0s autopkgtest [11:03:26]: starting date and time: 2024-03-20 11:03:26+0000 0s autopkgtest [11:03:26]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [11:03:26]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.s756l92i/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:minimap2 --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=minimap2/2.26+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-21.secgroup --name adt-noble-s390x-tombo-20240320-110326-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 98s autopkgtest [11:05:04]: testbed dpkg architecture: s390x 99s autopkgtest [11:05:05]: testbed apt version: 2.7.12 99s autopkgtest [11:05:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 99s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 100s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 100s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.7 kB] 100s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3766 kB] 100s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 100s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [653 kB] 100s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 100s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 100s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 100s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4051 kB] 100s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 100s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [34.4 kB] 100s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 103s Fetched 9188 kB in 2s (3886 kB/s) 103s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s Calculating upgrade... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 106s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 107s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 107s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 108s Reading package lists... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Calculating upgrade... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s autopkgtest [11:05:18]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 112s autopkgtest [11:05:18]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 115s Get:1 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (dsc) [2292 B] 115s Get:2 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (tar) [22.3 MB] 115s Get:3 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (diff) [7024 B] 115s gpgv: Signature made Sun Dec 17 19:23:46 2023 UTC 115s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 115s gpgv: issuer "tille@debian.org" 115s gpgv: Can't check signature: No public key 115s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6.dsc: no acceptable signature found 116s autopkgtest [11:05:22]: testing package tombo version 1.5.1-6 116s autopkgtest [11:05:22]: build not needed 123s autopkgtest [11:05:29]: test run-unit-test: preparing testbed 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s Starting pkgProblemResolver with broken count: 0 125s Starting 2 pkgProblemResolver with broken count: 0 125s Done 125s The following additional packages will be installed: 125s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 125s libhdf5-103-1 libhdf5-hl-100 libjs-jquery libjs-mathjax libjs-sphinxdoc 125s libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 python3-decorator 125s python3-h5py python3-h5py-serial python3-mappy python3-numpy python3-scipy 125s python3-tqdm sphinx-rtd-theme-common tombo tombo-doc 125s Suggested packages: 125s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 125s gfortran python3-dev python3-pytest python-scipy-doc 125s Recommended packages: 125s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 125s python3-rpy2 125s The following NEW packages will be installed: 125s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 125s libblas3 libgfortran5 libhdf5-103-1 libhdf5-hl-100 libjs-jquery 125s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 125s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 125s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 125s tombo-doc 125s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 125s Need to get 67.5 MB/67.5 MB of archives. 125s After this operation, 241 MB of additional disk space will be used. 125s Get:1 /tmp/autopkgtest.CY6TBv/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [712 B] 126s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x fonts-lato all 2.015-1 [2781 kB] 126s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 126s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 126s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libaec0 s390x 1.1.2-1 [25.7 kB] 126s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 126s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 126s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libsz2 s390x 1.1.2-1 [5346 B] 126s Get:9 http://ftpmaster.internal/ubuntu noble/universe s390x libhdf5-103-1 s390x 1.10.10+repack-3ubuntu1 [1425 kB] 126s Get:10 http://ftpmaster.internal/ubuntu noble/universe s390x libhdf5-hl-100 s390x 1.10.10+repack-3ubuntu1 [57.5 kB] 126s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 126s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 126s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libjs-sphinxdoc all 7.2.6-4 [149 kB] 126s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 127s Get:15 http://ftpmaster.internal/ubuntu noble/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1 [28.4 kB] 127s Get:16 http://ftpmaster.internal/ubuntu noble/universe s390x liblzf1 s390x 3.6-4 [7020 B] 127s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 127s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x python3-numpy s390x 1:1.24.2-2 [5137 kB] 127s Get:19 http://ftpmaster.internal/ubuntu noble/universe s390x python3-h5py-serial s390x 3.10.0-1ubuntu1 [1535 kB] 127s Get:20 http://ftpmaster.internal/ubuntu noble/universe s390x python3-h5py all 3.10.0-1ubuntu1 [7970 B] 127s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x python3-mappy s390x 2.26+dfsg-1 [207 kB] 127s Get:22 http://ftpmaster.internal/ubuntu noble/universe s390x python3-tqdm all 4.64.1-2 [95.2 kB] 127s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] 127s Get:24 http://ftpmaster.internal/ubuntu noble/universe s390x python3-scipy s390x 1.11.4-6 [20.1 MB] 127s Get:25 http://ftpmaster.internal/ubuntu noble/universe s390x tombo s390x 1.5.1-6 [502 kB] 127s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 128s Get:27 http://ftpmaster.internal/ubuntu noble/universe s390x tombo-doc all 1.5.1-6 [21.7 MB] 128s Fetched 67.5 MB in 3s (25.4 MB/s) 128s Selecting previously unselected package fonts-lato. 128s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52171 files and directories currently installed.) 128s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 128s Unpacking fonts-lato (2.015-1) ... 129s Selecting previously unselected package fonts-font-awesome. 129s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 129s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 129s Selecting previously unselected package fonts-mathjax. 129s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 129s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 129s Selecting previously unselected package libaec0:s390x. 129s Preparing to unpack .../03-libaec0_1.1.2-1_s390x.deb ... 129s Unpacking libaec0:s390x (1.1.2-1) ... 129s Selecting previously unselected package libblas3:s390x. 129s Preparing to unpack .../04-libblas3_3.12.0-3_s390x.deb ... 129s Unpacking libblas3:s390x (3.12.0-3) ... 129s Selecting previously unselected package libgfortran5:s390x. 129s Preparing to unpack .../05-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 129s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 129s Selecting previously unselected package libsz2:s390x. 129s Preparing to unpack .../06-libsz2_1.1.2-1_s390x.deb ... 129s Unpacking libsz2:s390x (1.1.2-1) ... 129s Selecting previously unselected package libhdf5-103-1:s390x. 129s Preparing to unpack .../07-libhdf5-103-1_1.10.10+repack-3ubuntu1_s390x.deb ... 129s Unpacking libhdf5-103-1:s390x (1.10.10+repack-3ubuntu1) ... 129s Selecting previously unselected package libhdf5-hl-100:s390x. 129s Preparing to unpack .../08-libhdf5-hl-100_1.10.10+repack-3ubuntu1_s390x.deb ... 129s Unpacking libhdf5-hl-100:s390x (1.10.10+repack-3ubuntu1) ... 129s Selecting previously unselected package libjs-jquery. 129s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 129s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 129s Selecting previously unselected package libjs-underscore. 129s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 129s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 129s Selecting previously unselected package libjs-sphinxdoc. 129s Preparing to unpack .../11-libjs-sphinxdoc_7.2.6-4_all.deb ... 129s Unpacking libjs-sphinxdoc (7.2.6-4) ... 129s Selecting previously unselected package liblapack3:s390x. 129s Preparing to unpack .../12-liblapack3_3.12.0-3_s390x.deb ... 129s Unpacking liblapack3:s390x (3.12.0-3) ... 129s Selecting previously unselected package liblbfgsb0:s390x. 129s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1_s390x.deb ... 129s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1) ... 129s Selecting previously unselected package liblzf1:s390x. 129s Preparing to unpack .../14-liblzf1_3.6-4_s390x.deb ... 129s Unpacking liblzf1:s390x (3.6-4) ... 129s Selecting previously unselected package python3-decorator. 129s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 129s Unpacking python3-decorator (5.1.1-5) ... 129s Selecting previously unselected package python3-numpy. 129s Preparing to unpack .../16-python3-numpy_1%3a1.24.2-2_s390x.deb ... 129s Unpacking python3-numpy (1:1.24.2-2) ... 130s Selecting previously unselected package python3-h5py-serial. 130s Preparing to unpack .../17-python3-h5py-serial_3.10.0-1ubuntu1_s390x.deb ... 130s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 130s Selecting previously unselected package python3-h5py. 130s Preparing to unpack .../18-python3-h5py_3.10.0-1ubuntu1_all.deb ... 130s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 130s Selecting previously unselected package python3-mappy. 130s Preparing to unpack .../19-python3-mappy_2.26+dfsg-1_s390x.deb ... 130s Unpacking python3-mappy (2.26+dfsg-1) ... 130s Selecting previously unselected package python3-tqdm. 130s Preparing to unpack .../20-python3-tqdm_4.64.1-2_all.deb ... 130s Unpacking python3-tqdm (4.64.1-2) ... 130s Selecting previously unselected package sphinx-rtd-theme-common. 130s Preparing to unpack .../21-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... 130s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 130s Selecting previously unselected package python3-scipy. 130s Preparing to unpack .../22-python3-scipy_1.11.4-6_s390x.deb ... 130s Unpacking python3-scipy (1.11.4-6) ... 131s Selecting previously unselected package tombo. 131s Preparing to unpack .../23-tombo_1.5.1-6_s390x.deb ... 131s Unpacking tombo (1.5.1-6) ... 131s Selecting previously unselected package libjs-mathjax. 