0s autopkgtest [17:50:34]: starting date and time: 2025-11-03 17:50:34+0000 0s autopkgtest [17:50:34]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [17:50:34]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.uczdk6bd/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-5.secgroup --name adt-resolute-ppc64el-tombo-20251103-175034-juju-7f2275-prod-proposed-migration-environment-15-57c4b15c-bb98-4432-b6c8-6b1239c1227b --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-ppc64el-tombo-20251103-175034-juju-7f2275-prod-proposed-migration-environment-15-57c4b15c-bb98-4432-b6c8-6b1239c1227b from image adt/ubuntu-resolute-ppc64el-server-20251103.img (UUID f10a73b5-42f3-44c3-8dca-a9a68322386d)... 54s autopkgtest [17:51:28]: testbed dpkg architecture: ppc64el 54s autopkgtest [17:51:28]: testbed apt version: 3.1.11 55s autopkgtest [17:51:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 55s autopkgtest [17:51:29]: testbed release detected to be: None 56s autopkgtest [17:51:30]: updating testbed package index (apt update) 56s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 56s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 56s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 56s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 57s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1066 kB] 57s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [88.2 kB] 57s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 57s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [24.2 kB] 57s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [128 kB] 57s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted ppc64el Packages [940 B] 57s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [667 kB] 57s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [12.4 kB] 57s Fetched 2084 kB in 1s (1675 kB/s) 58s Reading package lists... 59s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 59s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 59s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 59s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 60s Reading package lists... 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Calculating upgrade... 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s autopkgtest [17:51:34]: upgrading testbed (apt dist-upgrade and autopurge) 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Calculating upgrade... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Solving dependencies... 62s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 64s autopkgtest [17:51:38]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:02:41 UTC 2025 64s autopkgtest [17:51:38]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 69s Get:1 http://ftpmaster.internal/ubuntu resolute/universe tombo 1.5.1-7build3 (dsc) [2291 B] 69s Get:2 http://ftpmaster.internal/ubuntu resolute/universe tombo 1.5.1-7build3 (tar) [22.3 MB] 69s Get:3 http://ftpmaster.internal/ubuntu resolute/universe tombo 1.5.1-7build3 (diff) [9656 B] 70s gpgv: Signature made Tue Oct 21 17:53:35 2025 UTC 70s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 70s gpgv: Can't check signature: No public key 70s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7build3.dsc: no acceptable signature found 70s autopkgtest [17:51:44]: testing package tombo version 1.5.1-7build3 70s autopkgtest [17:51:44]: build not needed 74s autopkgtest [17:51:48]: test run-unit-test: preparing testbed 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Solving dependencies... 75s The following NEW packages will be installed: 75s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 75s libhdf5-310 libhdf5-hl-310 libjs-jquery libjs-mathjax libjs-sphinxdoc 75s libjs-underscore liblapack3 liblzf1 libqhull-r8.0 libsz2 python3-decorator 75s python3-h5py python3-h5py-serial python3-mappy python3-numpy 75s python3-numpy-dev python3-packaging python3-scipy python3-tqdm 75s sphinx-rtd-theme-common tombo tombo-doc 75s 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded. 75s Need to get 67.9 MB of archives. 75s After this operation, 271 MB of additional disk space will be used. 75s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-lato all 2.015-1 [2781 kB] 76s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy-dev ppc64el 1:2.2.4+ds-1ubuntu1 [153 kB] 76s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-6build1 [291 kB] 76s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-7ubuntu1 [620 kB] 76s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-6build1 [2960 kB] 76s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy ppc64el 1:2.2.4+ds-1ubuntu1 [4887 kB] 77s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 77s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 77s Get:9 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libaec0 ppc64el 1.1.4-2 [30.3 kB] 77s Get:10 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libsz2 ppc64el 1.1.4-2 [5646 B] 77s Get:11 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhdf5-310 ppc64el 1.14.5+repack-3build1 [1516 kB] 78s Get:12 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhdf5-hl-310 ppc64el 1.14.5+repack-3build1 [74.6 kB] 78s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 78s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 78s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 78s Get:16 http://ftpmaster.internal/ubuntu resolute/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 78s Get:17 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libqhull-r8.0 ppc64el 2020.2-7 [227 kB] 78s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-decorator all 5.2.1-2 [28.1 kB] 78s Get:19 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-h5py-serial ppc64el 3.13.0-1ubuntu1 [1187 kB] 78s Get:20 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-h5py all 3.13.0-1ubuntu1 [8230 B] 78s Get:21 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-mappy ppc64el 2.27+dfsg-1build3 [237 kB] 78s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-packaging all 25.0-1 [52.8 kB] 78s Get:23 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-tqdm all 4.67.1-5 [92.1 kB] 78s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 78s Get:25 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el python3-scipy ppc64el 1.16.3-1 [20.6 MB] 80s Get:26 http://ftpmaster.internal/ubuntu resolute/universe ppc64el tombo ppc64el 1.5.1-7build3 [512 kB] 80s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 81s Get:28 http://ftpmaster.internal/ubuntu resolute/universe ppc64el tombo-doc all 1.5.1-7build3 [21.7 MB] 83s Fetched 67.9 MB in 8s (8702 kB/s) 83s Selecting previously unselected package fonts-lato. 83s (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 ... 76579 files and directories currently installed.) 83s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 83s Unpacking fonts-lato (2.015-1) ... 83s Selecting previously unselected package python3-numpy-dev:ppc64el. 83s Preparing to unpack .../01-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 83s Unpacking python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 83s Selecting previously unselected package libblas3:ppc64el. 83s Preparing to unpack .../02-libblas3_3.12.1-6build1_ppc64el.deb ... 83s Unpacking libblas3:ppc64el (3.12.1-6build1) ... 83s Selecting previously unselected package libgfortran5:ppc64el. 83s Preparing to unpack .../03-libgfortran5_15.2.0-7ubuntu1_ppc64el.deb ... 83s Unpacking libgfortran5:ppc64el (15.2.0-7ubuntu1) ... 83s Selecting previously unselected package liblapack3:ppc64el. 83s Preparing to unpack .../04-liblapack3_3.12.1-6build1_ppc64el.deb ... 83s Unpacking liblapack3:ppc64el (3.12.1-6build1) ... 84s Selecting previously unselected package python3-numpy. 84s Preparing to unpack .../05-python3-numpy_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 84s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 84s Selecting previously unselected package fonts-font-awesome. 84s Preparing to unpack .../06-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 84s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 84s Selecting previously unselected package fonts-mathjax. 84s Preparing to unpack .../07-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 84s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 84s Selecting previously unselected package libaec0:ppc64el. 84s Preparing to unpack .../08-libaec0_1.1.4-2_ppc64el.deb ... 84s Unpacking libaec0:ppc64el (1.1.4-2) ... 84s Selecting previously unselected package libsz2:ppc64el. 84s Preparing to unpack .../09-libsz2_1.1.4-2_ppc64el.deb ... 84s Unpacking libsz2:ppc64el (1.1.4-2) ... 84s Selecting previously unselected package libhdf5-310:ppc64el. 84s Preparing to unpack .../10-libhdf5-310_1.14.5+repack-3build1_ppc64el.deb ... 84s Unpacking libhdf5-310:ppc64el (1.14.5+repack-3build1) ... 84s Selecting previously unselected package libhdf5-hl-310:ppc64el. 84s Preparing to unpack .../11-libhdf5-hl-310_1.14.5+repack-3build1_ppc64el.deb ... 84s Unpacking libhdf5-hl-310:ppc64el (1.14.5+repack-3build1) ... 84s Selecting previously unselected package libjs-jquery. 84s Preparing to unpack .../12-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 84s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 84s Selecting previously unselected package libjs-underscore. 84s Preparing to unpack .../13-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 84s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 84s Selecting previously unselected package libjs-sphinxdoc. 84s Preparing to unpack .../14-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 84s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 84s Selecting previously unselected package liblzf1:ppc64el. 84s Preparing to unpack .../15-liblzf1_3.6-4_ppc64el.deb ... 84s Unpacking liblzf1:ppc64el (3.6-4) ... 84s Selecting previously unselected package libqhull-r8.0:ppc64el. 84s Preparing to unpack .../16-libqhull-r8.0_2020.2-7_ppc64el.deb ... 84s Unpacking libqhull-r8.0:ppc64el (2020.2-7) ... 84s Selecting previously unselected package python3-decorator. 84s Preparing to unpack .../17-python3-decorator_5.2.1-2_all.deb ... 84s Unpacking python3-decorator (5.2.1-2) ... 84s Selecting previously unselected package python3-h5py-serial. 84s Preparing to unpack .../18-python3-h5py-serial_3.13.0-1ubuntu1_ppc64el.deb ... 84s Unpacking python3-h5py-serial (3.13.0-1ubuntu1) ... 84s Selecting previously unselected package python3-h5py. 84s Preparing to unpack .../19-python3-h5py_3.13.0-1ubuntu1_all.deb ... 84s Unpacking python3-h5py (3.13.0-1ubuntu1) ... 84s Selecting previously unselected package python3-mappy. 84s Preparing to unpack .../20-python3-mappy_2.27+dfsg-1build3_ppc64el.deb ... 84s Unpacking python3-mappy (2.27+dfsg-1build3) ... 84s Selecting previously unselected package python3-packaging. 