5s 56s --rna Explicitly select canonical RNA model. Default: 56s Automatically determine from FAST5s 56s 56s Significance Test Arguments: 56s --fishers-method-context FISHERS_METHOD_CONTEXT 56s Number of context bases up and downstream over which 56s to compute Fisher's method combined p-values. Note: 56s Not applicable for alternative model likelihood ratio 56s tests. Default: 1. 56s --minimum-test-reads MINIMUM_TEST_READS 56s Number of reads required at a position to perform 56s significance testing or contribute to model 56s estimation. Default: 1 56s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 56s P-value threshold when computing fraction of 56s significant reads at each genomic position. If two 56s values are provided, statistics between these values 56s are not considered. Default thresholds: DNA:0.15-0.5 , 56s RNA:0.05-0.4 56s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 56s Dampen fraction modified estimates for low coverage 56s sites. Two parameters are unmodified and modified 56s pseudo read counts. This is equivalent to a beta prior 56s on the fraction estimate. Set to "0 0" to disable 56s dampened fraction estimation. Default: [2, 0] 56s 56s Output Argument: 56s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 56s Base for binary files containing per-read statistics 56s from statistical testing. Filenames will be [--per- 56s read-statistics-basename].[--alternate- 56s bases]?.tombo.per_read_stats 56s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 56s Number of the most significant sites to store for 56s faster access. If a longer list of most significant 56s sites is required the list must be re-computed from 56s all batches. Very large values can increase RAM usage. 56s Default: 100000 56s 56s Multiprocessing Arguments: 56s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 56s Size of regions over which to multiprocesses statistic 56s computation. For very deep samples a smaller value is 56s recommmended in order to control memory consumption. 56s Default: 10000 56s --processes PROCESSES 56s Number of processes. Default: 1 56s 56s FAST5 Data Arguments: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 56s FAST5 subgroup(s) (under /Analyses/[--basecall- 56s group]/) containing basecalls and created within 56s [--corrected-group] containing re-squiggle results. 56s Default: ['BaseCalled_template'] 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo detect_modifications level_sample_compare 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s --statistics-file-basename STATISTICS_FILE_BASENAME 56s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 56s [--fishers-method-context FISHERS_METHOD_CONTEXT] 56s [--minimum-test-reads MINIMUM_TEST_READS] 56s [--statistic-type {ks,u,t}] 56s [--store-p-value] 56s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 56s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 56s [--processes PROCESSES] 56s [--corrected-group CORRECTED_GROUP] 56s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 56s [--quiet] [--help] 56s 56s Required Argument: 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s Directories containing fast5 files. 56s --statistics-file-basename STATISTICS_FILE_BASENAME 56s File base name to save base by base statistics from 56s testing. Filenames will be [--statistics-file- 56s basename].[--alternate-bases]?.tombo.stats 56s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 56s Set of directories containing fast5 files for 56s alternate set of reads. 56s 56s Significance Test Arguments: 56s --fishers-method-context FISHERS_METHOD_CONTEXT 56s Number of context bases up and downstream over which 56s to compute Fisher's method combined p-values. Note: 56s Not applicable for alternative model likelihood ratio 56s tests. Default: 1. 56s --minimum-test-reads MINIMUM_TEST_READS 56s Number of reads required at a position to perform 56s significance testing or contribute to model 56s estimation. Default: 50 56s --statistic-type {ks,u,t} 56s Type of statistical test to apply. Default: "ks" 56s --store-p-value Store p-value instead of effect-size statistic. 56s Statistics are D-statistic (KS-test), deviation from 56s even common language effect size (u-test), and Cohen's 56s D (t-test). 56s 56s Output Argument: 56s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 56s Number of the most significant sites to store for 56s faster access. If a longer list of most significant 56s sites is required the list must be re-computed from 56s all batches. Very large values can increase RAM usage. 56s Default: 100000 56s 56s Multiprocessing Arguments: 56s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 56s Size of regions over which to multiprocesses statistic 56s computation. For very deep samples a smaller value is 56s recommmended in order to control memory consumption. 56s Default: 10000 56s --processes PROCESSES 56s Number of processes. Default: 1 56s 56s FAST5 Data Arguments: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 56s FAST5 subgroup(s) (under /Analyses/[--basecall- 56s group]/) containing basecalls and created within 56s [--corrected-group] containing re-squiggle results. 56s Default: ['BaseCalled_template'] 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo detect_modifications aggregate_per_read_stats 56s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 56s --statistics-filename STATISTICS_FILENAME 56s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 56s [--minimum-test-reads MINIMUM_TEST_READS] 56s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 56s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 56s [--processes PROCESSES] 56s [--corrected-group CORRECTED_GROUP] 56s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 56s [--quiet] [--help] 56s 56s Required Argument: 56s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 56s Binary file containing per-read statistics from 56s statistical testing. 56s --statistics-filename STATISTICS_FILENAME 56s File to save/load genomic base anchored statistics. 56s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 56s P-value or log likelihood ratio threshold when 56s computing fraction of significant reads at each 56s genomic position. If two values are provided, 56s statistics between these values are not considered. 