131s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 131s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 132s Selecting previously unselected package tombo-doc. 132s Preparing to unpack .../25-tombo-doc_1.5.1-6_all.deb ... 132s Unpacking tombo-doc (1.5.1-6) ... 132s Selecting previously unselected package autopkgtest-satdep. 132s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 132s Unpacking autopkgtest-satdep (0) ... 132s Setting up fonts-lato (2.015-1) ... 132s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 132s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 132s Setting up python3-tqdm (4.64.1-2) ... 132s Setting up python3-mappy (2.26+dfsg-1) ... 132s Setting up libaec0:s390x (1.1.2-1) ... 132s Setting up python3-decorator (5.1.1-5) ... 132s Setting up libblas3:s390x (3.12.0-3) ... 132s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 132s Setting up liblzf1:s390x (3.6-4) ... 132s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 132s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 132s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 132s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 132s Setting up libsz2:s390x (1.1.2-1) ... 132s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 132s Setting up liblapack3:s390x (3.12.0-3) ... 132s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 132s Setting up python3-numpy (1:1.24.2-2) ... 134s Setting up libjs-sphinxdoc (7.2.6-4) ... 134s Setting up tombo-doc (1.5.1-6) ... 134s Setting up libhdf5-103-1:s390x (1.10.10+repack-3ubuntu1) ... 134s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1) ... 134s Setting up libhdf5-hl-100:s390x (1.10.10+repack-3ubuntu1) ... 134s Setting up python3-scipy (1.11.4-6) ... 136s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 137s Setting up python3-h5py (3.10.0-1ubuntu1) ... 137s Setting up tombo (1.5.1-6) ... 137s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 137s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 137s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 137s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 137s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 137s re.match('\+', fastq_rec[2]) is None): 137s Setting up autopkgtest-satdep (0) ... 137s Processing triggers for man-db (2.12.0-3) ... 137s Processing triggers for libc-bin (2.39-0ubuntu2) ... 140s (Reading database ... 59570 files and directories currently installed.) 140s Removing autopkgtest-satdep (0) ... 141s autopkgtest [11:05:47]: test run-unit-test: [----------------------- 141s ********* Testing help commands ********** 141s usage: tombo [-h] [-v] 141s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 141s ... 141s 141s ********** Tombo ********* 141s 141s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 141s 141s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 141s 141s Tombo command groups (additional help available within each command group): 141s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 141s preprocess Pre-process nanopore reads for Tombo processing. 141s filter Apply filter to Tombo index file for specified criterion. 141s detect_modifications Perform statistical testing to detect non-standard nucleotides. 141s text_output Output Tombo results in text files. 141s build_model Create canonical and alternative base Tombo models. 141s plot Save plots to visualize raw nanopore signal or testing results. 141s 141s options: 141s -h, --help show this help message and exit 141s -v, --version show Tombo version and exit. 141s usage: tombo resquiggle [--dna] [--rna] 141s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 141s [--q-score Q_SCORE] 141s [--signal-matching-score SIGNAL_MATCHING_SCORE] 141s [--processes PROCESSES] 141s [--corrected-group CORRECTED_GROUP] 141s [--basecall-group BASECALL_GROUP] 141s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 141s [--overwrite] 141s [--failed-reads-filename FAILED_READS_FILENAME] 141s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 141s [--print-advanced-arguments] [--quiet] [--help] 141s fast5s_basedir reference 141s 141s Required Arguments: 141s fast5s_basedir Directory containing fast5 files. All files ending in 141s "fast5" found recursively within this base directory 141s will be processed. 141s reference Reference genome/transcriptome FASTA file or minimap2 141s index (with "map-ont" preset) for mapping. 141s 141s Model Parameters: 141s --dna Explicitly select canonical DNA model. Default: 141s Automatically determine from FAST5s 141s --rna Explicitly select canonical RNA model. Default: 141s Automatically determine from FAST5s 141s 141s Read Filtering Argument: 141s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 141s Filter reads based on observations per base percentile 141s thresholds. Format thresholds as "percentile:thresh 141s [pctl2:thresh2 ...]". For example to filter reads with 141s 99th pctl > 200 obs/base or max > 5k obs/base use 141s "99:200 100:5000". 141s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 141s Default: 0.000000 141s --signal-matching-score SIGNAL_MATCHING_SCORE 141s Observed to expected signal matching score (higher 141s score indicates poor matching). Sample type defaults: 141s RNA : 2 || DNA : 1.1 141s 141s Multiprocessing Arguments: 141s --processes PROCESSES 141s Number of processes. Default: 1 141s 141s FAST5 Data Arguments: 141s --corrected-group CORRECTED_GROUP 141s FAST5 group created by resquiggle command. Default: 141s RawGenomeCorrected_000 141s --basecall-group BASECALL_GROUP 141s FAST5 group obtain original basecalls (under Analyses 141s group). Default: Basecall_1D_000 141s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 141s FAST5 subgroup(s) (under /Analyses/[--basecall- 141s group]/) containing basecalls and created within 141s [--corrected-group] containing re-squiggle results. 141s Default: ['BaseCalled_template'] 141s --overwrite Overwrite previous corrected group in FAST5 files. 141s Note: only effects --corrected-group or --new- 141s corrected-group. 141s 141s Input/Output Arguments: 141s --failed-reads-filename FAILED_READS_FILENAME 141s Output failed read filenames with assoicated error. 141s Default: Do not store failed reads. 141s --num-most-common-errors NUM_MOST_COMMON_ERRORS 141s Dynamically show this many most common errors so far 141s through run. Default: 0; Just show progress 141s 141s Advanced Arguments: 141s --print-advanced-arguments 141s Print advanced re-squiggle arguments and exit. 141s 141s Miscellaneous Arguments: 141s --quiet, -q Don't print status information. 141s --help, -h Print this help message and exit 141s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 141s --fastq-filenames 141s FASTQ_FILENAMES 141s [FASTQ_FILENAMES ...] 141s [--basecall-group BASECALL_GROUP] 141s [--basecall-subgroup BASECALL_SUBGROUP] 141s [--overwrite] 141s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 141s [--processes PROCESSES] 141s [--quiet] [--help] 141s 141s Required Arguments: 141s --fast5-basedir FAST5_BASEDIR 141s Directory containing fast5 files. 141s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 141s FASTQ filenames containing basecalls to be added to 141s raw FAST5 files. 141s 141s FAST5 Data Arguments: 141s --basecall-group BASECALL_GROUP 141s FAST5 group obtain original basecalls (under Analyses 141s group). Default: Basecall_1D_000 141s --basecall-subgroup BASECALL_SUBGROUP 141s FAST5 subgroup (under /Analyses/[--basecall-group]/) 141s under which to store basecalls from FASTQs. Default: 141s BaseCalled_template 141s --overwrite Overwrite previous corrected group in FAST5 files. 141s Note: only effects --corrected-group or --new- 141s corrected-group. 141s 141s Sequencing Summary Argument: 141s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 141s Sequencing summary filenames produced by albacore. 141s These can make annotation of raw FAST5 files with 141s FASTQ sequence much faster. 141s 141s Multiprocessing Argument: 141s --processes PROCESSES 141s Number of processes. Default: 1 141s 141s Miscellaneous Arguments: 141s --quiet, -q Don't print status information. 141s --help, -h Print this help message and exit 141s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 141s [FAST5_BASEDIRS ...] 141s [--corrected-group CORRECTED_GROUP] 141s [--quiet] [--help] 141s 141s Required Argument: 141s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 141s Directories containing fast5 files. 141s 141s FAST5 Data Argument: 141s --corrected-group CORRECTED_GROUP 141s FAST5 group created by resquiggle command. Default: 141s RawGenomeCorrected_000 141s 141s Miscellaneous Arguments: 141s --quiet, -q Don't print status information. 141s --help, -h Print this help message and exit 141s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 141s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 141s [--corrected-group CORRECTED_GROUP] [--quiet] 141s [--help] 141s 141s Required Argument: 141s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 141s Directories containing fast5 files. 141s 141s Read Filtering Argument: 141s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 141s Filter reads based on observations per base percentile 141s thresholds. Format thresholds as "percentile:thresh 141s [pctl2:thresh2 ...]". For example to filter reads with 141s 99th pctl > 200 obs/base or max > 5k obs/base use 141s "99:200 100:5000". 141s 141s FAST5 Data Argument: 141s --corrected-group CORRECTED_GROUP 141s FAST5 group created by resquiggle command. Default: 141s RawGenomeCorrected_000 141s 141s Miscellaneous Arguments: 141s --quiet, -q Don't print status information. 141s --help, -h Print this help message and exit 141s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 141s [FAST5_BASEDIRS ...] 141s [--percent-to-filter PERCENT_TO_FILTER] 141s [--corrected-group CORRECTED_GROUP] 141s [--quiet] [--help] 141s 141s Required Arguments: 141s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 141s Directories containing fast5 files. 141s 141s Read Filtering Argument: 141s --percent-to-filter PERCENT_TO_FILTER 141s Percentage of all reads to filter. Reads are randomly 141s selected weighted according to the approximate 141s coverage at the mapped genomic location. This can be 141s useful in modeling and testing. Default: 10.000000 141s 141s FAST5 Data Arguments: 141s --corrected-group CORRECTED_GROUP 141s FAST5 group created by resquiggle command. Default: 141s RawGenomeCorrected_000 141s 141s Miscellaneous Arguments: 141s --quiet, -q Don't print status information. 141s --help, -h Print this help message and exit 141s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 141s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 141s [--corrected-group CORRECTED_GROUP] 141s [--basecall-group BASECALL_GROUP] [--quiet] 141s [--help] 141s 141s Required Arguments: 141s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 141s Directories containing fast5 files. 