84s Preparing to unpack .../21-python3-packaging_25.0-1_all.deb ... 84s Unpacking python3-packaging (25.0-1) ... 84s Selecting previously unselected package python3-tqdm. 84s Preparing to unpack .../22-python3-tqdm_4.67.1-5_all.deb ... 84s Unpacking python3-tqdm (4.67.1-5) ... 84s Selecting previously unselected package sphinx-rtd-theme-common. 84s Preparing to unpack .../23-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 84s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 84s Selecting previously unselected package python3-scipy. 84s Preparing to unpack .../24-python3-scipy_1.16.3-1_ppc64el.deb ... 84s Unpacking python3-scipy (1.16.3-1) ... 85s Selecting previously unselected package tombo. 85s Preparing to unpack .../25-tombo_1.5.1-7build3_ppc64el.deb ... 85s Unpacking tombo (1.5.1-7build3) ... 85s Selecting previously unselected package libjs-mathjax. 85s Preparing to unpack .../26-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 85s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 86s Selecting previously unselected package tombo-doc. 86s Preparing to unpack .../27-tombo-doc_1.5.1-7build3_all.deb ... 86s Unpacking tombo-doc (1.5.1-7build3) ... 86s Setting up fonts-lato (2.015-1) ... 86s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 86s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 86s Setting up python3-tqdm (4.67.1-5) ... 86s Setting up libqhull-r8.0:ppc64el (2020.2-7) ... 86s Setting up python3-mappy (2.27+dfsg-1build3) ... 86s Setting up libaec0:ppc64el (1.1.4-2) ... 86s Setting up python3-decorator (5.2.1-2) ... 86s Setting up libblas3:ppc64el (3.12.1-6build1) ... 86s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 86s Setting up python3-packaging (25.0-1) ... 86s Setting up liblzf1:ppc64el (3.6-4) ... 86s Setting up python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 86s Setting up libgfortran5:ppc64el (15.2.0-7ubuntu1) ... 86s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 86s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 86s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 86s Setting up libsz2:ppc64el (1.1.4-2) ... 86s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 86s Setting up liblapack3:ppc64el (3.12.1-6build1) ... 86s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 86s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 88s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 88s Setting up tombo-doc (1.5.1-7build3) ... 88s Setting up libhdf5-310:ppc64el (1.14.5+repack-3build1) ... 88s Setting up libhdf5-hl-310:ppc64el (1.14.5+repack-3build1) ... 88s Setting up python3-scipy (1.16.3-1) ... 92s Setting up python3-h5py-serial (3.13.0-1ubuntu1) ... 92s Setting up python3-h5py (3.13.0-1ubuntu1) ... 92s Setting up tombo (1.5.1-7build3) ... 93s Processing triggers for man-db (2.13.1-1) ... 93s Processing triggers for libc-bin (2.42-0ubuntu3) ... 95s autopkgtest [17:52:09]: test run-unit-test: [----------------------- 95s ********* Testing help commands ********** 95s usage: tombo [-h] [-v] 95s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} ... 95s 95s ********** Tombo ********* 95s 95s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 95s 95s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 95s 95s Tombo command groups (additional help available within each command group): 95s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 95s preprocess Pre-process nanopore reads for Tombo processing. 95s filter Apply filter to Tombo index file for specified criterion. 95s detect_modifications Perform statistical testing to detect non-standard nucleotides. 95s text_output Output Tombo results in text files. 95s build_model Create canonical and alternative base Tombo models. 95s plot Save plots to visualize raw nanopore signal or testing results. 95s 95s options: 95s -h, --help show this help message and exit 95s -v, --version show Tombo version and exit. 95s usage: tombo resquiggle [--dna] [--rna] 95s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 95s [--q-score Q_SCORE] 95s [--signal-matching-score SIGNAL_MATCHING_SCORE] 95s [--processes PROCESSES] 95s [--corrected-group CORRECTED_GROUP] 95s [--basecall-group BASECALL_GROUP] 95s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 95s [--overwrite] 95s [--failed-reads-filename FAILED_READS_FILENAME] 95s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 95s [--print-advanced-arguments] [--quiet] [--help] 95s fast5s_basedir reference 95s 95s Required Arguments: 95s fast5s_basedir Directory containing fast5 files. All files ending in 95s "fast5" found recursively within this base directory 95s will be processed. 95s reference Reference genome/transcriptome FASTA file or minimap2 95s index (with "map-ont" preset) for mapping. 95s 95s Model Parameters: 95s --dna Explicitly select canonical DNA model. Default: 95s Automatically determine from FAST5s 95s --rna Explicitly select canonical RNA model. Default: 95s Automatically determine from FAST5s 95s 95s Read Filtering Argument: 95s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 95s Filter reads based on observations per base percentile 95s thresholds. Format thresholds as "percentile:thresh 95s [pctl2:thresh2 ...]". For example to filter reads with 95s 99th pctl > 200 obs/base or max > 5k obs/base use 95s "99:200 100:5000". 95s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 95s Default: 0.000000 95s --signal-matching-score SIGNAL_MATCHING_SCORE 95s Observed to expected signal matching score (higher 95s score indicates poor matching). Sample type defaults: 95s RNA : 2 || DNA : 1.1 95s 95s Multiprocessing Arguments: 95s --processes PROCESSES 95s Number of processes. Default: 1 95s 95s FAST5 Data Arguments: 95s --corrected-group CORRECTED_GROUP 95s FAST5 group created by resquiggle command. Default: 95s RawGenomeCorrected_000 95s --basecall-group BASECALL_GROUP 95s FAST5 group obtain original basecalls (under Analyses 95s group). Default: Basecall_1D_000 95s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 95s FAST5 subgroup(s) (under /Analyses/[--basecall- 95s group]/) containing basecalls and created within 95s [--corrected-group] containing re-squiggle results. 95s Default: ['BaseCalled_template'] 95s --overwrite Overwrite previous corrected group in FAST5 files. 95s Note: only effects --corrected-group or --new- 95s corrected-group. 95s 95s Input/Output Arguments: 95s --failed-reads-filename FAILED_READS_FILENAME 95s Output failed read filenames with assoicated error. 95s Default: Do not store failed reads. 95s --num-most-common-errors NUM_MOST_COMMON_ERRORS 95s Dynamically show this many most common errors so far 95s through run. Default: 0; Just show progress 95s 95s Advanced Arguments: 95s --print-advanced-arguments 95s Print advanced re-squiggle arguments and exit. 95s 95s Miscellaneous Arguments: 95s --quiet, -q Don't print status information. 95s --help, -h Print this help message and exit 95s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 95s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 95s [--basecall-group BASECALL_GROUP] 95s [--basecall-subgroup BASECALL_SUBGROUP] 95s [--overwrite] 95s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 95s [--processes PROCESSES] 95s [--quiet] [--help] 95s 95s Required Arguments: 95s --fast5-basedir FAST5_BASEDIR 95s Directory containing fast5 files. 95s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 95s FASTQ filenames containing basecalls to be added to 95s raw FAST5 files. 95s 95s FAST5 Data Arguments: 95s --basecall-group BASECALL_GROUP 95s FAST5 group obtain original basecalls (under Analyses 95s group). Default: Basecall_1D_000 95s --basecall-subgroup BASECALL_SUBGROUP 95s FAST5 subgroup (under /Analyses/[--basecall-group]/) 95s under which to store basecalls from FASTQs. Default: 95s BaseCalled_template 95s --overwrite Overwrite previous corrected group in FAST5 files. 95s Note: only effects --corrected-group or --new- 95s corrected-group. 95s 95s Sequencing Summary Argument: 95s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 95s Sequencing summary filenames produced by albacore. 95s These can make annotation of raw FAST5 files with 95s FASTQ sequence much faster. 95s 95s Multiprocessing Argument: 95s --processes PROCESSES 95s Number of processes. Default: 1 95s 95s Miscellaneous Arguments: 95s --quiet, -q Don't print status information. 95s --help, -h Print this help message and exit 95s usage: tombo filter clear_filters 95s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 95s [--corrected-group CORRECTED_GROUP] 95s [--quiet] [--help] 95s 95s Required Argument: 95s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 95s Directories containing fast5 files. 95s 95s FAST5 Data Argument: 95s --corrected-group CORRECTED_GROUP 95s FAST5 group created by resquiggle command. Default: 95s RawGenomeCorrected_000 95s 95s Miscellaneous Arguments: 95s --quiet, -q Don't print status information. 95s --help, -h Print this help message and exit 95s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 95s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 95s [--corrected-group CORRECTED_GROUP] [--quiet] 95s [--help] 95s 95s Required Argument: 95s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 95s Directories containing fast5 files. 95s 95s Read Filtering Argument: 95s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 95s Filter reads based on observations per base percentile 95s thresholds. Format thresholds as "percentile:thresh 95s [pctl2:thresh2 ...]". For example to filter reads with 95s 99th pctl > 200 obs/base or max > 5k obs/base use 95s "99:200 100:5000". 95s 95s FAST5 Data Argument: 95s --corrected-group CORRECTED_GROUP 95s FAST5 group created by resquiggle command. Default: 95s RawGenomeCorrected_000 95s 95s Miscellaneous Arguments: 95s --quiet, -q Don't print status information. 95s --help, -h Print this help message and exit 95s usage: tombo filter level_coverage 95s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 95s [--percent-to-filter PERCENT_TO_FILTER] 95s [--corrected-group CORRECTED_GROUP] 95s [--quiet] [--help] 95s 95s Required Arguments: 95s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 95s Directories containing fast5 files. 95s 95s Read Filtering Argument: 95s --percent-to-filter PERCENT_TO_FILTER 95s Percentage of all reads to filter. Reads are randomly 95s selected weighted according to the approximate 95s coverage at the mapped genomic location. This can be 95s useful in modeling and testing. Default: 10.000000 95s 95s FAST5 Data Arguments: 95s --corrected-group CORRECTED_GROUP 95s FAST5 group created by resquiggle command. Default: 95s RawGenomeCorrected_000 95s 95s Miscellaneous Arguments: 95s --quiet, -q Don't print status information. 