56s 56s Significance Test Arguments: 56s --minimum-test-reads MINIMUM_TEST_READS 56s Number of reads required at a position to perform 56s significance testing or contribute to model 56s estimation. Default: 1 56s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 56s Dampen fraction modified estimates for low coverage 56s sites. Two parameters are unmodified and modified 56s pseudo read counts. This is equivalent to a beta prior 56s on the fraction estimate. Set to "0 0" to disable 56s dampened fraction estimation. Default: [2, 0] 56s 56s Output Argument: 56s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 56s Number of the most significant sites to store for 56s faster access. If a longer list of most significant 56s sites is required the list must be re-computed from 56s all batches. Very large values can increase RAM usage. 56s Default: 100000 56s 56s Multiprocessing Arguments: 56s --processes PROCESSES 56s Number of processes. Default: 1 56s 56s FAST5 Data Arguments: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 56s FAST5 subgroup(s) (under /Analyses/[--basecall- 56s group]/) containing basecalls and created within 56s [--corrected-group] containing re-squiggle results. 56s Default: ['BaseCalled_template'] 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo text_output browser_files 56s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 56s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 56s [--statistics-filename STATISTICS_FILENAME] 56s [--genome-fasta GENOME_FASTA] 56s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 56s [--browser-file-basename BROWSER_FILE_BASENAME] 56s [--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} ...]] 56s [--corrected-group CORRECTED_GROUP] 56s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 56s [--quiet] [--help] 56s 56s Data Arguments: 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s Directories containing fast5 files. 56s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 56s Set of directories containing fast5 files for control 56s reads, containing only canonical nucleotides. 56s --statistics-filename STATISTICS_FILENAME 56s File to save/load genomic base anchored statistics. 56s 56s Statistic Motif Filter Arguments: 56s --genome-fasta GENOME_FASTA 56s FASTA file used to re-squiggle. For faster sequence 56s access. 56s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 56s Ground truth, motif centered, modified base 56s descriptions for output filtering. Format descriptions 56s as: "motif:mod_pos:name". The mod_pos indicates the 56s modified base within the motif (1-based index). 56s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 56s output for identification of E. coli dam and dcm 56s methylation. 56s 56s Output Arguments: 56s --browser-file-basename BROWSER_FILE_BASENAME 56s Basename for output browser files. Two files (plus and 56s minus strand) will be produced for each --file-types 56s supplied. Filenames formatted as "[browser-file- 56s basename].[file- 56s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 56s Default: tombo_results 56s --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} ...] 56s Data types of genome browser files to produce. 56s Produced coverage files are in bedGraph format, while 56s all other file types will be in wiggle format 56s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 56s Default: "coverage" 56s 56s FAST5 Data Arguments: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 56s FAST5 subgroup(s) (under /Analyses/[--basecall- 56s group]/) containing basecalls and created within 56s [--corrected-group] containing re-squiggle results. 56s Default: ['BaseCalled_template'] 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo text_output signif_sequence_context 56s --statistics-filename STATISTICS_FILENAME 56s [--genome-fasta GENOME_FASTA] 56s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 56s [--num-regions NUM_REGIONS] 56s [--num-bases NUM_BASES] 56s [--sequences-filename SEQUENCES_FILENAME] 56s [--corrected-group CORRECTED_GROUP] 56s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 56s [--quiet] [--help] 56s 56s Required Argument: 56s --statistics-filename STATISTICS_FILENAME 56s File to save/load genomic base anchored statistics. 56s 56s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 56s --genome-fasta GENOME_FASTA 56s FASTA file used to re-squiggle. For faster sequence 56s access. 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s Directories containing fast5 files. 56s 56s Region Selection Arguments: 56s --num-regions NUM_REGIONS 56s Number of regions to plot. Default: 100 56s --num-bases NUM_BASES 56s Number of bases to plot/output. Default: 15 56s 56s Output Arguments: 56s --sequences-filename SEQUENCES_FILENAME 56s File for sequences from selected regions. Sequences 56s will be stored in FASTA format. Default: 56s tombo_results.significant_regions.fasta. 56s 56s FAST5 Data Arguments: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 56s FAST5 subgroup(s) (under /Analyses/[--basecall- 56s group]/) containing basecalls and created within 56s [--corrected-group] containing re-squiggle results. 56s Default: ['BaseCalled_template'] 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo plot max_coverage 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 56s [--plot-standard-model] 56s [--plot-alternate-model {CpG,dcm,6mA,5mC,dam}] 56s [--overplot-threshold OVERPLOT_THRESHOLD] 56s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 56s [--num-regions NUM_REGIONS] 56s [--num-bases NUM_BASES] 56s [--pdf-filename PDF_FILENAME] 56s [--corrected-group CORRECTED_GROUP] 56s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 56s [--quiet] [--help] 56s 56s Required Argument: 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s Directories containing fast5 files. 56s 56s Comparison Arguments: 56s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 56s Set of directories containing fast5 files for control 56s reads, containing only canonical nucleotides. 