141s 141s Read Filtering Argument: 141s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 141s Default: 7.000000 141s 141s FAST5 Data Arguments: 141s --corrected-group CORRECTED_GROUP 141s FAST5 group created by resquiggle command. Default: 141s RawGenomeCorrected_000 141s --basecall-group BASECALL_GROUP 141s FAST5 group obtain original basecalls (under Analyses 141s group). Default: Basecall_1D_000 141s 141s Miscellaneous Arguments: 141s --quiet, -q Don't print status information. 141s --help, -h Print this help message and exit 141s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 141s [FAST5_BASEDIRS ...] 141s --signal-matching-score 141s SIGNAL_MATCHING_SCORE 141s [--corrected-group CORRECTED_GROUP] 141s [--quiet] [--help] 141s 141s Required Arguments: 141s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 141s Directories containing fast5 files. 141s --signal-matching-score SIGNAL_MATCHING_SCORE 141s Observed to expected signal matching score (higher 141s score indicates poor matching). Sample type defaults: 141s RNA : 2 || DNA : 1.1 141s 141s FAST5 Data Arguments: 141s --corrected-group CORRECTED_GROUP 141s FAST5 group created by resquiggle command. Default: 141s RawGenomeCorrected_000 141s 141s Miscellaneous Arguments: 141s --quiet, -q Don't print status information. 141s --help, -h Print this help message and exit 142s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 142s [FAST5_BASEDIRS ...] 142s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 142s [--include-partial-overlap] 142s [--corrected-group CORRECTED_GROUP] 142s [--quiet] [--help] 142s 142s Required Arguments: 142s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 142s Directories containing fast5 files. 142s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 142s Filter out reads not falling completely within include 142s regions. Omit start and end coordinates to include an 142s entire chromosome/sequence record. Format regions as 142s "chrm[:start-end] [chrm2[:start2-end2] ...]". 142s 142s Filter Argument: 142s --include-partial-overlap 142s Include reads that partially overlap the specified 142s region. Default: Only include reads completely 142s contained in a specified region 142s 142s FAST5 Data Argument: 142s --corrected-group CORRECTED_GROUP 142s FAST5 group created by resquiggle command. Default: 142s RawGenomeCorrected_000 142s 142s Miscellaneous Arguments: 142s --quiet, -q Don't print status information. 142s --help, -h Print this help message and exit 142s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 142s [FAST5_BASEDIRS ...] 142s --statistics-file-basename 142s STATISTICS_FILE_BASENAME [--dna] 142s [--rna] 142s [--fishers-method-context FISHERS_METHOD_CONTEXT] 142s [--minimum-test-reads MINIMUM_TEST_READS] 142s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 142s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 142s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 142s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 142s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 142s [--processes PROCESSES] 142s [--corrected-group CORRECTED_GROUP] 142s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 142s [--quiet] [--help] 142s 142s Required Argument: 142s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 142s Directories containing fast5 files. 142s --statistics-file-basename STATISTICS_FILE_BASENAME 142s File base name to save base by base statistics from 142s testing. Filenames will be [--statistics-file- 142s basename].[--alternate-bases]?.tombo.stats 142s 142s Comparison Model Arguments: 142s --dna Explicitly select canonical DNA model. Default: 142s Automatically determine from FAST5s 142s --rna Explicitly select canonical RNA model. Default: 142s Automatically determine from FAST5s 142s 142s Significance Test Arguments: 142s --fishers-method-context FISHERS_METHOD_CONTEXT 142s Number of context bases up and downstream over which 142s to compute Fisher's method combined p-values. Note: 142s Not applicable for alternative model likelihood ratio 142s tests. Default: 1. 142s --minimum-test-reads MINIMUM_TEST_READS 142s Number of reads required at a position to perform 142s significance testing or contribute to model 142s estimation. Default: 1 142s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 142s P-value threshold when computing fraction of 142s significant reads at each genomic position. If two 142s values are provided, statistics between these values 142s are not considered. Default thresholds: DNA:0.15-0.5 , 142s RNA:0.05-0.4 142s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 142s Dampen fraction modified estimates for low coverage 142s sites. Two parameters are unmodified and modified 142s pseudo read counts. This is equivalent to a beta prior 142s on the fraction estimate. Set to "0 0" to disable 142s dampened fraction estimation. Default: [2, 0] 142s 142s Output Argument: 142s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 142s Base for binary files containing per-read statistics 142s from statistical testing. Filenames will be [--per- 142s read-statistics-basename].[--alternate- 142s bases]?.tombo.per_read_stats 142s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 142s Number of the most significant sites to store for 142s faster access. If a longer list of most significant 142s sites is required the list must be re-computed from 142s all batches. Very large values can increase RAM usage. 142s Default: 100000 142s 142s Multiprocessing Arguments: 142s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 142s Size of regions over which to multiprocesses statistic 142s computation. For very deep samples a smaller value is 142s recommmended in order to control memory consumption. 142s Default: 10000 142s --processes PROCESSES 142s Number of processes. Default: 1 142s 142s FAST5 Data Arguments: 142s --corrected-group CORRECTED_GROUP 142s FAST5 group created by resquiggle command. Default: 142s RawGenomeCorrected_000 142s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 142s FAST5 subgroup(s) (under /Analyses/[--basecall- 142s group]/) containing basecalls and created within 142s [--corrected-group] containing re-squiggle results. 142s Default: ['BaseCalled_template'] 142s 142s Miscellaneous Arguments: 142s --quiet, -q Don't print status information. 142s --help, -h Print this help message and exit 142s usage: tombo detect_modifications alternative_model 142s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 142s [--statistics-file-basename STATISTICS_FILE_BASENAME] 142s [--alternate-bases {CpG,5mC,dcm,dam,6mA} [{CpG,5mC,dcm,dam,6mA} ...]] 142s [--print-available-models] 142s [--dna] [--rna] 142s [--minimum-test-reads MINIMUM_TEST_READS] 142s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 142s [--standard-log-likelihood-ratio] 142s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 142s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 142s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 142s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 142s [--processes PROCESSES] 142s [--corrected-group CORRECTED_GROUP] 142s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 142s [--quiet] [--help] 142s 142s Required Argument: 142s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 142s Directories containing fast5 files. 142s --statistics-file-basename STATISTICS_FILE_BASENAME 142s File base name to save base by base statistics from 142s testing. Filenames will be [--statistics-file- 142s basename].[--alternate-bases]?.tombo.stats 142s --alternate-bases {CpG,5mC,dcm,dam,6mA} [{CpG,5mC,dcm,dam,6mA} ...] 142s Default non-standard base model for testing (not 142s required if user created --alternate-model-filenames 142s is provided). 142s 142s Comparison Arguments: 142s --print-available-models 142s Print available alternative models and exit. 142s --dna Explicitly select canonical DNA model. Default: 142s Automatically determine from FAST5s 142s --rna Explicitly select canonical RNA model. Default: 142s Automatically determine from FAST5s 142s 142s Significance Test Arguments: 142s --minimum-test-reads MINIMUM_TEST_READS 142s Number of reads required at a position to perform 142s significance testing or contribute to model 142s estimation. Default: 1 142s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 142s Log likelihood ratio threshold when computing fraction 142s of significant reads at each genomic position. If two 142s values are provided, statistics between these values 142s are not considered. Default thresholds: DNA:-1.5-2.5 , 142s RNA:-2.5-2.5 142s --standard-log-likelihood-ratio 142s Use a standard log likelihood ratio (LLR) statistic. 142s Default is to use an outlier-robust LLR-like 142s statistic. Detail in full online documentation. 142s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 142s Dampen fraction modified estimates for low coverage 142s sites. Two parameters are unmodified and modified 142s pseudo read counts. This is equivalent to a beta prior 142s on the fraction estimate. Set to "0 0" to disable 142s dampened fraction estimation. Default: [2, 0] 142s 142s Output Argument: 142s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 142s Base for binary files containing per-read statistics 142s from statistical testing. Filenames will be [--per- 142s read-statistics-basename].[--alternate- 142s bases]?.tombo.per_read_stats 142s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 142s Number of the most significant sites to store for 142s faster access. If a longer list of most significant 142s sites is required the list must be re-computed from 142s all batches. Very large values can increase RAM usage. 142s Default: 100000 142s 142s Multiprocessing Arguments: 142s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 142s Size of regions over which to multiprocesses statistic 142s computation. For very deep samples a smaller value is 142s recommmended in order to control memory consumption. 142s Default: 10000 142s --processes PROCESSES 142s Number of processes. Default: 1 142s 142s FAST5 Data Arguments: 142s --corrected-group CORRECTED_GROUP 142s FAST5 group created by resquiggle command. Default: 142s RawGenomeCorrected_000 142s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 142s FAST5 subgroup(s) (under /Analyses/[--basecall- 142s group]/) containing basecalls and created within 142s [--corrected-group] containing re-squiggle results. 142s Default: ['BaseCalled_template'] 142s 142s Miscellaneous Arguments: 142s --quiet, -q Don't print status information. 142s --help, -h Print this help message and exit 142s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 142s FAST5_BASEDIRS 142s [FAST5_BASEDIRS ...] 142s --statistics-file-basename 142s STATISTICS_FILE_BASENAME 142s --control-fast5-basedirs 142s CONTROL_FAST5_BASEDIRS 142s [CONTROL_FAST5_BASEDIRS ...] 