95s --help, -h Print this help message and exit 95s usage: tombo filter q_score 95s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 95s [--q-score Q_SCORE] 95s [--corrected-group CORRECTED_GROUP] 95s [--basecall-group BASECALL_GROUP] [--quiet] 95s [--help] 95s 95s Required Arguments: 95s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 95s Directories containing fast5 files. 95s 95s Read Filtering Argument: 95s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 95s Default: 7.000000 95s 95s FAST5 Data Arguments: 95s --corrected-group CORRECTED_GROUP 95s FAST5 group created by resquiggle command. Default: 95s RawGenomeCorrected_000 95s --basecall-group BASECALL_GROUP 95s FAST5 group obtain original basecalls (under Analyses 95s group). Default: Basecall_1D_000 95s 95s Miscellaneous Arguments: 95s --quiet, -q Don't print status information. 95s --help, -h Print this help message and exit 95s usage: tombo filter raw_signal_matching 95s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 95s --signal-matching-score SIGNAL_MATCHING_SCORE 95s [--corrected-group CORRECTED_GROUP] 95s [--quiet] [--help] 95s 95s Required Arguments: 95s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 95s Directories containing fast5 files. 95s --signal-matching-score SIGNAL_MATCHING_SCORE 95s Observed to expected signal matching score (higher 95s score indicates poor matching). Sample type defaults: 95s RNA : 2 || DNA : 1.1 95s 95s FAST5 Data Arguments: 95s --corrected-group CORRECTED_GROUP 95s FAST5 group created by resquiggle command. Default: 95s RawGenomeCorrected_000 95s 95s Miscellaneous Arguments: 95s --quiet, -q Don't print status information. 95s --help, -h Print this help message and exit 95s usage: tombo filter genome_locations 95s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 95s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 95s [--include-partial-overlap] 95s [--corrected-group CORRECTED_GROUP] 95s [--quiet] [--help] 95s 95s Required Arguments: 95s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 95s Directories containing fast5 files. 95s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 95s Filter out reads not falling completely within include 95s regions. Omit start and end coordinates to include an 95s entire chromosome/sequence record. Format regions as 95s "chrm[:start-end] [chrm2[:start2-end2] ...]". 95s 95s Filter Argument: 95s --include-partial-overlap 95s Include reads that partially overlap the specified 95s region. Default: Only include reads completely 95s contained in a specified region 95s 95s FAST5 Data Argument: 95s --corrected-group CORRECTED_GROUP 95s FAST5 group created by resquiggle command. Default: 95s RawGenomeCorrected_000 95s 95s Miscellaneous Arguments: 95s --quiet, -q Don't print status information. 95s --help, -h Print this help message and exit 96s usage: tombo detect_modifications de_novo 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s --statistics-file-basename STATISTICS_FILE_BASENAME 96s [--dna] [--rna] 96s [--fishers-method-context FISHERS_METHOD_CONTEXT] 96s [--minimum-test-reads MINIMUM_TEST_READS] 96s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 96s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 96s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 96s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 96s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 96s [--processes PROCESSES] 96s [--corrected-group CORRECTED_GROUP] 96s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 96s [--quiet] [--help] 96s 96s Required Argument: 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s Directories containing fast5 files. 96s --statistics-file-basename STATISTICS_FILE_BASENAME 96s File base name to save base by base statistics from 96s testing. Filenames will be [--statistics-file- 96s basename].[--alternate-bases]?.tombo.stats 96s 96s Comparison Model Arguments: 96s --dna Explicitly select canonical DNA model. Default: 96s Automatically determine from FAST5s 96s --rna Explicitly select canonical RNA model. Default: 96s Automatically determine from FAST5s 96s 96s Significance Test Arguments: 96s --fishers-method-context FISHERS_METHOD_CONTEXT 96s Number of context bases up and downstream over which 96s to compute Fisher's method combined p-values. Note: 96s Not applicable for alternative model likelihood ratio 96s tests. Default: 1. 96s --minimum-test-reads MINIMUM_TEST_READS 96s Number of reads required at a position to perform 96s significance testing or contribute to model 96s estimation. Default: 1 96s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 96s P-value threshold when computing fraction of 96s significant reads at each genomic position. If two 96s values are provided, statistics between these values 96s are not considered. Default thresholds: DNA:0.15-0.5 , 96s RNA:0.05-0.4 96s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 96s Dampen fraction modified estimates for low coverage 96s sites. Two parameters are unmodified and modified 96s pseudo read counts. This is equivalent to a beta prior 96s on the fraction estimate. Set to "0 0" to disable 96s dampened fraction estimation. Default: [2, 0] 96s 96s Output Argument: 96s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 96s Base for binary files containing per-read statistics 96s from statistical testing. Filenames will be [--per- 96s read-statistics-basename].[--alternate- 96s bases]?.tombo.per_read_stats 96s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 96s Number of the most significant sites to store for 96s faster access. If a longer list of most significant 96s sites is required the list must be re-computed from 96s all batches. Very large values can increase RAM usage. 96s Default: 100000 96s 96s Multiprocessing Arguments: 96s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 96s Size of regions over which to multiprocesses statistic 96s computation. For very deep samples a smaller value is 96s recommmended in order to control memory consumption. 96s Default: 10000 96s --processes PROCESSES 96s Number of processes. Default: 1 96s 96s FAST5 Data Arguments: 96s --corrected-group CORRECTED_GROUP 96s FAST5 group created by resquiggle command. Default: 96s RawGenomeCorrected_000 96s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 96s FAST5 subgroup(s) (under /Analyses/[--basecall- 96s group]/) containing basecalls and created within 96s [--corrected-group] containing re-squiggle results. 96s Default: ['BaseCalled_template'] 96s 96s Miscellaneous Arguments: 96s --quiet, -q Don't print status information. 96s --help, -h Print this help message and exit 96s usage: tombo detect_modifications alternative_model 96s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 96s [--statistics-file-basename STATISTICS_FILE_BASENAME] 96s [--alternate-bases {5mC,6mA,CpG,dcm,dam} [{5mC,6mA,CpG,dcm,dam} ...]] 96s [--print-available-models] 96s [--dna] [--rna] 96s [--minimum-test-reads MINIMUM_TEST_READS] 96s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 96s [--standard-log-likelihood-ratio] 96s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 96s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 96s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 96s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 96s [--processes PROCESSES] 96s [--corrected-group CORRECTED_GROUP] 96s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 96s [--quiet] [--help] 96s 96s Required Argument: 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s Directories containing fast5 files. 96s --statistics-file-basename STATISTICS_FILE_BASENAME 96s File base name to save base by base statistics from 96s testing. Filenames will be [--statistics-file- 96s basename].[--alternate-bases]?.tombo.stats 96s --alternate-bases {5mC,6mA,CpG,dcm,dam} [{5mC,6mA,CpG,dcm,dam} ...] 96s Default non-standard base model for testing (not 96s required if user created --alternate-model-filenames 96s is provided). 96s 96s Comparison Arguments: 96s --print-available-models 96s Print available alternative models and exit. 96s --dna Explicitly select canonical DNA model. Default: 96s Automatically determine from FAST5s 96s --rna Explicitly select canonical RNA model. Default: 96s Automatically determine from FAST5s 96s 96s Significance Test Arguments: 96s --minimum-test-reads MINIMUM_TEST_READS 96s Number of reads required at a position to perform 96s significance testing or contribute to model 96s estimation. Default: 1 96s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 96s Log likelihood ratio threshold when computing fraction 96s of significant reads at each genomic position. If two 96s values are provided, statistics between these values 96s are not considered. Default thresholds: DNA:-1.5-2.5 , 96s RNA:-2.5-2.5 96s --standard-log-likelihood-ratio 96s Use a standard log likelihood ratio (LLR) statistic. 96s Default is to use an outlier-robust LLR-like 96s statistic. Detail in full online documentation. 96s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 96s Dampen fraction modified estimates for low coverage 96s sites. Two parameters are unmodified and modified 96s pseudo read counts. This is equivalent to a beta prior 96s on the fraction estimate. Set to "0 0" to disable 96s dampened fraction estimation. Default: [2, 0] 96s 96s Output Argument: 96s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 96s Base for binary files containing per-read statistics 96s from statistical testing. Filenames will be [--per- 96s read-statistics-basename].[--alternate- 96s bases]?.tombo.per_read_stats 96s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 96s Number of the most significant sites to store for 96s faster access. If a longer list of most significant 96s sites is required the list must be re-computed from 96s all batches. Very large values can increase RAM usage. 96s Default: 100000 96s 96s Multiprocessing Arguments: 96s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 96s Size of regions over which to multiprocesses statistic 96s computation. For very deep samples a smaller value is 96s recommmended in order to control memory consumption. 96s Default: 10000 96s --processes PROCESSES 96s Number of processes. Default: 1 96s 96s FAST5 Data Arguments: 96s --corrected-group CORRECTED_GROUP 96s FAST5 group created by resquiggle command. Default: 96s RawGenomeCorrected_000 96s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 96s FAST5 subgroup(s) (under /Analyses/[--basecall- 96s group]/) containing basecalls and created within 96s [--corrected-group] containing re-squiggle results. 96s Default: ['BaseCalled_template'] 96s 96s Miscellaneous Arguments: 96s --quiet, -q Don't print status information. 