56s --plot-standard-model 56s Add default standard model distribution to the plot. 56s --plot-alternate-model {CpG,dcm,6mA,5mC,dam} 56s Add alternative model distribution to the plot. 56s 56s Overplotting Arguments: 56s --overplot-threshold OVERPLOT_THRESHOLD 56s Coverage level to trigger alternative plot type 56s instead of raw signal. Default: 50 56s --overplot-type {Downsample,Boxplot,Quantile,Density} 56s Plot type for regions with higher coverage. Default: 56s Downsample 56s 56s Plotting Region Arguments: 56s --num-regions NUM_REGIONS 56s Number of regions to plot. Default: 10 56s --num-bases NUM_BASES 56s Number of bases to plot/output. Default: 21 56s 56s Output Argument: 56s --pdf-filename PDF_FILENAME 56s PDF filename to store plot(s). Default: 56s tombo_results.max_coverage.pdf 56s 56s FAST5 Data Arguments: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 56s FAST5 subgroup(s) (under /Analyses/[--basecall- 56s group]/) containing basecalls and created within 56s [--corrected-group] containing re-squiggle results. 56s Default: ['BaseCalled_template'] 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 56s usage: tombo plot genome_locations 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 56s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 56s [--plot-standard-model] 56s [--plot-alternate-model {dcm,5mC,6mA,CpG,dam}] 56s [--overplot-threshold OVERPLOT_THRESHOLD] 56s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 56s [--num-bases NUM_BASES] 56s [--pdf-filename PDF_FILENAME] 56s [--corrected-group CORRECTED_GROUP] 56s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 56s [--quiet] [--help] 56s 56s Required Arguments: 56s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 56s Directories containing fast5 files. 56s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 56s Genomic locations at which to plot signal. Format 56s locations as "chrm:position[:strand] 56s [chrm2:position2[:strand2] ...]" (strand not 56s applicable for all applications) 56s 56s Comparison Arguments: 56s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 56s Set of directories containing fast5 files for control 56s reads, containing only canonical nucleotides. 56s --plot-standard-model 56s Add default standard model distribution to the plot. 56s --plot-alternate-model {dcm,5mC,6mA,CpG,dam} 56s Add alternative model distribution to the plot. 56s 56s Overplotting Arguments: 56s --overplot-threshold OVERPLOT_THRESHOLD 56s Coverage level to trigger alternative plot type 56s instead of raw signal. Default: 50 56s --overplot-type {Downsample,Boxplot,Quantile,Density} 56s Plot type for regions with higher coverage. Default: 56s Downsample 56s 56s Plotting Region Argument: 56s --num-bases NUM_BASES 56s Number of bases to plot/output. Default: 21 56s 56s Output Argument: 56s --pdf-filename PDF_FILENAME 56s PDF filename to store plot(s). Default: 56s tombo_results.genome_locations.pdf 56s 56s FAST5 Data Arguments: 56s --corrected-group CORRECTED_GROUP 56s FAST5 group created by resquiggle command. Default: 56s RawGenomeCorrected_000 56s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 56s FAST5 subgroup(s) (under /Analyses/[--basecall- 56s group]/) containing basecalls and created within 56s [--corrected-group] containing re-squiggle results. 56s Default: ['BaseCalled_template'] 56s 56s Miscellaneous Arguments: 56s --quiet, -q Don't print status information. 56s --help, -h Print this help message and exit 57s usage: tombo plot motif_centered 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s --motif MOTIF --genome-fasta GENOME_FASTA 57s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 57s [--plot-standard-model] 57s [--plot-alternate-model {dcm,dam,CpG,6mA,5mC}] 57s [--overplot-threshold OVERPLOT_THRESHOLD] 57s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 57s [--num-regions NUM_REGIONS] 57s [--num-bases NUM_BASES] [--deepest-coverage] 57s [--pdf-filename PDF_FILENAME] 57s [--corrected-group CORRECTED_GROUP] 57s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 57s [--quiet] [--help] 57s 57s Required Arguments: 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s Directories containing fast5 files. 57s --motif MOTIF Motif of interest at which to plot signal and 57s statsitics. Supports IUPAC single letter codes (use T 57s for RNA). 57s --genome-fasta GENOME_FASTA 57s FASTA file used to re-squiggle. For faster sequence 57s access. 57s 57s Comparison Arguments: 57s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 57s Set of directories containing fast5 files for control 57s reads, containing only canonical nucleotides. 57s --plot-standard-model 57s Add default standard model distribution to the plot. 57s --plot-alternate-model {dcm,dam,CpG,6mA,5mC} 57s Add alternative model distribution to the plot. 57s 57s Overplotting Arguments: 57s --overplot-threshold OVERPLOT_THRESHOLD 57s Coverage level to trigger alternative plot type 57s instead of raw signal. Default: 50 57s --overplot-type {Downsample,Boxplot,Quantile,Density} 57s Plot type for regions with higher coverage. Default: 57s Downsample 57s 57s Plotting Region Arguments: 57s --num-regions NUM_REGIONS 57s Number of regions to plot. Default: 10 57s --num-bases NUM_BASES 57s Number of bases to plot/output. Default: 21 57s --deepest-coverage Plot the deepest coverage regions. 57s 57s Output Argument: 57s --pdf-filename PDF_FILENAME 57s PDF filename to store plot(s). Default: 57s tombo_results.motif_centered.pdf 57s 57s FAST5 Data Arguments: 57s --corrected-group CORRECTED_GROUP 57s FAST5 group created by resquiggle command. Default: 57s RawGenomeCorrected_000 57s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 57s FAST5 subgroup(s) (under /Analyses/[--basecall- 57s group]/) containing basecalls and created within 57s [--corrected-group] containing re-squiggle results. 57s Default: ['BaseCalled_template'] 57s 57s Miscellaneous Arguments: 57s --quiet, -q Don't print status information. 57s --help, -h Print this help message and exit 57s usage: tombo plot max_difference 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 57s [--overplot-threshold OVERPLOT_THRESHOLD] 57s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 57s [--num-regions NUM_REGIONS] 57s [--num-bases NUM_BASES] 57s [--pdf-filename PDF_FILENAME] 57s [--sequences-filename SEQUENCES_FILENAME] 57s [--corrected-group CORRECTED_GROUP] 57s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 57s [--quiet] [--help] 57s 57s Required Arguments: 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s Directories containing fast5 files. 57s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 57s Set of directories containing fast5 files for control 57s reads, containing only canonical nucleotides. 