142s [--sample-only-estimates] 142s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 142s [--dna] [--rna] 142s [--fishers-method-context FISHERS_METHOD_CONTEXT] 142s [--minimum-test-reads MINIMUM_TEST_READS] 142s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 142s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 142s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 142s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 142s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 142s [--processes PROCESSES] 142s [--corrected-group CORRECTED_GROUP] 142s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 142s [--quiet] [--help] 142s 142s Required Argument: 142s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 142s Directories containing fast5 files. 142s --statistics-file-basename STATISTICS_FILE_BASENAME 142s File base name to save base by base statistics from 142s testing. Filenames will be [--statistics-file- 142s basename].[--alternate-bases]?.tombo.stats 142s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 142s Set of directories containing fast5 files for control 142s reads, containing only canonical nucleotides. 142s 142s Model Prior Arguments: 142s --sample-only-estimates 142s Only use canonical sample to estimate expected signal 142s level and spread. Default: Use canonical model to 142s improve estimtates (esp. for low coverage regions) 142s using baysian posterior estimates. 142s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 142s Prior weights (one each for mean and spread) applied 142s to canonical base model for estimating posterior model 142s parameters for sample comparison. Default: [5, 40] 142s --dna Explicitly select canonical DNA model. Default: 142s Automatically determine from FAST5s 142s --rna Explicitly select canonical RNA model. Default: 142s Automatically determine from FAST5s 142s 142s Significance Test Arguments: 142s --fishers-method-context FISHERS_METHOD_CONTEXT 142s Number of context bases up and downstream over which 142s to compute Fisher's method combined p-values. Note: 142s Not applicable for alternative model likelihood ratio 142s tests. Default: 1. 142s --minimum-test-reads MINIMUM_TEST_READS 142s Number of reads required at a position to perform 142s significance testing or contribute to model 142s estimation. Default: 1 142s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 142s P-value threshold when computing fraction of 142s significant reads at each genomic position. If two 142s values are provided, statistics between these values 142s are not considered. Default thresholds: DNA:0.15-0.5 , 142s RNA:0.05-0.4 142s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 142s Dampen fraction modified estimates for low coverage 142s sites. Two parameters are unmodified and modified 142s pseudo read counts. This is equivalent to a beta prior 142s on the fraction estimate. Set to "0 0" to disable 142s dampened fraction estimation. Default: [2, 0] 142s 142s Output Argument: 142s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 142s Base for binary files containing per-read statistics 142s from statistical testing. Filenames will be [--per- 142s read-statistics-basename].[--alternate- 142s bases]?.tombo.per_read_stats 142s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 142s Number of the most significant sites to store for 142s faster access. If a longer list of most significant 142s sites is required the list must be re-computed from 142s all batches. Very large values can increase RAM usage. 142s Default: 100000 142s 142s Multiprocessing Arguments: 142s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 142s Size of regions over which to multiprocesses statistic 142s computation. For very deep samples a smaller value is 142s recommmended in order to control memory consumption. 142s Default: 10000 142s --processes PROCESSES 142s Number of processes. Default: 1 142s 142s FAST5 Data Arguments: 142s --corrected-group CORRECTED_GROUP 142s FAST5 group created by resquiggle command. Default: 142s RawGenomeCorrected_000 142s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 142s FAST5 subgroup(s) (under /Analyses/[--basecall- 142s group]/) containing basecalls and created within 142s [--corrected-group] containing re-squiggle results. 142s Default: ['BaseCalled_template'] 142s 142s Miscellaneous Arguments: 142s --quiet, -q Don't print status information. 142s --help, -h Print this help message and exit 142s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 142s FAST5_BASEDIRS 142s [FAST5_BASEDIRS ...] 142s --statistics-file-basename 142s STATISTICS_FILE_BASENAME 142s --alternate-fast5-basedirs 142s ALTERNATE_FAST5_BASEDIRS 142s [ALTERNATE_FAST5_BASEDIRS ...] 142s [--fishers-method-context FISHERS_METHOD_CONTEXT] 142s [--minimum-test-reads MINIMUM_TEST_READS] 142s [--statistic-type {ks,u,t}] 142s [--store-p-value] 142s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 142s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 142s [--processes PROCESSES] 142s [--corrected-group CORRECTED_GROUP] 142s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 142s [--quiet] [--help] 142s 142s Required Argument: 142s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 142s Directories containing fast5 files. 142s --statistics-file-basename STATISTICS_FILE_BASENAME 142s File base name to save base by base statistics from 142s testing. Filenames will be [--statistics-file- 142s basename].[--alternate-bases]?.tombo.stats 142s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 142s Set of directories containing fast5 files for 142s alternate set of reads. 142s 142s Significance Test Arguments: 142s --fishers-method-context FISHERS_METHOD_CONTEXT 142s Number of context bases up and downstream over which 142s to compute Fisher's method combined p-values. Note: 142s Not applicable for alternative model likelihood ratio 142s tests. Default: 1. 142s --minimum-test-reads MINIMUM_TEST_READS 142s Number of reads required at a position to perform 142s significance testing or contribute to model 142s estimation. Default: 50 142s --statistic-type {ks,u,t} 142s Type of statistical test to apply. Default: "ks" 142s --store-p-value Store p-value instead of effect-size statistic. 142s Statistics are D-statistic (KS-test), deviation from 142s even common language effect size (u-test), and Cohen's 142s D (t-test). 142s 142s Output Argument: 142s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 142s Number of the most significant sites to store for 142s faster access. If a longer list of most significant 142s sites is required the list must be re-computed from 142s all batches. Very large values can increase RAM usage. 142s Default: 100000 142s 142s Multiprocessing Arguments: 142s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 142s Size of regions over which to multiprocesses statistic 142s computation. For very deep samples a smaller value is 142s recommmended in order to control memory consumption. 142s Default: 10000 142s --processes PROCESSES 142s Number of processes. Default: 1 142s 142s FAST5 Data Arguments: 142s --corrected-group CORRECTED_GROUP 142s FAST5 group created by resquiggle command. Default: 142s RawGenomeCorrected_000 142s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 142s FAST5 subgroup(s) (under /Analyses/[--basecall- 142s group]/) containing basecalls and created within 142s [--corrected-group] containing re-squiggle results. 142s Default: ['BaseCalled_template'] 142s 142s Miscellaneous Arguments: 142s --quiet, -q Don't print status information. 142s --help, -h Print this help message and exit 142s usage: tombo detect_modifications aggregate_per_read_stats 142s --per-read-statistics-filename 142s PER_READ_STATISTICS_FILENAME 142s --statistics-filename 142s STATISTICS_FILENAME 142s --single-read-threshold 142s SINGLE_READ_THRESHOLD 142s [SINGLE_READ_THRESHOLD ...] 142s [--minimum-test-reads MINIMUM_TEST_READS] 142s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 142s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 142s [--processes PROCESSES] 142s [--corrected-group CORRECTED_GROUP] 142s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 142s [--quiet] [--help] 142s 142s Required Argument: 142s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 142s Binary file containing per-read statistics from 142s statistical testing. 142s --statistics-filename STATISTICS_FILENAME 142s File to save/load genomic base anchored statistics. 142s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 142s P-value or log likelihood ratio threshold when 142s computing fraction of significant reads at each 142s genomic position. If two values are provided, 142s statistics between these values are not considered. 142s 142s Significance Test Arguments: 142s --minimum-test-reads MINIMUM_TEST_READS 142s Number of reads required at a position to perform 142s significance testing or contribute to model 142s estimation. Default: 1 142s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 142s Dampen fraction modified estimates for low coverage 142s sites. Two parameters are unmodified and modified 142s pseudo read counts. This is equivalent to a beta prior 142s on the fraction estimate. Set to "0 0" to disable 142s dampened fraction estimation. Default: [2, 0] 142s 142s Output Argument: 142s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 142s Number of the most significant sites to store for 142s faster access. If a longer list of most significant 142s sites is required the list must be re-computed from 142s all batches. Very large values can increase RAM usage. 142s Default: 100000 142s 142s Multiprocessing Arguments: 142s --processes PROCESSES 142s Number of processes. Default: 1 142s 142s FAST5 Data Arguments: 142s --corrected-group CORRECTED_GROUP 142s FAST5 group created by resquiggle command. Default: 142s RawGenomeCorrected_000 142s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 142s FAST5 subgroup(s) (under /Analyses/[--basecall- 142s group]/) containing basecalls and created within 142s [--corrected-group] containing re-squiggle results. 142s Default: ['BaseCalled_template'] 142s 142s Miscellaneous Arguments: 142s --quiet, -q Don't print status information. 142s --help, -h Print this help message and exit 142s usage: tombo text_output browser_files 142s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 142s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 142s [--statistics-filename STATISTICS_FILENAME] 142s [--genome-fasta GENOME_FASTA] 142s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 142s [--browser-file-basename BROWSER_FILE_BASENAME] 142s [--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} ...]] 142s [--corrected-group CORRECTED_GROUP] 142s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 142s [--quiet] [--help] 142s 142s Data Arguments: 142s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 142s Directories containing fast5 files. 142s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 142s Set of directories containing fast5 files for control 142s reads, containing only canonical nucleotides. 142s --statistics-filename STATISTICS_FILENAME 142s File to save/load genomic base anchored statistics. 142s 142s Statistic Motif Filter Arguments: 142s --genome-fasta GENOME_FASTA 142s FASTA file used to re-squiggle. For faster sequence 142s access. 