0s autopkgtest [12:12:01]: starting date and time: 2024-11-15 12:12:01+0000 0s autopkgtest [12:12:01]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [12:12:01]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.61q932n8/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-71.secgroup --name adt-plucky-amd64-tombo-20241115-121201-juju-7f2275-prod-proposed-migration-environment-2-a2a2bbdb-f31b-4c2f-bfdc-7f342b6df3bc --image adt/ubuntu-plucky-amd64-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,keyserver.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/ 42s autopkgtest [12:12:43]: testbed dpkg architecture: amd64 42s autopkgtest [12:12:43]: testbed apt version: 2.9.8 42s autopkgtest [12:12:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 42s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 42s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [94.5 kB] 42s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 42s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 42s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1052 kB] 42s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [176 kB] 42s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [109 kB] 42s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 42s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [831 kB] 42s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [295 kB] 42s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9416 B] 42s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 43s Fetched 2696 kB in 0s (8005 kB/s) 43s Reading package lists... 44s Reading package lists... 44s Building dependency tree... 44s Reading state information... 45s Calculating upgrade... 45s The following packages will be upgraded: 45s python3-markupsafe 45s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 45s Need to get 13.0 kB of archives. 45s After this operation, 15.4 kB of additional disk space will be used. 45s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build3 [13.0 kB] 45s Fetched 13.0 kB in 0s (882 kB/s) 45s (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 ... 75575 files and directories currently installed.) 45s Preparing to unpack .../python3-markupsafe_2.1.5-1build3_amd64.deb ... 46s Unpacking python3-markupsafe (2.1.5-1build3) over (2.1.5-1build2) ... 46s Setting up python3-markupsafe (2.1.5-1build3) ... 46s Reading package lists... 46s Building dependency tree... 46s Reading state information... 46s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 47s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 47s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 47s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 47s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 48s Reading package lists... 48s Reading package lists... 48s Building dependency tree... 48s Reading state information... 48s Calculating upgrade... 48s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 49s Reading package lists... 49s Building dependency tree... 49s Reading state information... 49s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 50s autopkgtest [12:12:51]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 50s autopkgtest [12:12:51]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 51s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (dsc) [2291 B] 51s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (tar) [22.3 MB] 51s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (diff) [7100 B] 51s gpgv: Signature made Wed Apr 10 17:15:32 2024 UTC 51s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 51s gpgv: Can't check signature: No public key 51s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6build1.dsc: no acceptable signature found 51s autopkgtest [12:12:52]: testing package tombo version 1.5.1-6build1 51s autopkgtest [12:12:52]: build not needed 52s autopkgtest [12:12:53]: test run-unit-test: preparing testbed 52s Reading package lists... 52s Building dependency tree... 52s Reading state information... 53s Starting pkgProblemResolver with broken count: 0 53s Starting 2 pkgProblemResolver with broken count: 0 53s Done 53s The following additional packages will be installed: 53s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 53s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 53s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 53s python3-decorator python3-h5py python3-h5py-serial python3-mappy 53s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 53s tombo-doc 53s Suggested packages: 53s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 53s gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 53s Recommended packages: 53s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 53s python3-rpy2 53s The following NEW packages will be installed: 53s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 53s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 53s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 53s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 53s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 53s tombo-doc 53s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 53s Need to get 65.0 MB/65.0 MB of archives. 