96s --help, -h Print this help message and exit 96s usage: tombo detect_modifications model_sample_compare 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s --statistics-file-basename STATISTICS_FILE_BASENAME 96s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 96s [--sample-only-estimates] 96s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 96s [--dna] [--rna] 96s [--fishers-method-context FISHERS_METHOD_CONTEXT] 96s [--minimum-test-reads MINIMUM_TEST_READS] 96s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 96s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 96s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 96s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 96s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 96s [--processes PROCESSES] 96s [--corrected-group CORRECTED_GROUP] 96s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 96s [--quiet] [--help] 96s 96s Required Argument: 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s Directories containing fast5 files. 96s --statistics-file-basename STATISTICS_FILE_BASENAME 96s File base name to save base by base statistics from 96s testing. Filenames will be [--statistics-file- 96s basename].[--alternate-bases]?.tombo.stats 96s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 96s Set of directories containing fast5 files for control 96s reads, containing only canonical nucleotides. 96s 96s Model Prior Arguments: 96s --sample-only-estimates 96s Only use canonical sample to estimate expected signal 96s level and spread. Default: Use canonical model to 96s improve estimtates (esp. for low coverage regions) 96s using baysian posterior estimates. 96s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 96s Prior weights (one each for mean and spread) applied 96s to canonical base model for estimating posterior model 96s parameters for sample comparison. Default: [5, 40] 96s --dna Explicitly select canonical DNA model. Default: 96s Automatically determine from FAST5s 96s --rna Explicitly select canonical RNA model. Default: 96s Automatically determine from FAST5s 96s 96s Significance Test Arguments: 96s --fishers-method-context FISHERS_METHOD_CONTEXT 96s Number of context bases up and downstream over which 96s to compute Fisher's method combined p-values. Note: 96s Not applicable for alternative model likelihood ratio 96s tests. Default: 1. 96s --minimum-test-reads MINIMUM_TEST_READS 96s Number of reads required at a position to perform 96s significance testing or contribute to model 96s estimation. Default: 1 96s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 96s P-value threshold when computing fraction of 96s significant reads at each genomic position. If two 96s values are provided, statistics between these values 96s are not considered. Default thresholds: DNA:0.15-0.5 , 96s RNA:0.05-0.4 96s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 96s Dampen fraction modified estimates for low coverage 96s sites. Two parameters are unmodified and modified 96s pseudo read counts. This is equivalent to a beta prior 96s on the fraction estimate. Set to "0 0" to disable 96s dampened fraction estimation. Default: [2, 0] 96s 96s Output Argument: 96s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 96s Base for binary files containing per-read statistics 96s from statistical testing. Filenames will be [--per- 96s read-statistics-basename].[--alternate- 96s bases]?.tombo.per_read_stats 96s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 96s Number of the most significant sites to store for 96s faster access. If a longer list of most significant 96s sites is required the list must be re-computed from 96s all batches. Very large values can increase RAM usage. 96s Default: 100000 96s 96s Multiprocessing Arguments: 96s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 96s Size of regions over which to multiprocesses statistic 96s computation. For very deep samples a smaller value is 96s recommmended in order to control memory consumption. 96s Default: 10000 96s --processes PROCESSES 96s Number of processes. Default: 1 96s 96s FAST5 Data Arguments: 96s --corrected-group CORRECTED_GROUP 96s FAST5 group created by resquiggle command. Default: 96s RawGenomeCorrected_000 96s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 96s FAST5 subgroup(s) (under /Analyses/[--basecall- 96s group]/) containing basecalls and created within 96s [--corrected-group] containing re-squiggle results. 96s Default: ['BaseCalled_template'] 96s 96s Miscellaneous Arguments: 96s --quiet, -q Don't print status information. 96s --help, -h Print this help message and exit 96s usage: tombo detect_modifications level_sample_compare 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s --statistics-file-basename STATISTICS_FILE_BASENAME 96s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 96s [--fishers-method-context FISHERS_METHOD_CONTEXT] 96s [--minimum-test-reads MINIMUM_TEST_READS] 96s [--statistic-type {ks,u,t}] 96s [--store-p-value] 96s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 96s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 96s [--processes PROCESSES] 96s [--corrected-group CORRECTED_GROUP] 96s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 96s [--quiet] [--help] 96s 96s Required Argument: 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s Directories containing fast5 files. 96s --statistics-file-basename STATISTICS_FILE_BASENAME 96s File base name to save base by base statistics from 96s testing. Filenames will be [--statistics-file- 96s basename].[--alternate-bases]?.tombo.stats 96s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 96s Set of directories containing fast5 files for 96s alternate set of reads. 96s 96s Significance Test Arguments: 96s --fishers-method-context FISHERS_METHOD_CONTEXT 96s Number of context bases up and downstream over which 96s to compute Fisher's method combined p-values. Note: 96s Not applicable for alternative model likelihood ratio 96s tests. Default: 1. 96s --minimum-test-reads MINIMUM_TEST_READS 96s Number of reads required at a position to perform 96s significance testing or contribute to model 96s estimation. Default: 50 96s --statistic-type {ks,u,t} 96s Type of statistical test to apply. Default: "ks" 96s --store-p-value Store p-value instead of effect-size statistic. 96s Statistics are D-statistic (KS-test), deviation from 96s even common language effect size (u-test), and Cohen's 96s D (t-test). 96s 96s Output Argument: 96s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 96s Number of the most significant sites to store for 96s faster access. If a longer list of most significant 96s sites is required the list must be re-computed from 96s all batches. Very large values can increase RAM usage. 96s Default: 100000 96s 96s Multiprocessing Arguments: 96s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 96s Size of regions over which to multiprocesses statistic 96s computation. For very deep samples a smaller value is 96s recommmended in order to control memory consumption. 96s Default: 10000 96s --processes PROCESSES 96s Number of processes. Default: 1 96s 96s FAST5 Data Arguments: 96s --corrected-group CORRECTED_GROUP 96s FAST5 group created by resquiggle command. Default: 96s RawGenomeCorrected_000 96s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 96s FAST5 subgroup(s) (under /Analyses/[--basecall- 96s group]/) containing basecalls and created within 96s [--corrected-group] containing re-squiggle results. 96s Default: ['BaseCalled_template'] 96s 96s Miscellaneous Arguments: 96s --quiet, -q Don't print status information. 96s --help, -h Print this help message and exit 96s usage: tombo detect_modifications aggregate_per_read_stats 96s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 96s --statistics-filename STATISTICS_FILENAME 96s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 96s [--minimum-test-reads MINIMUM_TEST_READS] 96s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 96s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 96s [--processes PROCESSES] 96s [--corrected-group CORRECTED_GROUP] 96s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 96s [--quiet] [--help] 96s 96s Required Argument: 96s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 96s Binary file containing per-read statistics from 96s statistical testing. 96s --statistics-filename STATISTICS_FILENAME 96s File to save/load genomic base anchored statistics. 96s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 96s P-value or log likelihood ratio threshold when 96s computing fraction of significant reads at each 96s genomic position. If two values are provided, 96s statistics between these values are not considered. 96s 96s Significance Test Arguments: 96s --minimum-test-reads MINIMUM_TEST_READS 96s Number of reads required at a position to perform 96s significance testing or contribute to model 96s estimation. Default: 1 96s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 96s Dampen fraction modified estimates for low coverage 96s sites. Two parameters are unmodified and modified 96s pseudo read counts. This is equivalent to a beta prior 96s on the fraction estimate. Set to "0 0" to disable 96s dampened fraction estimation. Default: [2, 0] 96s 96s Output Argument: 96s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 96s Number of the most significant sites to store for 96s faster access. If a longer list of most significant 96s sites is required the list must be re-computed from 96s all batches. Very large values can increase RAM usage. 96s Default: 100000 96s 96s Multiprocessing Arguments: 96s --processes PROCESSES 96s Number of processes. Default: 1 96s 96s FAST5 Data Arguments: 96s --corrected-group CORRECTED_GROUP 96s FAST5 group created by resquiggle command. Default: 96s RawGenomeCorrected_000 96s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 96s FAST5 subgroup(s) (under /Analyses/[--basecall- 96s group]/) containing basecalls and created within 96s [--corrected-group] containing re-squiggle results. 96s Default: ['BaseCalled_template'] 96s 96s Miscellaneous Arguments: 96s --quiet, -q Don't print status information. 96s --help, -h Print this help message and exit 96s usage: tombo text_output browser_files 96s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 96s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 96s [--statistics-filename STATISTICS_FILENAME] 96s [--genome-fasta GENOME_FASTA] 96s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 96s [--browser-file-basename BROWSER_FILE_BASENAME] 96s [--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} ...]] 96s [--corrected-group CORRECTED_GROUP] 96s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 96s [--quiet] [--help] 96s 96s Data Arguments: 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s Directories containing fast5 files. 96s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 96s Set of directories containing fast5 files for control 96s reads, containing only canonical nucleotides. 