142s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 142s Ground truth, motif centered, modified base 142s descriptions for output filtering. Format descriptions 142s as: "motif:mod_pos:name". The mod_pos indicates the 142s modified base within the motif (1-based index). 142s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 142s output for identification of E. coli dam and dcm 142s methylation. 142s 142s Output Arguments: 142s --browser-file-basename BROWSER_FILE_BASENAME 142s Basename for output browser files. Two files (plus and 142s minus strand) will be produced for each --file-types 142s supplied. Filenames formatted as "[browser-file- 142s basename].[file- 142s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 142s Default: tombo_results 142s --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} ...] 142s Data types of genome browser files to produce. 142s Produced coverage files are in bedGraph format, while 142s all other file types will be in wiggle format 142s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 142s Default: "coverage" 142s 142s FAST5 Data Arguments: 142s --corrected-group CORRECTED_GROUP 142s FAST5 group created by resquiggle command. Default: 142s RawGenomeCorrected_000 142s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 142s FAST5 subgroup(s) (under /Analyses/[--basecall- 142s group]/) containing basecalls and created within 142s [--corrected-group] containing re-squiggle results. 142s Default: ['BaseCalled_template'] 142s 142s Miscellaneous Arguments: 142s --quiet, -q Don't print status information. 142s --help, -h Print this help message and exit 142s usage: tombo text_output signif_sequence_context --statistics-filename 142s STATISTICS_FILENAME 142s [--genome-fasta GENOME_FASTA] 142s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 142s [--num-regions NUM_REGIONS] 142s [--num-bases NUM_BASES] 142s [--sequences-filename SEQUENCES_FILENAME] 142s [--corrected-group CORRECTED_GROUP] 142s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 142s [--quiet] [--help] 142s 142s Required Argument: 142s --statistics-filename STATISTICS_FILENAME 142s File to save/load genomic base anchored statistics. 142s 142s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 142s --genome-fasta GENOME_FASTA 142s FASTA file used to re-squiggle. For faster sequence 142s access. 142s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 142s Directories containing fast5 files. 142s 142s Region Selection Arguments: 142s --num-regions NUM_REGIONS 142s Number of regions to plot. Default: 100 142s --num-bases NUM_BASES 142s Number of bases to plot/output. Default: 15 142s 142s Output Arguments: 142s --sequences-filename SEQUENCES_FILENAME 142s File for sequences from selected regions. Sequences 142s will be stored in FASTA format. Default: 142s tombo_results.significant_regions.fasta. 142s 142s FAST5 Data Arguments: 142s --corrected-group CORRECTED_GROUP 142s FAST5 group created by resquiggle command. Default: 142s RawGenomeCorrected_000 142s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 142s FAST5 subgroup(s) (under /Analyses/[--basecall- 142s group]/) containing basecalls and created within 142s [--corrected-group] containing re-squiggle results. 142s Default: ['BaseCalled_template'] 142s 142s Miscellaneous Arguments: 142s --quiet, -q Don't print status information. 142s --help, -h Print this help message and exit 142s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 142s [FAST5_BASEDIRS ...] 142s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 142s [--plot-standard-model] 142s [--plot-alternate-model {dcm,6mA,dam,CpG,5mC}] 142s [--overplot-threshold OVERPLOT_THRESHOLD] 142s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 142s [--num-regions NUM_REGIONS] 142s [--num-bases NUM_BASES] 142s [--pdf-filename PDF_FILENAME] 142s [--corrected-group CORRECTED_GROUP] 142s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 142s [--quiet] [--help] 142s 142s Required Argument: 142s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 142s Directories containing fast5 files. 142s 142s Comparison Arguments: 142s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 142s Set of directories containing fast5 files for control 142s reads, containing only canonical nucleotides. 142s --plot-standard-model 142s Add default standard model distribution to the plot. 142s --plot-alternate-model {dcm,6mA,dam,CpG,5mC} 142s Add alternative model distribution to the plot. 142s 142s Overplotting Arguments: 142s --overplot-threshold OVERPLOT_THRESHOLD 142s Coverage level to trigger alternative plot type 142s instead of raw signal. Default: 50 142s --overplot-type {Downsample,Boxplot,Quantile,Density} 142s Plot type for regions with higher coverage. Default: 142s Downsample 142s 142s Plotting Region Arguments: 142s --num-regions NUM_REGIONS 142s Number of regions to plot. Default: 10 142s --num-bases NUM_BASES 142s Number of bases to plot/output. Default: 21 142s 142s Output Argument: 142s --pdf-filename PDF_FILENAME 142s PDF filename to store plot(s). Default: 142s tombo_results.max_coverage.pdf 142s 142s FAST5 Data Arguments: 142s --corrected-group CORRECTED_GROUP 142s FAST5 group created by resquiggle command. Default: 142s RawGenomeCorrected_000 142s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 142s FAST5 subgroup(s) (under /Analyses/[--basecall- 142s group]/) containing basecalls and created within 142s [--corrected-group] containing re-squiggle results. 142s Default: ['BaseCalled_template'] 142s 142s Miscellaneous Arguments: 142s --quiet, -q Don't print status information. 142s --help, -h Print this help message and exit 142s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 142s [FAST5_BASEDIRS ...] --genome-locations 142s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 142s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 142s [--plot-standard-model] 142s [--plot-alternate-model {6mA,5mC,CpG,dcm,dam}] 142s [--overplot-threshold OVERPLOT_THRESHOLD] 142s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 142s [--num-bases NUM_BASES] 142s [--pdf-filename PDF_FILENAME] 142s [--corrected-group CORRECTED_GROUP] 142s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 142s [--quiet] [--help] 142s 142s Required Arguments: 142s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 142s Directories containing fast5 files. 142s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 142s Genomic locations at which to plot signal. Format 142s locations as "chrm:position[:strand] 142s [chrm2:position2[:strand2] ...]" (strand not 142s applicable for all applications) 142s 142s Comparison Arguments: 142s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 142s Set of directories containing fast5 files for control 142s reads, containing only canonical nucleotides. 142s --plot-standard-model 142s Add default standard model distribution to the plot. 142s --plot-alternate-model {6mA,5mC,CpG,dcm,dam} 142s Add alternative model distribution to the plot. 142s 142s Overplotting Arguments: 142s --overplot-threshold OVERPLOT_THRESHOLD 142s Coverage level to trigger alternative plot type 142s instead of raw signal. Default: 50 142s --overplot-type {Downsample,Boxplot,Quantile,Density} 142s Plot type for regions with higher coverage. Default: 142s Downsample 142s 142s Plotting Region Argument: 142s --num-bases NUM_BASES 142s Number of bases to plot/output. Default: 21 142s 142s Output Argument: 142s --pdf-filename PDF_FILENAME 142s PDF filename to store plot(s). Default: 142s tombo_results.genome_locations.pdf 142s 142s FAST5 Data Arguments: 142s --corrected-group CORRECTED_GROUP 142s FAST5 group created by resquiggle command. Default: 142s RawGenomeCorrected_000 142s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 142s FAST5 subgroup(s) (under /Analyses/[--basecall- 142s group]/) containing basecalls and created within 142s [--corrected-group] containing re-squiggle results. 142s Default: ['BaseCalled_template'] 142s 142s Miscellaneous Arguments: 142s --quiet, -q Don't print status information. 142s --help, -h Print this help message and exit 142s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 142s [FAST5_BASEDIRS ...] --motif MOTIF 142s --genome-fasta GENOME_FASTA 142s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 142s [--plot-standard-model] 142s [--plot-alternate-model {dam,dcm,6mA,CpG,5mC}] 142s [--overplot-threshold OVERPLOT_THRESHOLD] 142s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 142s [--num-regions NUM_REGIONS] 142s [--num-bases NUM_BASES] [--deepest-coverage] 142s [--pdf-filename PDF_FILENAME] 142s [--corrected-group CORRECTED_GROUP] 142s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 142s [--quiet] [--help] 142s 142s Required Arguments: 142s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 142s Directories containing fast5 files. 142s --motif MOTIF Motif of interest at which to plot signal and 142s statsitics. Supports IUPAC single letter codes (use T 142s for RNA). 142s --genome-fasta GENOME_FASTA 142s FASTA file used to re-squiggle. For faster sequence 142s access. 142s 142s Comparison Arguments: 142s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 142s Set of directories containing fast5 files for control 142s reads, containing only canonical nucleotides. 142s --plot-standard-model 142s Add default standard model distribution to the plot. 142s --plot-alternate-model {dam,dcm,6mA,CpG,5mC} 142s Add alternative model distribution to the plot. 142s 142s Overplotting Arguments: 142s --overplot-threshold OVERPLOT_THRESHOLD 142s Coverage level to trigger alternative plot type 142s instead of raw signal. Default: 50 142s --overplot-type {Downsample,Boxplot,Quantile,Density} 142s Plot type for regions with higher coverage. Default: 142s Downsample 142s 142s Plotting Region Arguments: 142s --num-regions NUM_REGIONS 142s Number of regions to plot. Default: 10 142s --num-bases NUM_BASES 142s Number of bases to plot/output. Default: 21 142s --deepest-coverage Plot the deepest coverage regions. 142s 142s Output Argument: 142s --pdf-filename PDF_FILENAME 142s PDF filename to store plot(s). Default: 142s tombo_results.motif_centered.pdf 142s 142s FAST5 Data Arguments: 142s --corrected-group CORRECTED_GROUP 142s FAST5 group created by resquiggle command. Default: 142s RawGenomeCorrected_000 142s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 142s FAST5 subgroup(s) (under /Analyses/[--basecall- 142s group]/) containing basecalls and created within 142s [--corrected-group] containing re-squiggle results. 142s Default: ['BaseCalled_template'] 142s 142s Miscellaneous Arguments: 142s --quiet, -q Don't print status information. 142s --help, -h Print this help message and exit 142s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 142s [FAST5_BASEDIRS ...] --control-fast5-basedirs 142s CONTROL_FAST5_BASEDIRS 142s [CONTROL_FAST5_BASEDIRS ...] 142s [--overplot-threshold OVERPLOT_THRESHOLD] 142s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 142s [--num-regions NUM_REGIONS] 142s [--num-bases NUM_BASES] 142s [--pdf-filename PDF_FILENAME] 142s [--sequences-filename SEQUENCES_FILENAME] 142s [--corrected-group CORRECTED_GROUP] 142s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 142s [--quiet] [--help] 142s 142s Required Arguments: 142s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 142s Directories containing fast5 files. 