53s After this operation, 222 MB of additional disk space will be used. 53s Get:1 /tmp/autopkgtest.iyP51h/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [708 B] 53s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-lato all 2.015-1 [2781 kB] 53s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 53s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 53s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 53s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 53s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 53s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 53s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 53s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB] 53s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 53s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 53s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 53s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 53s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 53s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 53s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 53s Get:18 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-numpy amd64 1:1.26.4+ds-11ubuntu1 [5319 kB] 53s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.11.0-5ubuntu1 [1107 kB] 53s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 53s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mappy amd64 2.27+dfsg-1 [150 kB] 53s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tqdm all 4.67.0-1 [91.6 kB] 53s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 53s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 54s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 tombo amd64 1.5.1-6build1 [450 kB] 54s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 54s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 tombo-doc all 1.5.1-6build1 [21.7 MB] 54s Fetched 65.0 MB in 1s (120 MB/s) 54s Selecting previously unselected package fonts-lato. 54s (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 ... 75576 files and directories currently installed.) 54s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 54s Unpacking fonts-lato (2.015-1) ... 54s Selecting previously unselected package fonts-font-awesome. 54s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 54s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 54s Selecting previously unselected package fonts-mathjax. 54s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 54s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 54s Selecting previously unselected package libaec0:amd64. 54s Preparing to unpack .../03-libaec0_1.1.3-1_amd64.deb ... 54s Unpacking libaec0:amd64 (1.1.3-1) ... 54s Selecting previously unselected package libblas3:amd64. 54s Preparing to unpack .../04-libblas3_3.12.0-3build2_amd64.deb ... 54s Unpacking libblas3:amd64 (3.12.0-3build2) ... 54s Selecting previously unselected package libgfortran5:amd64. 54s Preparing to unpack .../05-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 54s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 55s Selecting previously unselected package libsz2:amd64. 55s Preparing to unpack .../06-libsz2_1.1.3-1_amd64.deb ... 55s Unpacking libsz2:amd64 (1.1.3-1) ... 55s Selecting previously unselected package libhdf5-103-1t64:amd64. 55s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ... 55s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 55s Selecting previously unselected package libhdf5-hl-100t64:amd64. 55s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_amd64.deb ... 55s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 55s Selecting previously unselected package libjs-jquery. 55s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 55s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 55s Selecting previously unselected package libjs-underscore. 55s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 55s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 55s Selecting previously unselected package libjs-sphinxdoc. 55s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-4_all.deb ... 55s Unpacking libjs-sphinxdoc (7.4.7-4) ... 55s Selecting previously unselected package liblapack3:amd64. 55s Preparing to unpack .../12-liblapack3_3.12.0-3build2_amd64.deb ... 55s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 55s Selecting previously unselected package liblbfgsb0:amd64. 55s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 55s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 55s Selecting previously unselected package liblzf1:amd64. 55s Preparing to unpack .../14-liblzf1_3.6-4_amd64.deb ... 55s Unpacking liblzf1:amd64 (3.6-4) ... 55s Selecting previously unselected package python3-decorator. 55s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 55s Unpacking python3-decorator (5.1.1-5) ... 55s Selecting previously unselected package python3-numpy. 55s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-11ubuntu1_amd64.deb ... 55s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 55s Selecting previously unselected package python3-h5py-serial. 55s Preparing to unpack .../17-python3-h5py-serial_3.11.0-5ubuntu1_amd64.deb ... 55s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 55s Selecting previously unselected package python3-h5py. 55s Preparing to unpack .../18-python3-h5py_3.11.0-5ubuntu1_all.deb ... 55s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 55s Selecting previously unselected package python3-mappy. 55s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1_amd64.deb ... 