96s --statistics-filename STATISTICS_FILENAME 96s File to save/load genomic base anchored statistics. 96s 96s Statistic Motif Filter Arguments: 96s --genome-fasta GENOME_FASTA 96s FASTA file used to re-squiggle. For faster sequence 96s access. 96s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 96s Ground truth, motif centered, modified base 96s descriptions for output filtering. Format descriptions 96s as: "motif:mod_pos:name". The mod_pos indicates the 96s modified base within the motif (1-based index). 96s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 96s output for identification of E. coli dam and dcm 96s methylation. 96s 96s Output Arguments: 96s --browser-file-basename BROWSER_FILE_BASENAME 96s Basename for output browser files. Two files (plus and 96s minus strand) will be produced for each --file-types 96s supplied. Filenames formatted as "[browser-file- 96s basename].[file- 96s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 96s Default: tombo_results 96s --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} ...] 96s Data types of genome browser files to produce. 96s Produced coverage files are in bedGraph format, while 96s all other file types will be in wiggle format 96s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 96s Default: "coverage" 96s 96s FAST5 Data Arguments: 96s --corrected-group CORRECTED_GROUP 96s FAST5 group created by resquiggle command. Default: 96s RawGenomeCorrected_000 96s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 96s FAST5 subgroup(s) (under /Analyses/[--basecall- 96s group]/) containing basecalls and created within 96s [--corrected-group] containing re-squiggle results. 96s Default: ['BaseCalled_template'] 96s 96s Miscellaneous Arguments: 96s --quiet, -q Don't print status information. 96s --help, -h Print this help message and exit 96s usage: tombo text_output signif_sequence_context 96s --statistics-filename STATISTICS_FILENAME 96s [--genome-fasta GENOME_FASTA] 96s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 96s [--num-regions NUM_REGIONS] 96s [--num-bases NUM_BASES] 96s [--sequences-filename SEQUENCES_FILENAME] 96s [--corrected-group CORRECTED_GROUP] 96s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 96s [--quiet] [--help] 96s 96s Required Argument: 96s --statistics-filename STATISTICS_FILENAME 96s File to save/load genomic base anchored statistics. 96s 96s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 96s --genome-fasta GENOME_FASTA 96s FASTA file used to re-squiggle. For faster sequence 96s access. 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s Directories containing fast5 files. 96s 96s Region Selection Arguments: 96s --num-regions NUM_REGIONS 96s Number of regions to plot. Default: 100 96s --num-bases NUM_BASES 96s Number of bases to plot/output. Default: 15 96s 96s Output Arguments: 96s --sequences-filename SEQUENCES_FILENAME 96s File for sequences from selected regions. Sequences 96s will be stored in FASTA format. Default: 96s tombo_results.significant_regions.fasta. 96s 96s FAST5 Data Arguments: 96s --corrected-group CORRECTED_GROUP 96s FAST5 group created by resquiggle command. Default: 96s RawGenomeCorrected_000 96s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 96s FAST5 subgroup(s) (under /Analyses/[--basecall- 96s group]/) containing basecalls and created within 96s [--corrected-group] containing re-squiggle results. 96s Default: ['BaseCalled_template'] 96s 96s Miscellaneous Arguments: 96s --quiet, -q Don't print status information. 96s --help, -h Print this help message and exit 96s usage: tombo plot max_coverage 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 96s [--plot-standard-model] 96s [--plot-alternate-model {6mA,CpG,5mC,dam,dcm}] 96s [--overplot-threshold OVERPLOT_THRESHOLD] 96s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 96s [--num-regions NUM_REGIONS] 96s [--num-bases NUM_BASES] 96s [--pdf-filename PDF_FILENAME] 96s [--corrected-group CORRECTED_GROUP] 96s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 96s [--quiet] [--help] 96s 96s Required Argument: 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s Directories containing fast5 files. 96s 96s Comparison Arguments: 96s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 96s Set of directories containing fast5 files for control 96s reads, containing only canonical nucleotides. 96s --plot-standard-model 96s Add default standard model distribution to the plot. 96s --plot-alternate-model {6mA,CpG,5mC,dam,dcm} 96s Add alternative model distribution to the plot. 96s 96s Overplotting Arguments: 96s --overplot-threshold OVERPLOT_THRESHOLD 96s Coverage level to trigger alternative plot type 96s instead of raw signal. Default: 50 96s --overplot-type {Downsample,Boxplot,Quantile,Density} 96s Plot type for regions with higher coverage. Default: 96s Downsample 96s 96s Plotting Region Arguments: 96s --num-regions NUM_REGIONS 96s Number of regions to plot. Default: 10 96s --num-bases NUM_BASES 96s Number of bases to plot/output. Default: 21 96s 96s Output Argument: 96s --pdf-filename PDF_FILENAME 96s PDF filename to store plot(s). Default: 96s tombo_results.max_coverage.pdf 96s 96s FAST5 Data Arguments: 96s --corrected-group CORRECTED_GROUP 96s FAST5 group created by resquiggle command. Default: 96s RawGenomeCorrected_000 96s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 96s FAST5 subgroup(s) (under /Analyses/[--basecall- 96s group]/) containing basecalls and created within 96s [--corrected-group] containing re-squiggle results. 96s Default: ['BaseCalled_template'] 96s 96s Miscellaneous Arguments: 96s --quiet, -q Don't print status information. 96s --help, -h Print this help message and exit 96s usage: tombo plot genome_locations 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 96s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 96s [--plot-standard-model] 96s [--plot-alternate-model {dam,6mA,dcm,CpG,5mC}] 96s [--overplot-threshold OVERPLOT_THRESHOLD] 96s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 96s [--num-bases NUM_BASES] 96s [--pdf-filename PDF_FILENAME] 96s [--corrected-group CORRECTED_GROUP] 96s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 96s [--quiet] [--help] 96s 96s Required Arguments: 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s Directories containing fast5 files. 96s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 96s Genomic locations at which to plot signal. Format 96s locations as "chrm:position[:strand] 96s [chrm2:position2[:strand2] ...]" (strand not 96s applicable for all applications) 96s 96s Comparison Arguments: 96s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 96s Set of directories containing fast5 files for control 96s reads, containing only canonical nucleotides. 96s --plot-standard-model 96s Add default standard model distribution to the plot. 96s --plot-alternate-model {dam,6mA,dcm,CpG,5mC} 96s Add alternative model distribution to the plot. 96s 96s Overplotting Arguments: 96s --overplot-threshold OVERPLOT_THRESHOLD 96s Coverage level to trigger alternative plot type 96s instead of raw signal. Default: 50 96s --overplot-type {Downsample,Boxplot,Quantile,Density} 96s Plot type for regions with higher coverage. Default: 96s Downsample 96s 96s Plotting Region Argument: 96s --num-bases NUM_BASES 96s Number of bases to plot/output. Default: 21 96s 96s Output Argument: 96s --pdf-filename PDF_FILENAME 96s PDF filename to store plot(s). Default: 96s tombo_results.genome_locations.pdf 96s 96s FAST5 Data Arguments: 96s --corrected-group CORRECTED_GROUP 96s FAST5 group created by resquiggle command. Default: 96s RawGenomeCorrected_000 96s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 96s FAST5 subgroup(s) (under /Analyses/[--basecall- 96s group]/) containing basecalls and created within 96s [--corrected-group] containing re-squiggle results. 96s Default: ['BaseCalled_template'] 96s 96s Miscellaneous Arguments: 96s --quiet, -q Don't print status information. 96s --help, -h Print this help message and exit 96s usage: tombo plot motif_centered 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s --motif MOTIF --genome-fasta GENOME_FASTA 96s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 96s [--plot-standard-model] 96s [--plot-alternate-model {5mC,6mA,dcm,CpG,dam}] 96s [--overplot-threshold OVERPLOT_THRESHOLD] 96s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 96s [--num-regions NUM_REGIONS] 96s [--num-bases NUM_BASES] [--deepest-coverage] 96s [--pdf-filename PDF_FILENAME] 96s [--corrected-group CORRECTED_GROUP] 96s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 96s [--quiet] [--help] 96s 96s Required Arguments: 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s Directories containing fast5 files. 96s --motif MOTIF Motif of interest at which to plot signal and 96s statsitics. Supports IUPAC single letter codes (use T 96s for RNA). 96s --genome-fasta GENOME_FASTA 96s FASTA file used to re-squiggle. For faster sequence 96s access. 96s 96s Comparison Arguments: 96s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 96s Set of directories containing fast5 files for control 96s reads, containing only canonical nucleotides. 96s --plot-standard-model 96s Add default standard model distribution to the plot. 96s --plot-alternate-model {5mC,6mA,dcm,CpG,dam} 96s Add alternative model distribution to the plot. 96s 96s Overplotting Arguments: 96s --overplot-threshold OVERPLOT_THRESHOLD 96s Coverage level to trigger alternative plot type 96s instead of raw signal. Default: 50 96s --overplot-type {Downsample,Boxplot,Quantile,Density} 96s Plot type for regions with higher coverage. Default: 96s Downsample 96s 96s Plotting Region Arguments: 96s --num-regions NUM_REGIONS 96s Number of regions to plot. Default: 10 96s --num-bases NUM_BASES 96s Number of bases to plot/output. Default: 21 96s --deepest-coverage Plot the deepest coverage regions. 96s 96s Output Argument: 96s --pdf-filename PDF_FILENAME 96s PDF filename to store plot(s). Default: 96s tombo_results.motif_centered.pdf 96s 96s FAST5 Data Arguments: 96s --corrected-group CORRECTED_GROUP 96s FAST5 group created by resquiggle command. Default: 96s RawGenomeCorrected_000 96s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 96s FAST5 subgroup(s) (under /Analyses/[--basecall- 96s group]/) containing basecalls and created within 96s [--corrected-group] containing re-squiggle results. 96s Default: ['BaseCalled_template'] 96s 96s Miscellaneous Arguments: 96s --quiet, -q Don't print status information. 