57s 57s Overplotting Arguments: 57s --overplot-threshold OVERPLOT_THRESHOLD 57s Coverage level to trigger alternative plot type 57s instead of raw signal. Default: 50 57s --overplot-type {Downsample,Boxplot,Quantile,Density} 57s Plot type for regions with higher coverage. Default: 57s Downsample 57s 57s Plotting Region Arguments: 57s --num-regions NUM_REGIONS 57s Number of regions to plot. Default: 10 57s --num-bases NUM_BASES 57s Number of bases to plot/output. Default: 21 57s 57s Output Arguments: 57s --pdf-filename PDF_FILENAME 57s PDF filename to store plot(s). Default: 57s tombo_results.max_difference.pdf 57s --sequences-filename SEQUENCES_FILENAME 57s File for sequences from selected regions. Sequences 57s will be stored in FASTA format. Default: None. 57s 57s FAST5 Data Arguments: 57s --corrected-group CORRECTED_GROUP 57s FAST5 group created by resquiggle command. Default: 57s RawGenomeCorrected_000 57s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 57s FAST5 subgroup(s) (under /Analyses/[--basecall- 57s group]/) containing basecalls and created within 57s [--corrected-group] containing re-squiggle results. 57s Default: ['BaseCalled_template'] 57s 57s Miscellaneous Arguments: 57s --quiet, -q Don't print status information. 57s --help, -h Print this help message and exit 57s usage: tombo plot most_significant 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s --statistics-filename STATISTICS_FILENAME 57s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 57s [--plot-standard-model] 57s [--plot-alternate-model {5mC,CpG,dam,dcm,6mA}] 57s [--overplot-threshold OVERPLOT_THRESHOLD] 57s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 57s [--num-regions NUM_REGIONS] 57s [--num-bases NUM_BASES] 57s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 57s [--pdf-filename PDF_FILENAME] 57s [--sequences-filename SEQUENCES_FILENAME] 57s [--corrected-group CORRECTED_GROUP] 57s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 57s [--quiet] [--help] 57s 57s Required Arguments: 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s Directories containing fast5 files. 57s --statistics-filename STATISTICS_FILENAME 57s File to save/load genomic base anchored statistics. 57s 57s Comparison Arguments: 57s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 57s Set of directories containing fast5 files for control 57s reads, containing only canonical nucleotides. 57s --plot-standard-model 57s Add default standard model distribution to the plot. 57s --plot-alternate-model {5mC,CpG,dam,dcm,6mA} 57s Add alternative model distribution to the plot. 57s 57s Overplotting Arguments: 57s --overplot-threshold OVERPLOT_THRESHOLD 57s Coverage level to trigger alternative plot type 57s instead of raw signal. Default: 50 57s --overplot-type {Downsample,Boxplot,Quantile,Density} 57s Plot type for regions with higher coverage. Default: 57s Downsample 57s 57s Plotting Region Arguments: 57s --num-regions NUM_REGIONS 57s Number of regions to plot. Default: 10 57s --num-bases NUM_BASES 57s Number of bases to plot/output. Default: 21 57s 57s Statistical Argument: 57s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 57s Dampen fraction modified estimates for low coverage 57s sites. Two parameters are unmodified and modified 57s pseudo read counts. This is equivalent to a beta prior 57s on the fraction estimate. Set to "0 0" to disable 57s dampened fraction estimation. Default: [2, 0] 57s 57s Output Arguments: 57s --pdf-filename PDF_FILENAME 57s PDF filename to store plot(s). Default: 57s tombo_results.significant_difference.pdf 57s --sequences-filename SEQUENCES_FILENAME 57s File for sequences from selected regions. Sequences 57s will be stored in FASTA format. Default: None. 57s 57s FAST5 Data Arguments: 57s --corrected-group CORRECTED_GROUP 57s FAST5 group created by resquiggle command. Default: 57s RawGenomeCorrected_000 57s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 57s FAST5 subgroup(s) (under /Analyses/[--basecall- 57s group]/) containing basecalls and created within 57s [--corrected-group] containing re-squiggle results. 57s Default: ['BaseCalled_template'] 57s 57s Miscellaneous Arguments: 57s --quiet, -q Don't print status information. 57s --help, -h Print this help message and exit 57s usage: tombo plot motif_with_stats 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s --motif MOTIF 57s --statistics-filename STATISTICS_FILENAME 57s --genome-fasta GENOME_FASTA 57s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 57s [--plot-standard-model] 57s [--plot-alternate-model {6mA,dam,dcm,CpG,5mC}] 57s [--overplot-threshold OVERPLOT_THRESHOLD] 57s [--num-regions NUM_REGIONS] 57s [--num-context NUM_CONTEXT] 57s [--num-statistics NUM_STATISTICS] 57s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 57s [--pdf-filename PDF_FILENAME] 57s [--corrected-group CORRECTED_GROUP] 57s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 57s [--quiet] [--help] 57s 57s Required Arguments: 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s Directories containing fast5 files. 57s --motif MOTIF Motif of interest at which to plot signal and 57s statsitics. Supports IUPAC single letter codes (use T 57s for RNA). 57s --statistics-filename STATISTICS_FILENAME 57s File to save/load genomic base anchored statistics. 57s --genome-fasta GENOME_FASTA 57s FASTA file used to re-squiggle. For faster sequence 57s access. 57s 57s Comparison Arguments: 57s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 57s Set of directories containing fast5 files for control 57s reads, containing only canonical nucleotides. 