55s Unpacking python3-mappy (2.27+dfsg-1) ... 55s Selecting previously unselected package python3-tqdm. 55s Preparing to unpack .../20-python3-tqdm_4.67.0-1_all.deb ... 55s Unpacking python3-tqdm (4.67.0-1) ... 55s Selecting previously unselected package sphinx-rtd-theme-common. 55s Preparing to unpack .../21-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 55s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 55s Selecting previously unselected package python3-scipy. 55s Preparing to unpack .../22-python3-scipy_1.13.1-5_amd64.deb ... 55s Unpacking python3-scipy (1.13.1-5) ... 56s Selecting previously unselected package tombo. 56s Preparing to unpack .../23-tombo_1.5.1-6build1_amd64.deb ... 56s Unpacking tombo (1.5.1-6build1) ... 56s Selecting previously unselected package libjs-mathjax. 56s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 56s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 56s Selecting previously unselected package tombo-doc. 56s Preparing to unpack .../25-tombo-doc_1.5.1-6build1_all.deb ... 56s Unpacking tombo-doc (1.5.1-6build1) ... 57s Selecting previously unselected package autopkgtest-satdep. 57s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 57s Unpacking autopkgtest-satdep (0) ... 57s Setting up fonts-lato (2.015-1) ... 57s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 57s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 57s Setting up python3-tqdm (4.67.0-1) ... 57s Setting up python3-mappy (2.27+dfsg-1) ... 57s Setting up libaec0:amd64 (1.1.3-1) ... 57s Setting up python3-decorator (5.1.1-5) ... 57s Setting up libblas3:amd64 (3.12.0-3build2) ... 57s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 57s Setting up liblzf1:amd64 (3.6-4) ... 57s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 57s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 57s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 57s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 57s Setting up libsz2:amd64 (1.1.3-1) ... 57s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 57s Setting up liblapack3:amd64 (3.12.0-3build2) ... 57s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 57s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 59s Setting up libjs-sphinxdoc (7.4.7-4) ... 59s Setting up tombo-doc (1.5.1-6build1) ... 59s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 59s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 59s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 59s Setting up python3-scipy (1.13.1-5) ... 62s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 62s Setting up python3-h5py (3.11.0-5ubuntu1) ... 62s Setting up tombo (1.5.1-6build1) ... 62s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 62s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 62s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 62s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 62s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 62s re.match('\+', fastq_rec[2]) is None): 63s Setting up autopkgtest-satdep (0) ... 63s Processing triggers for man-db (2.13.0-1) ... 63s Processing triggers for libc-bin (2.40-1ubuntu3) ... 66s (Reading database ... 82798 files and directories currently installed.) 66s Removing autopkgtest-satdep (0) ... 66s autopkgtest [12:13:07]: test run-unit-test: [----------------------- 66s ********* Testing help commands ********** 66s usage: tombo [-h] [-v] 66s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 66s ... 66s 66s ********** Tombo ********* 66s 66s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 66s 66s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 66s 66s Tombo command groups (additional help available within each command group): 66s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 66s preprocess Pre-process nanopore reads for Tombo processing. 66s filter Apply filter to Tombo index file for specified criterion. 66s detect_modifications Perform statistical testing to detect non-standard nucleotides. 66s text_output Output Tombo results in text files. 66s build_model Create canonical and alternative base Tombo models. 66s plot Save plots to visualize raw nanopore signal or testing results. 66s 66s options: 66s -h, --help show this help message and exit 66s -v, --version show Tombo version and exit. 66s usage: tombo resquiggle [--dna] [--rna] 66s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 66s [--q-score Q_SCORE] 66s [--signal-matching-score SIGNAL_MATCHING_SCORE] 66s [--processes PROCESSES] 66s [--corrected-group CORRECTED_GROUP] 66s [--basecall-group BASECALL_GROUP] 66s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 66s [--overwrite] 66s [--failed-reads-filename FAILED_READS_FILENAME] 66s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 66s [--print-advanced-arguments] [--quiet] [--help] 66s fast5s_basedir reference 66s 66s Required Arguments: 66s fast5s_basedir Directory containing fast5 files. All files ending in 66s "fast5" found recursively within this base directory 66s will be processed. 66s reference Reference genome/transcriptome FASTA file or minimap2 66s index (with "map-ont" preset) for mapping. 