96s --help, -h Print this help message and exit 96s usage: tombo plot max_difference 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 96s [--overplot-threshold OVERPLOT_THRESHOLD] 96s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 96s [--num-regions NUM_REGIONS] 96s [--num-bases NUM_BASES] 96s [--pdf-filename PDF_FILENAME] 96s [--sequences-filename SEQUENCES_FILENAME] 96s [--corrected-group CORRECTED_GROUP] 96s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 96s [--quiet] [--help] 96s 96s Required Arguments: 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s Directories containing fast5 files. 96s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 96s Set of directories containing fast5 files for control 96s reads, containing only canonical nucleotides. 96s 96s Overplotting Arguments: 96s --overplot-threshold OVERPLOT_THRESHOLD 96s Coverage level to trigger alternative plot type 96s instead of raw signal. Default: 50 96s --overplot-type {Downsample,Boxplot,Quantile,Density} 96s Plot type for regions with higher coverage. Default: 96s Downsample 96s 96s Plotting Region Arguments: 96s --num-regions NUM_REGIONS 96s Number of regions to plot. Default: 10 96s --num-bases NUM_BASES 96s Number of bases to plot/output. Default: 21 96s 96s Output Arguments: 96s --pdf-filename PDF_FILENAME 96s PDF filename to store plot(s). Default: 96s tombo_results.max_difference.pdf 96s --sequences-filename SEQUENCES_FILENAME 96s File for sequences from selected regions. Sequences 96s will be stored in FASTA format. Default: None. 96s 96s FAST5 Data Arguments: 96s --corrected-group CORRECTED_GROUP 96s FAST5 group created by resquiggle command. Default: 96s RawGenomeCorrected_000 96s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 96s FAST5 subgroup(s) (under /Analyses/[--basecall- 96s group]/) containing basecalls and created within 96s [--corrected-group] containing re-squiggle results. 96s Default: ['BaseCalled_template'] 96s 96s Miscellaneous Arguments: 96s --quiet, -q Don't print status information. 96s --help, -h Print this help message and exit 96s usage: tombo plot most_significant 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s --statistics-filename STATISTICS_FILENAME 96s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 96s [--plot-standard-model] 96s [--plot-alternate-model {dcm,6mA,CpG,dam,5mC}] 96s [--overplot-threshold OVERPLOT_THRESHOLD] 96s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 96s [--num-regions NUM_REGIONS] 96s [--num-bases NUM_BASES] 96s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 96s [--pdf-filename PDF_FILENAME] 96s [--sequences-filename SEQUENCES_FILENAME] 96s [--corrected-group CORRECTED_GROUP] 96s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 96s [--quiet] [--help] 96s 96s Required Arguments: 96s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 96s Directories containing fast5 files. 96s --statistics-filename STATISTICS_FILENAME 96s File to save/load genomic base anchored statistics. 96s 96s Comparison Arguments: 96s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 96s Set of directories containing fast5 files for control 96s reads, containing only canonical nucleotides. 96s --plot-standard-model 96s Add default standard model distribution to the plot. 96s --plot-alternate-model {dcm,6mA,CpG,dam,5mC} 96s Add alternative model distribution to the plot. 96s 96s Overplotting Arguments: 96s --overplot-threshold OVERPLOT_THRESHOLD 96s Coverage level to trigger alternative plot type 96s instead of raw signal. Default: 50 96s --overplot-type {Downsample,Boxplot,Quantile,Density} 96s Plot type for regions with higher coverage. Default: 96s Downsample 96s 96s Plotting Region Arguments: 96s --num-regions NUM_REGIONS 96s Number of regions to plot. Default: 10 96s --num-bases NUM_BASES 96s Number of bases to plot/output. Default: 21 96s 96s Statistical Argument: 96s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 96s Dampen fraction modified estimates for low coverage 96s sites. Two parameters are unmodified and modified 96s pseudo read counts. This is equivalent to a beta prior 96s on the fraction estimate. Set to "0 0" to disable 96s dampened fraction estimation. Default: [2, 0] 96s 96s Output Arguments: 96s --pdf-filename PDF_FILENAME 96s PDF filename to store plot(s). Default: 96s tombo_results.significant_difference.pdf 96s --sequences-filename SEQUENCES_FILENAME 96s File for sequences from selected regions. Sequences 96s will be stored in FASTA format. Default: None. 96s 96s FAST5 Data Arguments: 96s --corrected-group CORRECTED_GROUP 96s FAST5 group created by resquiggle command. Default: 96s RawGenomeCorrected_000 96s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 96s FAST5 subgroup(s) (under /Analyses/[--basecall- 96s group]/) containing basecalls and created within 96s [--corrected-group] containing re-squiggle results. 96s Default: ['BaseCalled_template'] 96s 96s Miscellaneous Arguments: 96s --quiet, -q Don't print status information. 96s --help, -h Print this help message and exit 97s usage: tombo plot motif_with_stats 97s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 97s --motif MOTIF 97s --statistics-filename STATISTICS_FILENAME 97s --genome-fasta GENOME_FASTA 97s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 97s [--plot-standard-model] 97s [--plot-alternate-model {5mC,6mA,dcm,dam,CpG}] 97s [--overplot-threshold OVERPLOT_THRESHOLD] 97s [--num-regions NUM_REGIONS] 97s [--num-context NUM_CONTEXT] 97s [--num-statistics NUM_STATISTICS] 97s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 97s [--pdf-filename PDF_FILENAME] 97s [--corrected-group CORRECTED_GROUP] 97s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 97s [--quiet] [--help] 97s 97s Required Arguments: 97s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 97s Directories containing fast5 files. 97s --motif MOTIF Motif of interest at which to plot signal and 97s statsitics. Supports IUPAC single letter codes (use T 97s for RNA). 97s --statistics-filename STATISTICS_FILENAME 97s File to save/load genomic base anchored statistics. 97s --genome-fasta GENOME_FASTA 97s FASTA file used to re-squiggle. For faster sequence 97s access. 97s 97s Comparison Arguments: 97s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 97s Set of directories containing fast5 files for control 97s reads, containing only canonical nucleotides. 97s --plot-standard-model 97s Add default standard model distribution to the plot. 97s --plot-alternate-model {5mC,6mA,dcm,dam,CpG} 97s Add alternative model distribution to the plot. 97s 97s Overplotting Argument: 97s --overplot-threshold OVERPLOT_THRESHOLD 97s Coverage level to trigger alternative plot type 97s instead of raw signal. Default: 50 97s 97s Plotting Region Arguments: 97s --num-regions NUM_REGIONS 97s Number of regions to plot. Default: 3 97s --num-context NUM_CONTEXT 97s Number of context bases around motif. Default: 5 97s --num-statistics NUM_STATISTICS 97s Number of motif centered regions to include in 97s statistic distributions. Default: 200 97s 97s Statistical Argument: 97s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 97s Dampen fraction modified estimates for low coverage 97s sites. Two parameters are unmodified and modified 97s pseudo read counts. This is equivalent to a beta prior 97s on the fraction estimate. Set to "0 0" to disable 97s dampened fraction estimation. Default: [2, 0] 97s 97s Output Argument: 97s --pdf-filename PDF_FILENAME 97s PDF filename to store plot(s). Default: 97s tombo_results.motif_statistics.pdf 97s 97s FAST5 Data Arguments: 97s --corrected-group CORRECTED_GROUP 97s FAST5 group created by resquiggle command. Default: 97s RawGenomeCorrected_000 97s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 97s FAST5 subgroup(s) (under /Analyses/[--basecall- 97s group]/) containing basecalls and created within 97s [--corrected-group] containing re-squiggle results. 97s Default: ['BaseCalled_template'] 97s 97s Miscellaneous Arguments: 97s --quiet, -q Don't print status information. 97s --help, -h Print this help message and exit 97s usage: tombo plot per_read 97s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 97s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 97s [--genome-fasta GENOME_FASTA] 97s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 97s [--num-reads NUM_READS] [--num-bases NUM_BASES] 97s [--box-center] [--pdf-filename PDF_FILENAME] 97s [--corrected-group CORRECTED_GROUP] 97s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 97s [--quiet] [--help] 97s 97s Required Arguments: 97s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 97s Genomic locations at which to plot signal. Format 97s locations as "chrm:position[:strand] 97s [chrm2:position2[:strand2] ...]" (strand not 97s applicable for all applications) 97s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 97s Binary file containing per-read statistics from 97s statistical testing. 97s 97s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 97s --genome-fasta GENOME_FASTA 97s FASTA file used to re-squiggle. For faster sequence 97s access. 97s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 97s Directories containing fast5 files. 97s 97s Plotting Region Arguments: 97s --num-reads NUM_READS 97s Number of reads to plot. Default: 100 97s --num-bases NUM_BASES 97s Number of bases to plot/output. Default: 51 97s --box-center Plot a box around the central base. 97s 97s Output Argument: 97s --pdf-filename PDF_FILENAME 97s PDF filename to store plot(s). Default: 97s tombo_results.per_read_stats.pdf 97s 97s FAST5 Data Arguments: 97s --corrected-group CORRECTED_GROUP 97s FAST5 group created by resquiggle command. Default: 97s RawGenomeCorrected_000 97s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 97s FAST5 subgroup(s) (under /Analyses/[--basecall- 97s group]/) containing basecalls and created within 97s [--corrected-group] containing re-squiggle results. 97s Default: ['BaseCalled_template'] 97s 97s Miscellaneous Arguments: 97s --quiet, -q Don't print status information. 97s --help, -h Print this help message and exit 97s usage: tombo plot roc 97s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 97s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 97s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 97s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 97s [--genome-fasta GENOME_FASTA] 97s [--pdf-filename PDF_FILENAME] 97s [--statistics-per-block STATISTICS_PER_BLOCK] 97s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 97s [--quiet] [--help] 97s 97s Required Argument: 97s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 97s Files to load genomic base anchored statistics. 97s 97s Ground Truth Arguments (provide bed files or motifs): 97s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 97s Modification description and bed format files 97s containing single base locations of ground truth 97s modified sites. Bed files should contain 6 fields 97s including strand. Format descriptions as 97s "mod_name:locs.bed". Example: "CpG 97s bisulfite":bisulfite_locs.bed 97s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 97s Bed format files containing single base locations of 97s ground truth unmodified sites. Bed files should 97s contain 6 fields including strand. 