57s --plot-standard-model 57s Add default standard model distribution to the plot. 57s --plot-alternate-model {6mA,dam,dcm,CpG,5mC} 57s Add alternative model distribution to the plot. 57s 57s Overplotting Argument: 57s --overplot-threshold OVERPLOT_THRESHOLD 57s Coverage level to trigger alternative plot type 57s instead of raw signal. Default: 50 57s 57s Plotting Region Arguments: 57s --num-regions NUM_REGIONS 57s Number of regions to plot. Default: 3 57s --num-context NUM_CONTEXT 57s Number of context bases around motif. Default: 5 57s --num-statistics NUM_STATISTICS 57s Number of motif centered regions to include in 57s statistic distributions. Default: 200 57s 57s Statistical Argument: 57s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 57s Dampen fraction modified estimates for low coverage 57s sites. Two parameters are unmodified and modified 57s pseudo read counts. This is equivalent to a beta prior 57s on the fraction estimate. Set to "0 0" to disable 57s dampened fraction estimation. Default: [2, 0] 57s 57s Output Argument: 57s --pdf-filename PDF_FILENAME 57s PDF filename to store plot(s). Default: 57s tombo_results.motif_statistics.pdf 57s 57s FAST5 Data Arguments: 57s --corrected-group CORRECTED_GROUP 57s FAST5 group created by resquiggle command. Default: 57s RawGenomeCorrected_000 57s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 57s FAST5 subgroup(s) (under /Analyses/[--basecall- 57s group]/) containing basecalls and created within 57s [--corrected-group] containing re-squiggle results. 57s Default: ['BaseCalled_template'] 57s 57s Miscellaneous Arguments: 57s --quiet, -q Don't print status information. 57s --help, -h Print this help message and exit 57s usage: tombo plot per_read 57s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 57s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 57s [--genome-fasta GENOME_FASTA] 57s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 57s [--num-reads NUM_READS] [--num-bases NUM_BASES] 57s [--box-center] [--pdf-filename PDF_FILENAME] 57s [--corrected-group CORRECTED_GROUP] 57s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 57s [--quiet] [--help] 57s 57s Required Arguments: 57s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 57s Genomic locations at which to plot signal. Format 57s locations as "chrm:position[:strand] 57s [chrm2:position2[:strand2] ...]" (strand not 57s applicable for all applications) 57s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 57s Binary file containing per-read statistics from 57s statistical testing. 57s 57s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 57s --genome-fasta GENOME_FASTA 57s FASTA file used to re-squiggle. For faster sequence 57s access. 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s Directories containing fast5 files. 57s 57s Plotting Region Arguments: 57s --num-reads NUM_READS 57s Number of reads to plot. Default: 100 57s --num-bases NUM_BASES 57s Number of bases to plot/output. Default: 51 57s --box-center Plot a box around the central base. 57s 57s Output Argument: 57s --pdf-filename PDF_FILENAME 57s PDF filename to store plot(s). Default: 57s tombo_results.per_read_stats.pdf 57s 57s FAST5 Data Arguments: 57s --corrected-group CORRECTED_GROUP 57s FAST5 group created by resquiggle command. Default: 57s RawGenomeCorrected_000 57s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 57s FAST5 subgroup(s) (under /Analyses/[--basecall- 57s group]/) containing basecalls and created within 57s [--corrected-group] containing re-squiggle results. 57s Default: ['BaseCalled_template'] 57s 57s Miscellaneous Arguments: 57s --quiet, -q Don't print status information. 57s --help, -h Print this help message and exit 57s usage: tombo plot roc 57s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 57s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 57s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 57s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 57s [--genome-fasta GENOME_FASTA] 57s [--pdf-filename PDF_FILENAME] 57s [--statistics-per-block STATISTICS_PER_BLOCK] 57s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 57s [--quiet] [--help] 57s 57s Required Argument: 57s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 57s Files to load genomic base anchored statistics. 57s 57s Ground Truth Arguments (provide bed files or motifs): 57s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 57s Modification description and bed format files 57s containing single base locations of ground truth 57s modified sites. Bed files should contain 6 fields 57s including strand. Format descriptions as 57s "mod_name:locs.bed". Example: "CpG 57s bisulfite":bisulfite_locs.bed 57s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 57s Bed format files containing single base locations of 57s ground truth unmodified sites. Bed files should 57s contain 6 fields including strand. 57s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 57s Ground truth, motif centered, modified base 57s descriptions for computing ROC and PR curves. Each 57s statistics file is associated with a set of motif 57s descriptions. Format descriptions as: 57s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 57s mod_pos indicates the alternate-base within the motif 57s (1-based index). Example: CCWGG:2:"dcm 57s 5mC"::GATC:2:"dam 6mA" would assess the performance of 57s a single Tombo statistics file for identification of 57s E. coli dam and dcm methylation. 57s --genome-fasta GENOME_FASTA 57s FASTA file used to re-squiggle. For faster sequence 57s access. 57s 57s Output Arguments: 57s --pdf-filename PDF_FILENAME 57s PDF filename to store plot(s). Default: 57s tombo_results.roc.pdf 57s 57s Down-sampling Arguments: 57s --statistics-per-block STATISTICS_PER_BLOCK 57s Number of randomly selected per-read, per-base 57s statistics to extract from each genomic block for 57s plotting. Default: Include all stats 57s --total-statistics-limit TOTAL_STATISTICS_LIMIT 57s Total per-read statistics to be extracted for 57s plotting. Avoids memory overflow for large runs. 57s Default: 5000000 57s 57s Miscellaneous Arguments: 57s --quiet, -q Don't print status information. 57s --help, -h Print this help message and exit 57s usage: tombo plot per_read_roc 57s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 57s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 57s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 57s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 57s [--genome-fasta GENOME_FASTA] 57s [--statistics-per-block STATISTICS_PER_BLOCK] 57s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 57s [--pdf-filename PDF_FILENAME] [--quiet] 57s [--help] 57s 57s Required Argument: 57s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 57s Binary files containing per-read statistics from 57s statistical testing. 