66s 66s Model Parameters: 66s --dna Explicitly select canonical DNA model. Default: 66s Automatically determine from FAST5s 66s --rna Explicitly select canonical RNA model. Default: 66s Automatically determine from FAST5s 66s 66s Read Filtering Argument: 66s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 66s Filter reads based on observations per base percentile 66s thresholds. Format thresholds as "percentile:thresh 66s [pctl2:thresh2 ...]". For example to filter reads with 66s 99th pctl > 200 obs/base or max > 5k obs/base use 66s "99:200 100:5000". 66s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 66s Default: 0.000000 66s --signal-matching-score SIGNAL_MATCHING_SCORE 66s Observed to expected signal matching score (higher 66s score indicates poor matching). Sample type defaults: 66s RNA : 2 || DNA : 1.1 66s 66s Multiprocessing Arguments: 66s --processes PROCESSES 66s Number of processes. Default: 1 66s 66s FAST5 Data Arguments: 66s --corrected-group CORRECTED_GROUP 66s FAST5 group created by resquiggle command. Default: 66s RawGenomeCorrected_000 66s --basecall-group BASECALL_GROUP 66s FAST5 group obtain original basecalls (under Analyses 66s group). Default: Basecall_1D_000 66s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 66s FAST5 subgroup(s) (under /Analyses/[--basecall- 66s group]/) containing basecalls and created within 66s [--corrected-group] containing re-squiggle results. 66s Default: ['BaseCalled_template'] 66s --overwrite Overwrite previous corrected group in FAST5 files. 66s Note: only effects --corrected-group or --new- 66s corrected-group. 66s 66s Input/Output Arguments: 66s --failed-reads-filename FAILED_READS_FILENAME 66s Output failed read filenames with assoicated error. 66s Default: Do not store failed reads. 66s --num-most-common-errors NUM_MOST_COMMON_ERRORS 66s Dynamically show this many most common errors so far 66s through run. Default: 0; Just show progress 66s 66s Advanced Arguments: 66s --print-advanced-arguments 66s Print advanced re-squiggle arguments and exit. 66s 66s Miscellaneous Arguments: 66s --quiet, -q Don't print status information. 66s --help, -h Print this help message and exit 66s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 66s --fastq-filenames 66s FASTQ_FILENAMES 66s [FASTQ_FILENAMES ...] 66s [--basecall-group BASECALL_GROUP] 66s [--basecall-subgroup BASECALL_SUBGROUP] 66s [--overwrite] 66s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 66s [--processes PROCESSES] 66s [--quiet] [--help] 66s 66s Required Arguments: 66s --fast5-basedir FAST5_BASEDIR 66s Directory containing fast5 files. 66s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 66s FASTQ filenames containing basecalls to be added to 66s raw FAST5 files. 66s 66s FAST5 Data Arguments: 66s --basecall-group BASECALL_GROUP 66s FAST5 group obtain original basecalls (under Analyses 66s group). Default: Basecall_1D_000 66s --basecall-subgroup BASECALL_SUBGROUP 66s FAST5 subgroup (under /Analyses/[--basecall-group]/) 66s under which to store basecalls from FASTQs. Default: 66s BaseCalled_template 66s --overwrite Overwrite previous corrected group in FAST5 files. 66s Note: only effects --corrected-group or --new- 66s corrected-group. 66s 66s Sequencing Summary Argument: 66s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 66s Sequencing summary filenames produced by albacore. 66s These can make annotation of raw FAST5 files with 66s FASTQ sequence much faster. 66s 66s Multiprocessing Argument: 66s --processes PROCESSES 66s Number of processes. Default: 1 66s 66s Miscellaneous Arguments: 66s --quiet, -q Don't print status information. 66s --help, -h Print this help message and exit 66s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 66s [FAST5_BASEDIRS ...] 66s [--corrected-group CORRECTED_GROUP] 66s [--quiet] [--help] 66s 66s Required Argument: 66s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 66s Directories containing fast5 files. 66s 66s FAST5 Data Argument: 66s --corrected-group CORRECTED_GROUP 66s FAST5 group created by resquiggle command. Default: 66s RawGenomeCorrected_000 66s 66s Miscellaneous Arguments: 66s --quiet, -q Don't print status information. 66s --help, -h Print this help message and exit 66s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 66s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 66s [--corrected-group CORRECTED_GROUP] [--quiet] 66s [--help] 66s 66s Required Argument: 66s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 66s Directories containing fast5 files. 66s 66s Read Filtering Argument: 66s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 66s Filter reads based on observations per base percentile 66s thresholds. Format thresholds as "percentile:thresh 66s [pctl2:thresh2 ...]". For example to filter reads with 66s 99th pctl > 200 obs/base or max > 5k obs/base use 66s "99:200 100:5000". 66s 66s FAST5 Data Argument: 66s --corrected-group CORRECTED_GROUP 66s FAST5 group created by resquiggle command. Default: 66s RawGenomeCorrected_000 66s 66s Miscellaneous Arguments: 66s --quiet, -q Don't print status information. 66s --help, -h Print this help message and exit 66s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 66s [FAST5_BASEDIRS ...] 66s [--percent-to-filter PERCENT_TO_FILTER] 66s [--corrected-group CORRECTED_GROUP] 66s [--quiet] [--help] 66s 66s Required Arguments: 66s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 66s Directories containing fast5 files. 