97s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 97s Ground truth, motif centered, modified base 97s descriptions for computing ROC and PR curves. Each 97s statistics file is associated with a set of motif 97s descriptions. Format descriptions as: 97s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 97s mod_pos indicates the alternate-base within the motif 97s (1-based index). Example: CCWGG:2:"dcm 97s 5mC"::GATC:2:"dam 6mA" would assess the performance of 97s a single Tombo statistics file for identification of 97s E. coli dam and dcm methylation. 97s --genome-fasta GENOME_FASTA 97s FASTA file used to re-squiggle. For faster sequence 97s access. 97s 97s Output Arguments: 97s --pdf-filename PDF_FILENAME 97s PDF filename to store plot(s). Default: 97s tombo_results.roc.pdf 97s 97s Down-sampling Arguments: 97s --statistics-per-block STATISTICS_PER_BLOCK 97s Number of randomly selected per-read, per-base 97s statistics to extract from each genomic block for 97s plotting. Default: Include all stats 97s --total-statistics-limit TOTAL_STATISTICS_LIMIT 97s Total per-read statistics to be extracted for 97s plotting. Avoids memory overflow for large runs. 97s Default: 5000000 97s 97s Miscellaneous Arguments: 97s --quiet, -q Don't print status information. 97s --help, -h Print this help message and exit 97s usage: tombo plot per_read_roc 97s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 97s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 97s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 97s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 97s [--genome-fasta GENOME_FASTA] 97s [--statistics-per-block STATISTICS_PER_BLOCK] 97s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 97s [--pdf-filename PDF_FILENAME] [--quiet] 97s [--help] 97s 97s Required Argument: 97s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 97s Binary files containing per-read statistics from 97s statistical testing. 97s 97s Ground Truth Arguments (provide bed files or motifs): 97s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 97s Modification description and bed format files 97s containing single base locations of ground truth 97s modified sites. Bed files should contain 6 fields 97s including strand. Format descriptions as 97s "mod_name:locs.bed". Example: "CpG 97s bisulfite":bisulfite_locs.bed 97s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 97s Bed format files containing single base locations of 97s ground truth unmodified sites. Bed files should 97s contain 6 fields including strand. 97s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 97s Ground truth, motif centered, modified base 97s descriptions for computing ROC and PR curves. Each 97s statistics file is associated with a set of motif 97s descriptions. Format descriptions as: 97s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 97s mod_pos indicates the alternate-base within the motif 97s (1-based index). Example: CCWGG:2:"dcm 97s 5mC"::GATC:2:"dam 6mA" would assess the performance of 97s a single Tombo statistics file for identification of 97s E. coli dam and dcm methylation. 97s --genome-fasta GENOME_FASTA 97s FASTA file used to re-squiggle. For faster sequence 97s access. 97s 97s Down-sampling Arguments: 97s --statistics-per-block STATISTICS_PER_BLOCK 97s Number of randomly selected per-read, per-base 97s statistics to extract from each genomic block for 97s plotting. Default: 100000 97s --total-statistics-limit TOTAL_STATISTICS_LIMIT 97s Total per-read statistics to be extracted for 97s plotting. Avoids memory overflow for large runs. 97s Default: 5000000 97s 97s Output Arguments: 97s --pdf-filename PDF_FILENAME 97s PDF filename to store plot(s). Default: 97s tombo_results.per_reads_roc.pdf 97s 97s Miscellaneous Arguments: 97s --quiet, -q Don't print status information. 97s --help, -h Print this help message and exit 97s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 97s [--upstream-bases {0,1,2,3,4}] 97s [--downstream-bases {0,1,2,3,4}] [--read-mean] 97s [--num-kmer-threshold NUM_KMER_THRESHOLD] 97s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 97s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 97s [--corrected-group CORRECTED_GROUP] 97s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 97s [--quiet] [--help] 97s 97s Required Argument: 97s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 97s Directories containing fast5 files. 97s 97s Data Processing Arguments: 97s --upstream-bases {0,1,2,3,4} 97s Upstream bases in k-mer. Default: 1 97s --downstream-bases {0,1,2,3,4} 97s Downstream bases in k-mer. Default: 2 97s --read-mean Plot k-mer means across whole reads as opposed to 97s individual k-mer event levels. 97s --num-kmer-threshold NUM_KMER_THRESHOLD 97s Observations of each k-mer required to include a read 97s in read level averages. Default: 1 97s 97s Plotting Region Arguments: 97s --num-reads NUM_READS 97s Number of reads to plot. Default: 100 97s 97s Output Arguments: 97s --pdf-filename PDF_FILENAME 97s PDF filename to store plot(s). Default: 97s tombo_results.kmer_distribution.pdf 97s --r-data-filename R_DATA_FILENAME 97s Filename to save R data structure. Default: Don't save 97s --dont-plot Don't plot result. Useful to produce only R data file. 97s 97s FAST5 Data Arguments: 97s --corrected-group CORRECTED_GROUP 97s FAST5 group created by resquiggle command. Default: 97s RawGenomeCorrected_000 97s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 97s FAST5 subgroup(s) (under /Analyses/[--basecall- 97s group]/) containing basecalls and created within 97s [--corrected-group] containing re-squiggle results. 97s Default: ['BaseCalled_template'] 97s 97s Miscellaneous Arguments: 97s --quiet, -q Don't print status information. 97s --help, -h Print this help message and exit 97s usage: tombo plot cluster_most_significant 97s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 97s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 97s --statistics-filename STATISTICS_FILENAME 97s [--genome-fasta GENOME_FASTA] 97s [--processes PROCESSES] 97s [--num-regions NUM_REGIONS] 97s [--num-bases NUM_BASES] 97s [--slide-span SLIDE_SPAN] 97s [--pdf-filename PDF_FILENAME] 97s [--r-data-filename R_DATA_FILENAME] 97s [--corrected-group CORRECTED_GROUP] 97s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 97s [--quiet] [--help] 97s 97s Required Arguments: 97s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 97s Directories containing fast5 files. 97s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 97s Set of directories containing fast5 files for control 97s reads, containing only canonical nucleotides. 97s --statistics-filename STATISTICS_FILENAME 97s File to save/load genomic base anchored statistics. 97s 97s FASTA Sequence Argument: 97s --genome-fasta GENOME_FASTA 97s FASTA file used to re-squiggle. For faster sequence 97s access. 97s 97s Multiprocessing Argument: 97s --processes PROCESSES 97s Number of processes. Default: 1 97s 97s Plotting Region Arguments: 97s --num-regions NUM_REGIONS 97s Number of regions to plot. Default: 10 97s --num-bases NUM_BASES 97s Number of bases to plot/output. Default: 21 97s --slide-span SLIDE_SPAN 97s Number of bases offset over which to search when 97s computing distances for signal cluster plotting. 97s Default: 0 (exact position) 97s 97s Output Arguments: 97s --pdf-filename PDF_FILENAME 97s PDF filename to store plot(s). Default: 97s tombo_results.signal_clusters.pdf 97s --r-data-filename R_DATA_FILENAME 97s Filename to save R data structure. Default: Don't save 97s 97s FAST5 Data Arguments: 97s --corrected-group CORRECTED_GROUP 97s FAST5 group created by resquiggle command. Default: 97s RawGenomeCorrected_000 97s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 97s FAST5 subgroup(s) (under /Analyses/[--basecall- 97s group]/) containing basecalls and created within 97s [--corrected-group] containing re-squiggle results. 97s Default: ['BaseCalled_template'] 97s 97s Miscellaneous Arguments: 97s --quiet, -q Don't print status information. 97s --help, -h Print this help message and exit 97s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 97s 97s Required Arguments: 97s fast5s_basedir Directory containing fast5 files. All files ending in 97s "fast5" found recursively within this base directory will be 97s processed. 97s 97s Miscellaneous Arguments: 97s --quiet, -q Don't print status information. 97s --help, -h Print this help message and exit 97s usage: tombo build_model event_resquiggle 97s [--minimap2-executable MINIMAP2_EXECUTABLE] 97s [--minimap2-index MINIMAP2_INDEX] 97s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 97s [--graphmap-executable GRAPHMAP_EXECUTABLE] 97s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 97s [--normalization-type {median,pA,pA_raw,none}] 97s [--pore-model-filename PORE_MODEL_FILENAME] 97s [--outlier-threshold OUTLIER_THRESHOLD] 97s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 97s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 97s [--timeout TIMEOUT] 97s [--cpts-limit CPTS_LIMIT] 97s [--skip-index] [--overwrite] 97s [--failed-reads-filename FAILED_READS_FILENAME] 97s [--include-event-stdev] 97s [--corrected-group CORRECTED_GROUP] 97s [--basecall-group BASECALL_GROUP] 97s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 97s [--processes PROCESSES] 97s [--align-processes ALIGN_PROCESSES] 97s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 97s [--resquiggle-processes RESQUIGGLE_PROCESSES] 97s [--quiet] [--help] 97s fast5s_basedir reference_fasta 97s 97s Required Arguments: 97s fast5s_basedir Directory containing fast5 files. All files ending in 97s "fast5" found recursively within this base directory 97s will be processed. 97s reference_fasta Reference genome/transcriptome FASTA file for mapping. 97s 97s Mapper Arguments (One mapper is required): 97s --minimap2-executable MINIMAP2_EXECUTABLE 97s Path to minimap2 executable. 97s --minimap2-index MINIMAP2_INDEX 97s Path to minimap2 index (with map-ont preset) file 97s corresponding to the [genome_fasta] provided. 97s --bwa-mem-executable BWA_MEM_EXECUTABLE 97s Path to bwa-mem executable. 97s --graphmap-executable GRAPHMAP_EXECUTABLE 97s Path to graphmap executable. 97s --alignment-batch-size ALIGNMENT_BATCH_SIZE 97s Number of reads included in each alignment call. Note: 97s A new system mapping call is made for each batch 97s (including loading of the genome), so it is advised to 97s use larger values for larger genomes. Default: 1000 97s 97s Signal Processing Arguments: 97s --normalization-type {median,pA,pA_raw,none} 97s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 97s as in the ONT events (using offset, range and 97s digitization), "pA": k-mer-based correction for pA 97s drift as in nanopolish (requires [--pore-model- 97s filename]), "median": median and MAD from raw signal. 