142s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 142s Set of directories containing fast5 files for control 142s reads, containing only canonical nucleotides. 142s 142s Overplotting Arguments: 142s --overplot-threshold OVERPLOT_THRESHOLD 142s Coverage level to trigger alternative plot type 142s instead of raw signal. Default: 50 142s --overplot-type {Downsample,Boxplot,Quantile,Density} 142s Plot type for regions with higher coverage. Default: 142s Downsample 142s 142s Plotting Region Arguments: 142s --num-regions NUM_REGIONS 142s Number of regions to plot. Default: 10 142s --num-bases NUM_BASES 142s Number of bases to plot/output. Default: 21 142s 142s Output Arguments: 142s --pdf-filename PDF_FILENAME 142s PDF filename to store plot(s). Default: 142s tombo_results.max_difference.pdf 142s --sequences-filename SEQUENCES_FILENAME 142s File for sequences from selected regions. Sequences 142s will be stored in FASTA format. Default: None. 142s 142s FAST5 Data Arguments: 142s --corrected-group CORRECTED_GROUP 142s FAST5 group created by resquiggle command. Default: 142s RawGenomeCorrected_000 142s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 142s FAST5 subgroup(s) (under /Analyses/[--basecall- 142s group]/) containing basecalls and created within 142s [--corrected-group] containing re-squiggle results. 142s Default: ['BaseCalled_template'] 142s 142s Miscellaneous Arguments: 142s --quiet, -q Don't print status information. 142s --help, -h Print this help message and exit 142s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 142s [FAST5_BASEDIRS ...] --statistics-filename 142s STATISTICS_FILENAME 142s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 142s [--plot-standard-model] 142s [--plot-alternate-model {dcm,CpG,dam,6mA,5mC}] 142s [--overplot-threshold OVERPLOT_THRESHOLD] 142s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 142s [--num-regions NUM_REGIONS] 142s [--num-bases NUM_BASES] 142s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 142s [--pdf-filename PDF_FILENAME] 142s [--sequences-filename SEQUENCES_FILENAME] 142s [--corrected-group CORRECTED_GROUP] 142s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 142s [--quiet] [--help] 142s 142s Required Arguments: 142s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 142s Directories containing fast5 files. 142s --statistics-filename STATISTICS_FILENAME 142s File to save/load genomic base anchored statistics. 142s 142s Comparison Arguments: 142s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 142s Set of directories containing fast5 files for control 142s reads, containing only canonical nucleotides. 142s --plot-standard-model 142s Add default standard model distribution to the plot. 142s --plot-alternate-model {dcm,CpG,dam,6mA,5mC} 142s Add alternative model distribution to the plot. 142s 142s Overplotting Arguments: 142s --overplot-threshold OVERPLOT_THRESHOLD 142s Coverage level to trigger alternative plot type 142s instead of raw signal. Default: 50 142s --overplot-type {Downsample,Boxplot,Quantile,Density} 142s Plot type for regions with higher coverage. Default: 142s Downsample 142s 142s Plotting Region Arguments: 142s --num-regions NUM_REGIONS 142s Number of regions to plot. Default: 10 142s --num-bases NUM_BASES 142s Number of bases to plot/output. Default: 21 142s 142s Statistical Argument: 142s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 142s Dampen fraction modified estimates for low coverage 142s sites. Two parameters are unmodified and modified 142s pseudo read counts. This is equivalent to a beta prior 142s on the fraction estimate. Set to "0 0" to disable 142s dampened fraction estimation. Default: [2, 0] 142s 142s Output Arguments: 142s --pdf-filename PDF_FILENAME 142s PDF filename to store plot(s). Default: 142s tombo_results.significant_difference.pdf 142s --sequences-filename SEQUENCES_FILENAME 142s File for sequences from selected regions. Sequences 142s will be stored in FASTA format. Default: None. 142s 142s FAST5 Data Arguments: 142s --corrected-group CORRECTED_GROUP 142s FAST5 group created by resquiggle command. Default: 142s RawGenomeCorrected_000 142s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 142s FAST5 subgroup(s) (under /Analyses/[--basecall- 142s group]/) containing basecalls and created within 142s [--corrected-group] containing re-squiggle results. 142s Default: ['BaseCalled_template'] 142s 142s Miscellaneous Arguments: 142s --quiet, -q Don't print status information. 142s --help, -h Print this help message and exit 143s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 143s [FAST5_BASEDIRS ...] --motif MOTIF 143s --statistics-filename STATISTICS_FILENAME 143s --genome-fasta GENOME_FASTA 143s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 143s [--plot-standard-model] 143s [--plot-alternate-model {5mC,dam,dcm,6mA,CpG}] 143s [--overplot-threshold OVERPLOT_THRESHOLD] 143s [--num-regions NUM_REGIONS] 143s [--num-context NUM_CONTEXT] 143s [--num-statistics NUM_STATISTICS] 143s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 143s [--pdf-filename PDF_FILENAME] 143s [--corrected-group CORRECTED_GROUP] 143s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 143s [--quiet] [--help] 143s 143s Required Arguments: 143s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 143s Directories containing fast5 files. 143s --motif MOTIF Motif of interest at which to plot signal and 143s statsitics. Supports IUPAC single letter codes (use T 143s for RNA). 143s --statistics-filename STATISTICS_FILENAME 143s File to save/load genomic base anchored statistics. 143s --genome-fasta GENOME_FASTA 143s FASTA file used to re-squiggle. For faster sequence 143s access. 143s 143s Comparison Arguments: 143s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 143s Set of directories containing fast5 files for control 143s reads, containing only canonical nucleotides. 143s --plot-standard-model 143s Add default standard model distribution to the plot. 143s --plot-alternate-model {5mC,dam,dcm,6mA,CpG} 143s Add alternative model distribution to the plot. 143s 143s Overplotting Argument: 143s --overplot-threshold OVERPLOT_THRESHOLD 143s Coverage level to trigger alternative plot type 143s instead of raw signal. Default: 50 143s 143s Plotting Region Arguments: 143s --num-regions NUM_REGIONS 143s Number of regions to plot. Default: 3 143s --num-context NUM_CONTEXT 143s Number of context bases around motif. Default: 5 143s --num-statistics NUM_STATISTICS 143s Number of motif centered regions to include in 143s statistic distributions. Default: 200 143s 143s Statistical Argument: 143s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 143s Dampen fraction modified estimates for low coverage 143s sites. Two parameters are unmodified and modified 143s pseudo read counts. This is equivalent to a beta prior 143s on the fraction estimate. Set to "0 0" to disable 143s dampened fraction estimation. Default: [2, 0] 143s 143s Output Argument: 143s --pdf-filename PDF_FILENAME 143s PDF filename to store plot(s). Default: 143s tombo_results.motif_statistics.pdf 143s 143s FAST5 Data Arguments: 143s --corrected-group CORRECTED_GROUP 143s FAST5 group created by resquiggle command. Default: 143s RawGenomeCorrected_000 143s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 143s FAST5 subgroup(s) (under /Analyses/[--basecall- 143s group]/) containing basecalls and created within 143s [--corrected-group] containing re-squiggle results. 143s Default: ['BaseCalled_template'] 143s 143s Miscellaneous Arguments: 143s --quiet, -q Don't print status information. 143s --help, -h Print this help message and exit 143s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 143s [GENOME_LOCATIONS ...] 143s --per-read-statistics-filename 143s PER_READ_STATISTICS_FILENAME 143s [--genome-fasta GENOME_FASTA] 143s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 143s [--num-reads NUM_READS] [--num-bases NUM_BASES] 143s [--box-center] [--pdf-filename PDF_FILENAME] 143s [--corrected-group CORRECTED_GROUP] 143s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 143s [--quiet] [--help] 143s 143s Required Arguments: 143s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 143s Genomic locations at which to plot signal. Format 143s locations as "chrm:position[:strand] 143s [chrm2:position2[:strand2] ...]" (strand not 143s applicable for all applications) 143s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 143s Binary file containing per-read statistics from 143s statistical testing. 143s 143s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 143s --genome-fasta GENOME_FASTA 143s FASTA file used to re-squiggle. For faster sequence 143s access. 143s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 143s Directories containing fast5 files. 143s 143s Plotting Region Arguments: 143s --num-reads NUM_READS 143s Number of reads to plot. Default: 100 143s --num-bases NUM_BASES 143s Number of bases to plot/output. Default: 51 143s --box-center Plot a box around the central base. 143s 143s Output Argument: 143s --pdf-filename PDF_FILENAME 143s PDF filename to store plot(s). Default: 143s tombo_results.per_read_stats.pdf 143s 143s FAST5 Data Arguments: 143s --corrected-group CORRECTED_GROUP 143s FAST5 group created by resquiggle command. Default: 143s RawGenomeCorrected_000 143s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 143s FAST5 subgroup(s) (under /Analyses/[--basecall- 143s group]/) containing basecalls and created within 143s [--corrected-group] containing re-squiggle results. 143s Default: ['BaseCalled_template'] 143s 143s Miscellaneous Arguments: 143s --quiet, -q Don't print status information. 143s --help, -h Print this help message and exit 143s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 143s [STATISTICS_FILENAMES ...] 143s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 143s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 143s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 143s [--genome-fasta GENOME_FASTA] 143s [--pdf-filename PDF_FILENAME] 143s [--statistics-per-block STATISTICS_PER_BLOCK] 143s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 143s [--quiet] [--help] 143s 143s Required Argument: 143s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 143s Files to load genomic base anchored statistics. 143s 143s Ground Truth Arguments (provide bed files or motifs): 143s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 143s Modification description and bed format files 143s containing single base locations of ground truth 143s modified sites. Bed files should contain 6 fields 143s including strand. Format descriptions as 143s "mod_name:locs.bed". Example: "CpG 143s bisulfite":bisulfite_locs.bed 143s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 143s Bed format files containing single base locations of 143s ground truth unmodified sites. Bed files should 143s contain 6 fields including strand. 