57s 57s Ground Truth Arguments (provide bed files or motifs): 57s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 57s Modification description and bed format files 57s containing single base locations of ground truth 57s modified sites. Bed files should contain 6 fields 57s including strand. Format descriptions as 57s "mod_name:locs.bed". Example: "CpG 57s bisulfite":bisulfite_locs.bed 57s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 57s Bed format files containing single base locations of 57s ground truth unmodified sites. Bed files should 57s contain 6 fields including strand. 57s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 57s Ground truth, motif centered, modified base 57s descriptions for computing ROC and PR curves. Each 57s statistics file is associated with a set of motif 57s descriptions. Format descriptions as: 57s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 57s mod_pos indicates the alternate-base within the motif 57s (1-based index). Example: CCWGG:2:"dcm 57s 5mC"::GATC:2:"dam 6mA" would assess the performance of 57s a single Tombo statistics file for identification of 57s E. coli dam and dcm methylation. 57s --genome-fasta GENOME_FASTA 57s FASTA file used to re-squiggle. For faster sequence 57s access. 57s 57s Down-sampling Arguments: 57s --statistics-per-block STATISTICS_PER_BLOCK 57s Number of randomly selected per-read, per-base 57s statistics to extract from each genomic block for 57s plotting. Default: 100000 57s --total-statistics-limit TOTAL_STATISTICS_LIMIT 57s Total per-read statistics to be extracted for 57s plotting. Avoids memory overflow for large runs. 57s Default: 5000000 57s 57s Output Arguments: 57s --pdf-filename PDF_FILENAME 57s PDF filename to store plot(s). Default: 57s tombo_results.per_reads_roc.pdf 57s 57s Miscellaneous Arguments: 57s --quiet, -q Don't print status information. 57s --help, -h Print this help message and exit 57s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s [--upstream-bases {0,1,2,3,4}] 57s [--downstream-bases {0,1,2,3,4}] [--read-mean] 57s [--num-kmer-threshold NUM_KMER_THRESHOLD] 57s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 57s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 57s [--corrected-group CORRECTED_GROUP] 57s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 57s [--quiet] [--help] 57s 57s Required Argument: 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s Directories containing fast5 files. 57s 57s Data Processing Arguments: 57s --upstream-bases {0,1,2,3,4} 57s Upstream bases in k-mer. Default: 1 57s --downstream-bases {0,1,2,3,4} 57s Downstream bases in k-mer. Default: 2 57s --read-mean Plot k-mer means across whole reads as opposed to 57s individual k-mer event levels. 57s --num-kmer-threshold NUM_KMER_THRESHOLD 57s Observations of each k-mer required to include a read 57s in read level averages. Default: 1 57s 57s Plotting Region Arguments: 57s --num-reads NUM_READS 57s Number of reads to plot. Default: 100 57s 57s Output Arguments: 57s --pdf-filename PDF_FILENAME 57s PDF filename to store plot(s). Default: 57s tombo_results.kmer_distribution.pdf 57s --r-data-filename R_DATA_FILENAME 57s Filename to save R data structure. Default: Don't save 57s --dont-plot Don't plot result. Useful to produce only R data file. 57s 57s FAST5 Data Arguments: 57s --corrected-group CORRECTED_GROUP 57s FAST5 group created by resquiggle command. Default: 57s RawGenomeCorrected_000 57s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 57s FAST5 subgroup(s) (under /Analyses/[--basecall- 57s group]/) containing basecalls and created within 57s [--corrected-group] containing re-squiggle results. 57s Default: ['BaseCalled_template'] 57s 57s Miscellaneous Arguments: 57s --quiet, -q Don't print status information. 57s --help, -h Print this help message and exit 57s usage: tombo plot cluster_most_significant 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 57s --statistics-filename STATISTICS_FILENAME 57s [--genome-fasta GENOME_FASTA] 57s [--processes PROCESSES] 57s [--num-regions NUM_REGIONS] 57s [--num-bases NUM_BASES] 57s [--slide-span SLIDE_SPAN] 57s [--pdf-filename PDF_FILENAME] 57s [--r-data-filename R_DATA_FILENAME] 57s [--corrected-group CORRECTED_GROUP] 57s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 57s [--quiet] [--help] 57s 57s Required Arguments: 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s Directories containing fast5 files. 57s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 57s Set of directories containing fast5 files for control 57s reads, containing only canonical nucleotides. 57s --statistics-filename STATISTICS_FILENAME 57s File to save/load genomic base anchored statistics. 57s 57s FASTA Sequence Argument: 57s --genome-fasta GENOME_FASTA 57s FASTA file used to re-squiggle. For faster sequence 57s access. 57s 57s Multiprocessing Argument: 57s --processes PROCESSES 57s Number of processes. Default: 1 57s 57s Plotting Region Arguments: 57s --num-regions NUM_REGIONS 57s Number of regions to plot. Default: 10 57s --num-bases NUM_BASES 57s Number of bases to plot/output. Default: 21 57s --slide-span SLIDE_SPAN 57s Number of bases offset over which to search when 57s computing distances for signal cluster plotting. 57s Default: 0 (exact position) 57s 57s Output Arguments: 57s --pdf-filename PDF_FILENAME 57s PDF filename to store plot(s). Default: 57s tombo_results.signal_clusters.pdf 57s --r-data-filename R_DATA_FILENAME 57s Filename to save R data structure. Default: Don't save 57s 57s FAST5 Data Arguments: 57s --corrected-group CORRECTED_GROUP 57s FAST5 group created by resquiggle command. Default: 57s RawGenomeCorrected_000 57s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 57s FAST5 subgroup(s) (under /Analyses/[--basecall- 57s group]/) containing basecalls and created within 57s [--corrected-group] containing re-squiggle results. 57s Default: ['BaseCalled_template'] 57s 57s Miscellaneous Arguments: 57s --quiet, -q Don't print status information. 57s --help, -h Print this help message and exit 57s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 57s 57s Required Arguments: 57s fast5s_basedir Directory containing fast5 files. All files ending in 57s "fast5" found recursively within this base directory will be 57s processed. 57s 57s Miscellaneous Arguments: 57s --quiet, -q Don't print status information. 