97s Default: median 97s --pore-model-filename PORE_MODEL_FILENAME 97s File containing kmer model parameters (level_mean and 97s level_stdv) used in order to compute kmer-based 97s corrected pA values. E.g. https://github.com/jts/nanop 97s olish/blob/master/etc/r9- 97s models/template_median68pA.5mers.model 97s --outlier-threshold OUTLIER_THRESHOLD 97s Windosrize the signal at this number of scale values. 97s Negative value disables outlier clipping. Default: 97s 5.000000 97s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 97s Specify the 2 parameters for segmentation 1) running 97s neighboring windows width 2) minimum raw observations 97s per genomic base. Sample type defaults: RNA : 12 6 || 97s DNA : 5 3 97s 97s Read Filtering Arguments: 97s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 97s Filter reads based on observations per base percentile 97s thresholds. Format thresholds as "percentile:thresh 97s [pctl2:thresh2 ...]". For example to filter reads with 97s 99th pctl > 200 obs/base or max > 5k obs/base use 97s "99:200 100:5000". 97s --timeout TIMEOUT Timeout in seconds for processing a single read. 97s Default: No timeout. 97s --cpts-limit CPTS_LIMIT 97s Maximum number of changepoints to find within a single 97s indel group. Default: No limit. 97s 97s Input/Output Arguments: 97s --skip-index Skip creation of tombo index. This drastically slows 97s downstream tombo commands. Default stores tombo index 97s named ".[--fast5-basedir].[--corrected- 97s group].tombo.index" to be loaded automatically for 97s downstream commands. 97s --overwrite Overwrite previous corrected group in FAST5 files. 97s Note: only effects --corrected-group or --new- 97s corrected-group. 97s --failed-reads-filename FAILED_READS_FILENAME 97s Output failed read filenames with assoicated error. 97s Default: Do not store failed reads. 97s --include-event-stdev 97s Include corrected event standard deviation in output 97s FAST5 data. 97s 97s FAST5 Data Arguments: 97s --corrected-group CORRECTED_GROUP 97s FAST5 group created by resquiggle command. Default: 97s RawGenomeCorrected_000 97s --basecall-group BASECALL_GROUP 97s FAST5 group obtain original basecalls (under Analyses 97s group). Default: Basecall_1D_000 97s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 97s FAST5 subgroup(s) (under /Analyses/[--basecall- 97s group]/) containing basecalls and created within 97s [--corrected-group] containing re-squiggle results. 97s Default: ['BaseCalled_template'] 97s 97s Multiprocessing Arguments: 97s --processes PROCESSES 97s Number of processes. Default: 2 97s --align-processes ALIGN_PROCESSES 97s Number of processes to use for parsing and aligning 97s original basecalls. Each process will independently 97s load the genome into memory, so use caution with 97s larger genomes (e.g. human). Default: 1 97s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 97s Number of threads to use for aligner system call. 97s Default: [--processes] / (2 * [--align-processes)] 97s --resquiggle-processes RESQUIGGLE_PROCESSES 97s Number of processes to use for resquiggle algorithm. 97s Default: [--processes] / 2 97s 97s Miscellaneous Arguments: 97s --quiet, -q Don't print status information. 97s --help, -h Print this help message and exit 97s usage: tombo build_model estimate_reference 97s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 97s --tombo-model-filename TOMBO_MODEL_FILENAME 97s [--estimate-mean] 97s [--kmer-specific-sd] 97s [--upstream-bases {0,1,2,3,4}] 97s [--downstream-bases {0,1,2,3,4}] 97s [--minimum-test-reads MINIMUM_TEST_READS] 97s [--coverage-threshold COVERAGE_THRESHOLD] 97s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 97s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 97s [--processes PROCESSES] 97s [--corrected-group CORRECTED_GROUP] 97s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 97s [--quiet] [--help] 97s 97s Required Arguments: 97s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 97s Directories containing fast5 files. 97s --tombo-model-filename TOMBO_MODEL_FILENAME 97s Filename to save Tombo model. 97s 97s Modeling Arguments: 97s --estimate-mean Use the mean instead of median for model level 97s estimation. Note: This can cause poor fits due to 97s outliers 97s --kmer-specific-sd Estimate standard deviation for each k-mers 97s individually. 97s --upstream-bases {0,1,2,3,4} 97s Upstream bases in k-mer. Default: 1 97s --downstream-bases {0,1,2,3,4} 97s Downstream bases in k-mer. Default: 2 97s 97s Filtering Arguments: 97s --minimum-test-reads MINIMUM_TEST_READS 97s Number of reads required at a position to perform 97s significance testing or contribute to model 97s estimation. Default: 10 97s --coverage-threshold COVERAGE_THRESHOLD 97s Maximum mean coverage per region when estimating k-mer 97s model (limits compute time for deep samples). Default: 97s 100 97s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 97s Number of each k-mer observations required in order to 97s produce a reference (genomic locations for standard 97s reference and per-read for alternative reference). 97s Default: 5 97s 97s Multiprocessing Arguments: 97s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 97s Size of regions over which to multiprocesses statistic 97s computation. For very deep samples a smaller value is 97s recommmended in order to control memory consumption. 97s Default: 10000 97s --processes PROCESSES 97s Number of processes. Default: 1 97s 97s FAST5 Data Arguments: 97s --corrected-group CORRECTED_GROUP 97s FAST5 group created by resquiggle command. Default: 97s RawGenomeCorrected_000 97s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 97s FAST5 subgroup(s) (under /Analyses/[--basecall- 97s group]/) containing basecalls and created within 97s [--corrected-group] containing re-squiggle results. 97s Default: ['BaseCalled_template'] 97s 97s Miscellaneous Arguments: 97s --quiet, -q Don't print status information. 97s --help, -h Print this help message and exit 97s usage: tombo build_model estimate_alt_reference 97s --alternate-model-filename ALTERNATE_MODEL_FILENAME 97s --alternate-model-name ALTERNATE_MODEL_NAME 97s --alternate-model-base {A,C,G,T} 97s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 97s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 97s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 97s [--control-density-filename CONTROL_DENSITY_FILENAME] 97s [--dna] [--rna] 97s [--tombo-model-filename TOMBO_MODEL_FILENAME] 97s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 97s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 97s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 97s [--save-density-basename SAVE_DENSITY_BASENAME] 97s [--processes PROCESSES] 97s [--corrected-group CORRECTED_GROUP] 97s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 97s [--quiet] [--help] 97s 97s Required Arguments: 97s --alternate-model-filename ALTERNATE_MODEL_FILENAME 97s Tombo model for alternative likelihood ratio 97s significance testing. 97s --alternate-model-name ALTERNATE_MODEL_NAME 97s A short name to associate with this alternate model 97s (e.g. 5mC, 6mA, etc.). This text will be included in 97s output filenames when this model is used for testing. 97s --alternate-model-base {A,C,G,T} 97s Non-standard base is an alternative to this base. 97s 97s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 97s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 97s Directories containing fast5 files. 97s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 97s Set of directories containing fast5 files for control 97s reads, containing only canonical nucleotides. 97s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 97s File containing k-mer level kernel density estimates 97s for the alternative sample saved using --save-density- 97s basename. 97s --control-density-filename CONTROL_DENSITY_FILENAME 97s File containing k-mer level kernel density estimates 97s for the control sample saved using --save-density- 97s basename. 97s 97s Standard Model Arguments: 97s --dna Explicitly select canonical DNA model. Default: 97s Automatically determine from FAST5s 97s --rna Explicitly select canonical RNA model. Default: 97s Automatically determine from FAST5s 97s --tombo-model-filename TOMBO_MODEL_FILENAME 97s Tombo model filename. If no file is provided, the 97s default DNA or RNA Tombo model will be used. 97s 97s Model Fitting Arguments: 97s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 97s When esitmating the alternative base incorporation 97s rate, this percent of k-mers are assumed to have 97s significantly shifted signal so the alternative 97s distribution minimally overlaps the standard base 97s distribution. Default: 5.000000 97s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 97s Bandwidth applied when performing Gaussian kernal 97s density esitmation on standard and alternative base 97s signal distributions. Default: 0.050000 97s 97s Filtering Argument: 97s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 97s Number of each k-mer observations required in order to 97s produce a reference (genomic locations for standard 97s reference and per-read for alternative reference). 97s Default: 1000 97s 97s Output Argument: 97s --save-density-basename SAVE_DENSITY_BASENAME 97s Basename to save alternative model estimation density 97s estimation information. See scripts/debug_est_alt.R 97s for info use example. Default: Don't save. 97s 97s Multiprocessing Arguments: 97s --processes PROCESSES 97s Number of processes. Default: 1 97s 97s FAST5 Data Arguments: 97s --corrected-group CORRECTED_GROUP 97s FAST5 group created by resquiggle command. Default: 97s RawGenomeCorrected_000 97s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 97s FAST5 subgroup(s) (under /Analyses/[--basecall- 97s group]/) containing basecalls and created within 97s [--corrected-group] containing re-squiggle results. 97s Default: ['BaseCalled_template'] 97s 97s Miscellaneous Arguments: 97s --quiet, -q Don't print status information. 97s --help, -h Print this help message and exit 97s This test only tests the help system 97s There is an extensive test in 97s 97s tombo/tests/shell_tests.sh 97s 97s but this requires to download larger data 97s sets which is not done for the moment. 98s autopkgtest [17:52:12]: test run-unit-test: -----------------------] 98s run-unit-test PASS 98s autopkgtest [17:52:12]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 99s autopkgtest [17:52:13]: @@@@@@@@@@@@@@@@@@@@ summary 99s run-unit-test PASS