143s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 143s Ground truth, motif centered, modified base 143s descriptions for computing ROC and PR curves. Each 143s statistics file is associated with a set of motif 143s descriptions. Format descriptions as: 143s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 143s mod_pos indicates the alternate-base within the motif 143s (1-based index). Example: CCWGG:2:"dcm 143s 5mC"::GATC:2:"dam 6mA" would assess the performance of 143s a single Tombo statistics file for identification of 143s E. coli dam and dcm methylation. 143s --genome-fasta GENOME_FASTA 143s FASTA file used to re-squiggle. For faster sequence 143s access. 143s 143s Output Arguments: 143s --pdf-filename PDF_FILENAME 143s PDF filename to store plot(s). Default: 143s tombo_results.roc.pdf 143s 143s Down-sampling Arguments: 143s --statistics-per-block STATISTICS_PER_BLOCK 143s Number of randomly selected per-read, per-base 143s statistics to extract from each genomic block for 143s plotting. Default: Include all stats 143s --total-statistics-limit TOTAL_STATISTICS_LIMIT 143s Total per-read statistics to be extracted for 143s plotting. Avoids memory overflow for large runs. 143s Default: 5000000 143s 143s Miscellaneous Arguments: 143s --quiet, -q Don't print status information. 143s --help, -h Print this help message and exit 143s usage: tombo plot per_read_roc --per-read-statistics-filenames 143s PER_READ_STATISTICS_FILENAMES 143s [PER_READ_STATISTICS_FILENAMES ...] 143s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 143s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 143s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 143s [--genome-fasta GENOME_FASTA] 143s [--statistics-per-block STATISTICS_PER_BLOCK] 143s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 143s [--pdf-filename PDF_FILENAME] [--quiet] 143s [--help] 143s 143s Required Argument: 143s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 143s Binary files containing per-read statistics from 143s statistical testing. 143s 143s Ground Truth Arguments (provide bed files or motifs): 143s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 143s Modification description and bed format files 143s containing single base locations of ground truth 143s modified sites. Bed files should contain 6 fields 143s including strand. Format descriptions as 143s "mod_name:locs.bed". Example: "CpG 143s bisulfite":bisulfite_locs.bed 143s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 143s Bed format files containing single base locations of 143s ground truth unmodified sites. Bed files should 143s contain 6 fields including strand. 143s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 143s Ground truth, motif centered, modified base 143s descriptions for computing ROC and PR curves. Each 143s statistics file is associated with a set of motif 143s descriptions. Format descriptions as: 143s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 143s mod_pos indicates the alternate-base within the motif 143s (1-based index). Example: CCWGG:2:"dcm 143s 5mC"::GATC:2:"dam 6mA" would assess the performance of 143s a single Tombo statistics file for identification of 143s E. coli dam and dcm methylation. 143s --genome-fasta GENOME_FASTA 143s FASTA file used to re-squiggle. For faster sequence 143s access. 143s 143s Down-sampling Arguments: 143s --statistics-per-block STATISTICS_PER_BLOCK 143s Number of randomly selected per-read, per-base 143s statistics to extract from each genomic block for 143s plotting. Default: 100000 143s --total-statistics-limit TOTAL_STATISTICS_LIMIT 143s Total per-read statistics to be extracted for 143s plotting. Avoids memory overflow for large runs. 143s Default: 5000000 143s 143s Output Arguments: 143s --pdf-filename PDF_FILENAME 143s PDF filename to store plot(s). Default: 143s tombo_results.per_reads_roc.pdf 143s 143s Miscellaneous Arguments: 143s --quiet, -q Don't print status information. 143s --help, -h Print this help message and exit 143s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 143s [--upstream-bases {0,1,2,3,4}] 143s [--downstream-bases {0,1,2,3,4}] [--read-mean] 143s [--num-kmer-threshold NUM_KMER_THRESHOLD] 143s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 143s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 143s [--corrected-group CORRECTED_GROUP] 143s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 143s [--quiet] [--help] 143s 143s Required Argument: 143s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 143s Directories containing fast5 files. 143s 143s Data Processing Arguments: 143s --upstream-bases {0,1,2,3,4} 143s Upstream bases in k-mer. Default: 1 143s --downstream-bases {0,1,2,3,4} 143s Downstream bases in k-mer. Default: 2 143s --read-mean Plot k-mer means across whole reads as opposed to 143s individual k-mer event levels. 143s --num-kmer-threshold NUM_KMER_THRESHOLD 143s Observations of each k-mer required to include a read 143s in read level averages. Default: 1 143s 143s Plotting Region Arguments: 143s --num-reads NUM_READS 143s Number of reads to plot. Default: 100 143s 143s Output Arguments: 143s --pdf-filename PDF_FILENAME 143s PDF filename to store plot(s). Default: 143s tombo_results.kmer_distribution.pdf 143s --r-data-filename R_DATA_FILENAME 143s Filename to save R data structure. Default: Don't save 143s --dont-plot Don't plot result. Useful to produce only R data file. 143s 143s FAST5 Data Arguments: 143s --corrected-group CORRECTED_GROUP 143s FAST5 group created by resquiggle command. Default: 143s RawGenomeCorrected_000 143s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 143s FAST5 subgroup(s) (under /Analyses/[--basecall- 143s group]/) containing basecalls and created within 143s [--corrected-group] containing re-squiggle results. 143s Default: ['BaseCalled_template'] 143s 143s Miscellaneous Arguments: 143s --quiet, -q Don't print status information. 143s --help, -h Print this help message and exit 143s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 143s [FAST5_BASEDIRS ...] 143s --control-fast5-basedirs 143s CONTROL_FAST5_BASEDIRS 143s [CONTROL_FAST5_BASEDIRS ...] 143s --statistics-filename 143s STATISTICS_FILENAME 143s [--genome-fasta GENOME_FASTA] 143s [--processes PROCESSES] 143s [--num-regions NUM_REGIONS] 143s [--num-bases NUM_BASES] 143s [--slide-span SLIDE_SPAN] 143s [--pdf-filename PDF_FILENAME] 143s [--r-data-filename R_DATA_FILENAME] 143s [--corrected-group CORRECTED_GROUP] 143s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 143s [--quiet] [--help] 143s 143s Required Arguments: 143s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 143s Directories containing fast5 files. 143s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 143s Set of directories containing fast5 files for control 143s reads, containing only canonical nucleotides. 143s --statistics-filename STATISTICS_FILENAME 143s File to save/load genomic base anchored statistics. 143s 143s FASTA Sequence Argument: 143s --genome-fasta GENOME_FASTA 143s FASTA file used to re-squiggle. For faster sequence 143s access. 143s 143s Multiprocessing Argument: 143s --processes PROCESSES 143s Number of processes. Default: 1 143s 143s Plotting Region Arguments: 143s --num-regions NUM_REGIONS 143s Number of regions to plot. Default: 10 143s --num-bases NUM_BASES 143s Number of bases to plot/output. Default: 21 143s --slide-span SLIDE_SPAN 143s Number of bases offset over which to search when 143s computing distances for signal cluster plotting. 143s Default: 0 (exact position) 143s 143s Output Arguments: 143s --pdf-filename PDF_FILENAME 143s PDF filename to store plot(s). Default: 143s tombo_results.signal_clusters.pdf 143s --r-data-filename R_DATA_FILENAME 143s Filename to save R data structure. Default: Don't save 143s 143s FAST5 Data Arguments: 143s --corrected-group CORRECTED_GROUP 143s FAST5 group created by resquiggle command. Default: 143s RawGenomeCorrected_000 143s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 143s FAST5 subgroup(s) (under /Analyses/[--basecall- 143s group]/) containing basecalls and created within 143s [--corrected-group] containing re-squiggle results. 143s Default: ['BaseCalled_template'] 143s 143s Miscellaneous Arguments: 143s --quiet, -q Don't print status information. 143s --help, -h Print this help message and exit 143s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 143s 143s Required Arguments: 143s fast5s_basedir Directory containing fast5 files. All files ending in 143s "fast5" found recursively within this base directory will be 143s processed. 143s 143s Miscellaneous Arguments: 143s --quiet, -q Don't print status information. 143s --help, -h Print this help message and exit 143s usage: tombo build_model event_resquiggle 143s [--minimap2-executable MINIMAP2_EXECUTABLE] 143s [--minimap2-index MINIMAP2_INDEX] 143s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 143s [--graphmap-executable GRAPHMAP_EXECUTABLE] 143s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 143s [--normalization-type {median,pA,pA_raw,none}] 143s [--pore-model-filename PORE_MODEL_FILENAME] 143s [--outlier-threshold OUTLIER_THRESHOLD] 143s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 143s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 143s [--timeout TIMEOUT] 143s [--cpts-limit CPTS_LIMIT] 143s [--skip-index] [--overwrite] 143s [--failed-reads-filename FAILED_READS_FILENAME] 143s [--include-event-stdev] 143s [--corrected-group CORRECTED_GROUP] 143s [--basecall-group BASECALL_GROUP] 143s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 143s [--processes PROCESSES] 143s [--align-processes ALIGN_PROCESSES] 143s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 143s [--resquiggle-processes RESQUIGGLE_PROCESSES] 143s [--quiet] [--help] 143s fast5s_basedir reference_fasta 143s 143s Required Arguments: 143s fast5s_basedir Directory containing fast5 files. All files ending in 143s "fast5" found recursively within this base directory 143s will be processed. 143s reference_fasta Reference genome/transcriptome FASTA file for mapping. 143s 143s Mapper Arguments (One mapper is required): 143s --minimap2-executable MINIMAP2_EXECUTABLE 143s Path to minimap2 executable. 143s --minimap2-index MINIMAP2_INDEX 143s Path to minimap2 index (with map-ont preset) file 143s corresponding to the [genome_fasta] provided. 143s --bwa-mem-executable BWA_MEM_EXECUTABLE 143s Path to bwa-mem executable. 143s --graphmap-executable GRAPHMAP_EXECUTABLE 143s Path to graphmap executable. 143s --alignment-batch-size ALIGNMENT_BATCH_SIZE 143s Number of reads included in each alignment call. Note: 143s A new system mapping call is made for each batch 143s (including loading of the genome), so it is advised to 143s use larger values for larger genomes. Default: 1000 143s 143s Signal Processing Arguments: 143s --normalization-type {median,pA,pA_raw,none} 143s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 143s as in the ONT events (using offset, range and 143s digitization), "pA": k-mer-based correction for pA 143s drift as in nanopolish (requires [--pore-model- 143s filename]), "median": median and MAD from raw signal. 