57s --help, -h Print this help message and exit 57s usage: tombo build_model event_resquiggle 57s [--minimap2-executable MINIMAP2_EXECUTABLE] 57s [--minimap2-index MINIMAP2_INDEX] 57s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 57s [--graphmap-executable GRAPHMAP_EXECUTABLE] 57s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 57s [--normalization-type {median,pA,pA_raw,none}] 57s [--pore-model-filename PORE_MODEL_FILENAME] 57s [--outlier-threshold OUTLIER_THRESHOLD] 57s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 57s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 57s [--timeout TIMEOUT] 57s [--cpts-limit CPTS_LIMIT] 57s [--skip-index] [--overwrite] 57s [--failed-reads-filename FAILED_READS_FILENAME] 57s [--include-event-stdev] 57s [--corrected-group CORRECTED_GROUP] 57s [--basecall-group BASECALL_GROUP] 57s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 57s [--processes PROCESSES] 57s [--align-processes ALIGN_PROCESSES] 57s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 57s [--resquiggle-processes RESQUIGGLE_PROCESSES] 57s [--quiet] [--help] 57s fast5s_basedir reference_fasta 57s 57s Required Arguments: 57s fast5s_basedir Directory containing fast5 files. All files ending in 57s "fast5" found recursively within this base directory 57s will be processed. 57s reference_fasta Reference genome/transcriptome FASTA file for mapping. 57s 57s Mapper Arguments (One mapper is required): 57s --minimap2-executable MINIMAP2_EXECUTABLE 57s Path to minimap2 executable. 57s --minimap2-index MINIMAP2_INDEX 57s Path to minimap2 index (with map-ont preset) file 57s corresponding to the [genome_fasta] provided. 57s --bwa-mem-executable BWA_MEM_EXECUTABLE 57s Path to bwa-mem executable. 57s --graphmap-executable GRAPHMAP_EXECUTABLE 57s Path to graphmap executable. 57s --alignment-batch-size ALIGNMENT_BATCH_SIZE 57s Number of reads included in each alignment call. Note: 57s A new system mapping call is made for each batch 57s (including loading of the genome), so it is advised to 57s use larger values for larger genomes. Default: 1000 57s 57s Signal Processing Arguments: 57s --normalization-type {median,pA,pA_raw,none} 57s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 57s as in the ONT events (using offset, range and 57s digitization), "pA": k-mer-based correction for pA 57s drift as in nanopolish (requires [--pore-model- 57s filename]), "median": median and MAD from raw signal. 57s Default: median 57s --pore-model-filename PORE_MODEL_FILENAME 57s File containing kmer model parameters (level_mean and 57s level_stdv) used in order to compute kmer-based 57s corrected pA values. E.g. https://github.com/jts/nanop 57s olish/blob/master/etc/r9- 57s models/template_median68pA.5mers.model 57s --outlier-threshold OUTLIER_THRESHOLD 57s Windosrize the signal at this number of scale values. 57s Negative value disables outlier clipping. Default: 57s 5.000000 57s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 57s Specify the 2 parameters for segmentation 1) running 57s neighboring windows width 2) minimum raw observations 57s per genomic base. Sample type defaults: RNA : 12 6 || 57s DNA : 5 3 57s 57s Read Filtering Arguments: 57s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 57s Filter reads based on observations per base percentile 57s thresholds. Format thresholds as "percentile:thresh 57s [pctl2:thresh2 ...]". For example to filter reads with 57s 99th pctl > 200 obs/base or max > 5k obs/base use 57s "99:200 100:5000". 57s --timeout TIMEOUT Timeout in seconds for processing a single read. 57s Default: No timeout. 57s --cpts-limit CPTS_LIMIT 57s Maximum number of changepoints to find within a single 57s indel group. Default: No limit. 57s 57s Input/Output Arguments: 57s --skip-index Skip creation of tombo index. This drastically slows 57s downstream tombo commands. Default stores tombo index 57s named ".[--fast5-basedir].[--corrected- 57s group].tombo.index" to be loaded automatically for 57s downstream commands. 57s --overwrite Overwrite previous corrected group in FAST5 files. 57s Note: only effects --corrected-group or --new- 57s corrected-group. 57s --failed-reads-filename FAILED_READS_FILENAME 57s Output failed read filenames with assoicated error. 57s Default: Do not store failed reads. 57s --include-event-stdev 57s Include corrected event standard deviation in output 57s FAST5 data. 57s 57s FAST5 Data Arguments: 57s --corrected-group CORRECTED_GROUP 57s FAST5 group created by resquiggle command. Default: 57s RawGenomeCorrected_000 57s --basecall-group BASECALL_GROUP 57s FAST5 group obtain original basecalls (under Analyses 57s group). Default: Basecall_1D_000 57s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 57s FAST5 subgroup(s) (under /Analyses/[--basecall- 57s group]/) containing basecalls and created within 57s [--corrected-group] containing re-squiggle results. 57s Default: ['BaseCalled_template'] 57s 57s Multiprocessing Arguments: 57s --processes PROCESSES 57s Number of processes. Default: 2 57s --align-processes ALIGN_PROCESSES 57s Number of processes to use for parsing and aligning 57s original basecalls. Each process will independently 57s load the genome into memory, so use caution with 57s larger genomes (e.g. human). Default: 1 57s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 57s Number of threads to use for aligner system call. 57s Default: [--processes] / (2 * [--align-processes)] 57s --resquiggle-processes RESQUIGGLE_PROCESSES 57s Number of processes to use for resquiggle algorithm. 57s Default: [--processes] / 2 57s 57s Miscellaneous Arguments: 57s --quiet, -q Don't print status information. 57s --help, -h Print this help message and exit 57s usage: tombo build_model estimate_reference 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s --tombo-model-filename TOMBO_MODEL_FILENAME 57s [--estimate-mean] 57s [--kmer-specific-sd] 57s [--upstream-bases {0,1,2,3,4}] 57s [--downstream-bases {0,1,2,3,4}] 57s [--minimum-test-reads MINIMUM_TEST_READS] 57s [--coverage-threshold COVERAGE_THRESHOLD] 57s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 57s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 57s [--processes PROCESSES] 57s [--corrected-group CORRECTED_GROUP] 57s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 57s [--quiet] [--help] 57s 57s Required Arguments: 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s Directories containing fast5 files. 57s --tombo-model-filename TOMBO_MODEL_FILENAME 57s Filename to save Tombo model. 