66s 66s Read Filtering Argument: 66s --percent-to-filter PERCENT_TO_FILTER 66s Percentage of all reads to filter. Reads are randomly 66s selected weighted according to the approximate 66s coverage at the mapped genomic location. This can be 66s useful in modeling and testing. Default: 10.000000 66s 66s FAST5 Data Arguments: 66s --corrected-group CORRECTED_GROUP 66s FAST5 group created by resquiggle command. Default: 66s RawGenomeCorrected_000 66s 66s Miscellaneous Arguments: 66s --quiet, -q Don't print status information. 66s --help, -h Print this help message and exit 67s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 67s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 67s [--corrected-group CORRECTED_GROUP] 67s [--basecall-group BASECALL_GROUP] [--quiet] 67s [--help] 67s 67s Required Arguments: 67s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 67s Directories containing fast5 files. 67s 67s Read Filtering Argument: 67s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 67s Default: 7.000000 67s 67s FAST5 Data Arguments: 67s --corrected-group CORRECTED_GROUP 67s FAST5 group created by resquiggle command. Default: 67s RawGenomeCorrected_000 67s --basecall-group BASECALL_GROUP 67s FAST5 group obtain original basecalls (under Analyses 67s group). Default: Basecall_1D_000 67s 67s Miscellaneous Arguments: 67s --quiet, -q Don't print status information. 67s --help, -h Print this help message and exit 67s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 67s [FAST5_BASEDIRS ...] 67s --signal-matching-score 67s SIGNAL_MATCHING_SCORE 67s [--corrected-group CORRECTED_GROUP] 67s [--quiet] [--help] 67s 67s Required Arguments: 67s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 67s Directories containing fast5 files. 67s --signal-matching-score SIGNAL_MATCHING_SCORE 67s Observed to expected signal matching score (higher 67s score indicates poor matching). Sample type defaults: 67s RNA : 2 || DNA : 1.1 67s 67s FAST5 Data Arguments: 67s --corrected-group CORRECTED_GROUP 67s FAST5 group created by resquiggle command. Default: 67s RawGenomeCorrected_000 67s 67s Miscellaneous Arguments: 67s --quiet, -q Don't print status information. 67s --help, -h Print this help message and exit 67s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 67s [FAST5_BASEDIRS ...] 67s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 67s [--include-partial-overlap] 67s [--corrected-group CORRECTED_GROUP] 67s [--quiet] [--help] 67s 67s Required Arguments: 67s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 67s Directories containing fast5 files. 67s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 67s Filter out reads not falling completely within include 67s regions. Omit start and end coordinates to include an 67s entire chromosome/sequence record. Format regions as 67s "chrm[:start-end] [chrm2[:start2-end2] ...]". 67s 67s Filter Argument: 67s --include-partial-overlap 67s Include reads that partially overlap the specified 67s region. Default: Only include reads completely 67s contained in a specified region 67s 67s FAST5 Data Argument: 67s --corrected-group CORRECTED_GROUP 67s FAST5 group created by resquiggle command. Default: 67s RawGenomeCorrected_000 67s 67s Miscellaneous Arguments: 67s --quiet, -q Don't print status information. 67s --help, -h Print this help message and exit 67s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 67s [FAST5_BASEDIRS ...] 67s --statistics-file-basename 67s STATISTICS_FILE_BASENAME [--dna] 67s [--rna] 67s [--fishers-method-context FISHERS_METHOD_CONTEXT] 67s [--minimum-test-reads MINIMUM_TEST_READS] 67s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 67s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 67s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 67s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 67s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 67s [--processes PROCESSES] 67s [--corrected-group CORRECTED_GROUP] 67s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 67s [--quiet] [--help] 67s 67s Required Argument: 67s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 67s Directories containing fast5 files. 67s --statistics-file-basename STATISTICS_FILE_BASENAME 67s File base name to save base by base statistics from 67s testing. Filenames will be [--statistics-file- 67s basename].[--alternate-bases]?.tombo.stats 67s 67s Comparison Model Arguments: 67s --dna Explicitly select canonical DNA model. Default: 67s Automatically determine from FAST5s 67s --rna Explicitly select canonical RNA model. Default: 67s Automatically determine from FAST5s 67s 67s Significance Test Arguments: 67s --fishers-method-context FISHERS_METHOD_CONTEXT 67s Number of context bases up and downstream over which 67s to compute Fisher's method combined p-values. Note: 67s Not applicable for alternative model likelihood ratio 67s tests. Default: 1. 67s --minimum-test-reads MINIMUM_TEST_READS 67s Number of reads required at a position to perform 67s significance testing or contribute to model 67s estimation. Default: 1 67s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 67s P-value threshold when computing fraction of 67s significant reads at each genomic position. If two 67s values are provided, statistics between these values 67s are not considered. Default thresholds: DNA:0.15-0.5 , 67s RNA:0.05-0.4 67s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 67s Dampen fraction modified estimates for low coverage 67s sites. Two parameters are unmodified and modified 67s pseudo read counts. This is equivalent to a beta prior 67s on the fraction estimate. Set to "0 0" to disable 67s dampened fraction estimation. Default: [2, 0] 67s 67s Output Argument: 67s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 67s Base for binary files containing per-read statistics 67s from statistical testing. Filenames will be [--per- 67s read-statistics-basename].