143s Default: median 143s --pore-model-filename PORE_MODEL_FILENAME 143s File containing kmer model parameters (level_mean and 143s level_stdv) used in order to compute kmer-based 143s corrected pA values. E.g. https://github.com/jts/nanop 143s olish/blob/master/etc/r9- 143s models/template_median68pA.5mers.model 143s --outlier-threshold OUTLIER_THRESHOLD 143s Windosrize the signal at this number of scale values. 143s Negative value disables outlier clipping. Default: 143s 5.000000 143s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 143s Specify the 2 parameters for segmentation 1) running 143s neighboring windows width 2) minimum raw observations 143s per genomic base. Sample type defaults: RNA : 12 6 || 143s DNA : 5 3 143s 143s Read Filtering Arguments: 143s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 143s Filter reads based on observations per base percentile 143s thresholds. Format thresholds as "percentile:thresh 143s [pctl2:thresh2 ...]". For example to filter reads with 143s 99th pctl > 200 obs/base or max > 5k obs/base use 143s "99:200 100:5000". 143s --timeout TIMEOUT Timeout in seconds for processing a single read. 143s Default: No timeout. 143s --cpts-limit CPTS_LIMIT 143s Maximum number of changepoints to find within a single 143s indel group. Default: No limit. 143s 143s Input/Output Arguments: 143s --skip-index Skip creation of tombo index. This drastically slows 143s downstream tombo commands. Default stores tombo index 143s named ".[--fast5-basedir].[--corrected- 143s group].tombo.index" to be loaded automatically for 143s downstream commands. 143s --overwrite Overwrite previous corrected group in FAST5 files. 143s Note: only effects --corrected-group or --new- 143s corrected-group. 143s --failed-reads-filename FAILED_READS_FILENAME 143s Output failed read filenames with assoicated error. 143s Default: Do not store failed reads. 143s --include-event-stdev 143s Include corrected event standard deviation in output 143s FAST5 data. 143s 143s FAST5 Data Arguments: 143s --corrected-group CORRECTED_GROUP 143s FAST5 group created by resquiggle command. Default: 143s RawGenomeCorrected_000 143s --basecall-group BASECALL_GROUP 143s FAST5 group obtain original basecalls (under Analyses 143s group). Default: Basecall_1D_000 143s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 143s FAST5 subgroup(s) (under /Analyses/[--basecall- 143s group]/) containing basecalls and created within 143s [--corrected-group] containing re-squiggle results. 143s Default: ['BaseCalled_template'] 143s 143s Multiprocessing Arguments: 143s --processes PROCESSES 143s Number of processes. Default: 2 143s --align-processes ALIGN_PROCESSES 143s Number of processes to use for parsing and aligning 143s original basecalls. Each process will independently 143s load the genome into memory, so use caution with 143s larger genomes (e.g. human). Default: 1 143s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 143s Number of threads to use for aligner system call. 143s Default: [--processes] / (2 * [--align-processes)] 143s --resquiggle-processes RESQUIGGLE_PROCESSES 143s Number of processes to use for resquiggle algorithm. 143s Default: [--processes] / 2 143s 143s Miscellaneous Arguments: 143s --quiet, -q Don't print status information. 143s --help, -h Print this help message and exit 143s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 143s [FAST5_BASEDIRS ...] 143s --tombo-model-filename 143s TOMBO_MODEL_FILENAME 143s [--estimate-mean] 143s [--kmer-specific-sd] 143s [--upstream-bases {0,1,2,3,4}] 143s [--downstream-bases {0,1,2,3,4}] 143s [--minimum-test-reads MINIMUM_TEST_READS] 143s [--coverage-threshold COVERAGE_THRESHOLD] 143s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 143s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 143s [--processes PROCESSES] 143s [--corrected-group CORRECTED_GROUP] 143s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 143s [--quiet] [--help] 143s 143s Required Arguments: 143s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 143s Directories containing fast5 files. 143s --tombo-model-filename TOMBO_MODEL_FILENAME 143s Filename to save Tombo model. 143s 143s Modeling Arguments: 143s --estimate-mean Use the mean instead of median for model level 143s estimation. Note: This can cause poor fits due to 143s outliers 143s --kmer-specific-sd Estimate standard deviation for each k-mers 143s individually. 143s --upstream-bases {0,1,2,3,4} 143s Upstream bases in k-mer. Default: 1 143s --downstream-bases {0,1,2,3,4} 143s Downstream bases in k-mer. Default: 2 143s 143s Filtering Arguments: 143s --minimum-test-reads MINIMUM_TEST_READS 143s Number of reads required at a position to perform 143s significance testing or contribute to model 143s estimation. Default: 10 143s --coverage-threshold COVERAGE_THRESHOLD 143s Maximum mean coverage per region when estimating k-mer 143s model (limits compute time for deep samples). Default: 143s 100 143s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 143s Number of each k-mer observations required in order to 143s produce a reference (genomic locations for standard 143s reference and per-read for alternative reference). 143s Default: 5 143s 143s Multiprocessing Arguments: 143s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 143s Size of regions over which to multiprocesses statistic 143s computation. For very deep samples a smaller value is 143s recommmended in order to control memory consumption. 143s Default: 10000 143s --processes PROCESSES 143s Number of processes. Default: 1 143s 143s FAST5 Data Arguments: 143s --corrected-group CORRECTED_GROUP 143s FAST5 group created by resquiggle command. Default: 143s RawGenomeCorrected_000 143s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 143s FAST5 subgroup(s) (under /Analyses/[--basecall- 143s group]/) containing basecalls and created within 143s [--corrected-group] containing re-squiggle results. 143s Default: ['BaseCalled_template'] 143s 143s Miscellaneous Arguments: 143s --quiet, -q Don't print status information. 143s --help, -h Print this help message and exit 143s usage: tombo build_model estimate_alt_reference --alternate-model-filename 143s ALTERNATE_MODEL_FILENAME 143s --alternate-model-name 143s ALTERNATE_MODEL_NAME 143s --alternate-model-base 143s {A,C,G,T} 143s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 143s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 143s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 143s [--control-density-filename CONTROL_DENSITY_FILENAME] 143s [--dna] [--rna] 143s [--tombo-model-filename TOMBO_MODEL_FILENAME] 143s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 143s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 143s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 143s [--save-density-basename SAVE_DENSITY_BASENAME] 143s [--processes PROCESSES] 143s [--corrected-group CORRECTED_GROUP] 143s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 143s [--quiet] [--help] 143s 143s Required Arguments: 143s --alternate-model-filename ALTERNATE_MODEL_FILENAME 143s Tombo model for alternative likelihood ratio 143s significance testing. 143s --alternate-model-name ALTERNATE_MODEL_NAME 143s A short name to associate with this alternate model 143s (e.g. 5mC, 6mA, etc.). This text will be included in 143s output filenames when this model is used for testing. 143s --alternate-model-base {A,C,G,T} 143s Non-standard base is an alternative to this base. 143s 143s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 143s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 143s Directories containing fast5 files. 143s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 143s Set of directories containing fast5 files for control 143s reads, containing only canonical nucleotides. 143s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 143s File containing k-mer level kernel density estimates 143s for the alternative sample saved using --save-density- 143s basename. 143s --control-density-filename CONTROL_DENSITY_FILENAME 143s File containing k-mer level kernel density estimates 143s for the control sample saved using --save-density- 143s basename. 143s 143s Standard Model Arguments: 143s --dna Explicitly select canonical DNA model. Default: 143s Automatically determine from FAST5s 143s --rna Explicitly select canonical RNA model. Default: 143s Automatically determine from FAST5s 143s --tombo-model-filename TOMBO_MODEL_FILENAME 143s Tombo model filename. If no file is provided, the 143s default DNA or RNA Tombo model will be used. 143s 143s Model Fitting Arguments: 143s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 143s When esitmating the alternative base incorporation 143s rate, this percent of k-mers are assumed to have 143s significantly shifted signal so the alternative 143s distribution minimally overlaps the standard base 143s distribution. Default: 5.000000 143s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 143s Bandwidth applied when performing Gaussian kernal 143s density esitmation on standard and alternative base 143s signal distributions. Default: 0.050000 143s 143s Filtering Argument: 143s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 143s Number of each k-mer observations required in order to 143s produce a reference (genomic locations for standard 143s reference and per-read for alternative reference). 143s Default: 1000 143s 143s Output Argument: 143s --save-density-basename SAVE_DENSITY_BASENAME 143s Basename to save alternative model estimation density 143s estimation information. See scripts/debug_est_alt.R 143s for info use example. Default: Don't save. 143s 143s Multiprocessing Arguments: 143s --processes PROCESSES 143s Number of processes. Default: 1 143s 143s FAST5 Data Arguments: 143s --corrected-group CORRECTED_GROUP 143s FAST5 group created by resquiggle command. Default: 143s RawGenomeCorrected_000 143s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 143s FAST5 subgroup(s) (under /Analyses/[--basecall- 143s group]/) containing basecalls and created within 143s [--corrected-group] containing re-squiggle results. 143s Default: ['BaseCalled_template'] 143s 143s Miscellaneous Arguments: 143s --quiet, -q Don't print status information. 143s --help, -h Print this help message and exit 143s This test only tests the help system 143s There is an extensive test in 143s 143s tombo/tests/shell_tests.sh 143s 143s but this requires to download larger data 143s sets which is not done for the moment. 144s autopkgtest [11:05:50]: test run-unit-test: -----------------------] 144s autopkgtest [11:05:50]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 144s run-unit-test PASS 145s autopkgtest [11:05:51]: @@@@@@@@@@@@@@@@@@@@ summary 145s run-unit-test PASS 157s Creating nova instance adt-noble-s390x-tombo-20240320-110326-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240320.img (UUID 6569a0ff-4984-4a4c-a4d0-b93f21cb5de9)...