57s 57s Modeling Arguments: 57s --estimate-mean Use the mean instead of median for model level 57s estimation. Note: This can cause poor fits due to 57s outliers 57s --kmer-specific-sd Estimate standard deviation for each k-mers 57s individually. 57s --upstream-bases {0,1,2,3,4} 57s Upstream bases in k-mer. Default: 1 57s --downstream-bases {0,1,2,3,4} 57s Downstream bases in k-mer. Default: 2 57s 57s Filtering Arguments: 57s --minimum-test-reads MINIMUM_TEST_READS 57s Number of reads required at a position to perform 57s significance testing or contribute to model 57s estimation. Default: 10 57s --coverage-threshold COVERAGE_THRESHOLD 57s Maximum mean coverage per region when estimating k-mer 57s model (limits compute time for deep samples). Default: 57s 100 57s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 57s Number of each k-mer observations required in order to 57s produce a reference (genomic locations for standard 57s reference and per-read for alternative reference). 57s Default: 5 57s 57s Multiprocessing Arguments: 57s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 57s Size of regions over which to multiprocesses statistic 57s computation. For very deep samples a smaller value is 57s recommmended in order to control memory consumption. 57s Default: 10000 57s --processes PROCESSES 57s Number of processes. Default: 1 57s 57s FAST5 Data Arguments: 57s --corrected-group CORRECTED_GROUP 57s FAST5 group created by resquiggle command. Default: 57s RawGenomeCorrected_000 57s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 57s FAST5 subgroup(s) (under /Analyses/[--basecall- 57s group]/) containing basecalls and created within 57s [--corrected-group] containing re-squiggle results. 57s Default: ['BaseCalled_template'] 57s 57s Miscellaneous Arguments: 57s --quiet, -q Don't print status information. 57s --help, -h Print this help message and exit 57s usage: tombo build_model estimate_alt_reference 57s --alternate-model-filename ALTERNATE_MODEL_FILENAME 57s --alternate-model-name ALTERNATE_MODEL_NAME 57s --alternate-model-base {A,C,G,T} 57s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 57s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 57s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 57s [--control-density-filename CONTROL_DENSITY_FILENAME] 57s [--dna] [--rna] 57s [--tombo-model-filename TOMBO_MODEL_FILENAME] 57s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 57s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 57s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 57s [--save-density-basename SAVE_DENSITY_BASENAME] 57s [--processes PROCESSES] 57s [--corrected-group CORRECTED_GROUP] 57s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 57s [--quiet] [--help] 57s 57s Required Arguments: 57s --alternate-model-filename ALTERNATE_MODEL_FILENAME 57s Tombo model for alternative likelihood ratio 57s significance testing. 57s --alternate-model-name ALTERNATE_MODEL_NAME 57s A short name to associate with this alternate model 57s (e.g. 5mC, 6mA, etc.). This text will be included in 57s output filenames when this model is used for testing. 57s --alternate-model-base {A,C,G,T} 57s Non-standard base is an alternative to this base. 57s 57s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 57s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 57s Directories containing fast5 files. 57s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 57s Set of directories containing fast5 files for control 57s reads, containing only canonical nucleotides. 57s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 57s File containing k-mer level kernel density estimates 57s for the alternative sample saved using --save-density- 57s basename. 57s --control-density-filename CONTROL_DENSITY_FILENAME 57s File containing k-mer level kernel density estimates 57s for the control sample saved using --save-density- 57s basename. 57s 57s Standard Model Arguments: 57s --dna Explicitly select canonical DNA model. Default: 57s Automatically determine from FAST5s 57s --rna Explicitly select canonical RNA model. Default: 57s Automatically determine from FAST5s 57s --tombo-model-filename TOMBO_MODEL_FILENAME 57s Tombo model filename. If no file is provided, the 57s default DNA or RNA Tombo model will be used. 57s 57s Model Fitting Arguments: 57s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 57s When esitmating the alternative base incorporation 57s rate, this percent of k-mers are assumed to have 57s significantly shifted signal so the alternative 57s distribution minimally overlaps the standard base 57s distribution. Default: 5.000000 57s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 57s Bandwidth applied when performing Gaussian kernal 57s density esitmation on standard and alternative base 57s signal distributions. Default: 0.050000 57s 57s Filtering Argument: 57s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 57s Number of each k-mer observations required in order to 57s produce a reference (genomic locations for standard 57s reference and per-read for alternative reference). 57s Default: 1000 57s 57s Output Argument: 57s --save-density-basename SAVE_DENSITY_BASENAME 57s Basename to save alternative model estimation density 57s estimation information. See scripts/debug_est_alt.R 57s for info use example. Default: Don't save. 57s 57s Multiprocessing Arguments: 57s --processes PROCESSES 57s Number of processes. Default: 1 57s 57s FAST5 Data Arguments: 57s --corrected-group CORRECTED_GROUP 57s FAST5 group created by resquiggle command. Default: 57s RawGenomeCorrected_000 57s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 57s FAST5 subgroup(s) (under /Analyses/[--basecall- 57s group]/) containing basecalls and created within 57s [--corrected-group] containing re-squiggle results. 57s Default: ['BaseCalled_template'] 57s 57s Miscellaneous Arguments: 57s --quiet, -q Don't print status information. 57s --help, -h Print this help message and exit 57s This test only tests the help system 57s There is an extensive test in 57s 57s tombo/tests/shell_tests.sh 57s 57s but this requires to download larger data 57s sets which is not done for the moment. 57s autopkgtest [05:46:17]: test run-unit-test: -----------------------] 58s run-unit-test PASS 58s autopkgtest [05:46:18]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 58s autopkgtest [05:46:18]: @@@@@@@@@@@@@@@@@@@@ summary 58s run-unit-test PASS