[--alternate- 67s bases]?.tombo.per_read_stats 67s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 67s Number of the most significant sites to store for 67s faster access. If a longer list of most significant 67s sites is required the list must be re-computed from 67s all batches. Very large values can increase RAM usage. 67s Default: 100000 67s 67s Multiprocessing Arguments: 67s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 67s Size of regions over which to multiprocesses statistic 67s computation. For very deep samples a smaller value is 67s recommmended in order to control memory consumption. 67s Default: 10000 67s --processes PROCESSES 67s Number of processes. Default: 1 67s 67s FAST5 Data Arguments: 67s --corrected-group CORRECTED_GROUP 67s FAST5 group created by resquiggle command. Default: 67s RawGenomeCorrected_000 67s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 67s FAST5 subgroup(s) (under /Analyses/[--basecall- 67s group]/) containing basecalls and created within 67s [--corrected-group] containing re-squiggle results. 67s Default: ['BaseCalled_template'] 67s 67s Miscellaneous Arguments: 67s --quiet, -q Don't print status information. 67s --help, -h Print this help message and exit 67s usage: tombo detect_modifications alternative_model 67s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 67s [--statistics-file-basename STATISTICS_FILE_BASENAME] 67s [--alternate-bases {CpG,dam,5mC,6mA,dcm} [{CpG,dam,5mC,6mA,dcm} ...]] 67s [--print-available-models] 67s [--dna] [--rna] 67s [--minimum-test-reads MINIMUM_TEST_READS] 67s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 67s [--standard-log-likelihood-ratio] 67s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 67s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 67s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 67s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 67s [--processes PROCESSES] 67s [--corrected-group CORRECTED_GROUP] 67s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 67s [--quiet] [--help] 67s 67s Required Argument: 67s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 67s Directories containing fast5 files. 67s --statistics-file-basename STATISTICS_FILE_BASENAME 67s File base name to save base by base statistics from 67s testing. Filenames will be [--statistics-file- 67s basename].[--alternate-bases]?.tombo.stats 67s --alternate-bases {CpG,dam,5mC,6mA,dcm} [{CpG,dam,5mC,6mA,dcm} ...] 67s Default non-standard base model for testing (not 67s required if user created --alternate-model-filenames 67s is provided). 67s 67s Comparison Arguments: 67s --print-available-models 67s Print available alternative models and exit. 67s --dna Explicitly select canonical DNA model. Default: 67s Automatically determine from FAST5s 67s --rna Explicitly select canonical RNA model. Default: 67s Automatically determine from FAST5s 67s 67s Significance Test Arguments: 67s --minimum-test-reads MINIMUM_TEST_READS 67s Number of reads required at a position to perform 67s significance testing or contribute to model 67s estimation. Default: 1 67s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 67s Log likelihood ratio threshold when computing fraction 67s of significant reads at each genomic position. If two 67s values are provided, statistics between these values 67s are not considered. Default thresholds: DNA:-1.5-2.5 , 67s RNA:-2.5-2.5 67s --standard-log-likelihood-ratio 67s Use a standard log likelihood ratio (LLR) statistic. 67s Default is to use an outlier-robust LLR-like 67s statistic. Detail in full online documentation. 67s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 67s Dampen fraction modified estimates for low coverage 67s sites. Two parameters are unmodified and modified 67s pseudo read counts. This is equivalent to a beta prior 67s on the fraction estimate. Set to "0 0" to disable 67s dampened fraction estimation. Default: [2, 0] 67s 67s Output Argument: 67s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 67s Base for binary files containing per-read statistics 67s from statistical testing. Filenames will be [--per- 67s read-statistics-basename].[--alternate- 67s bases]?.tombo.per_read_stats 67s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 67s Number of the most significant sites to store for 67s faster access. If a longer list of most significant 67s sites is required the list must be re-computed from 67s all batches. Very large values can increase RAM usage. 67s Default: 100000 67s 67s Multiprocessing Arguments: 67s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 67s Size of regions over which to multiprocesses statistic 67s computation. For very deep samples a smaller value is 67s recommmended in order to control memory consumption. 67s Default: 10000 67s --processes PROCESSES 67s Number of processes. Default: 1 67s 67s FAST5 Data Arguments: 67s --corrected-group CORRECTED_GROUP 67s FAST5 group created by resquiggle command. Default: 67s RawGenomeCorrected_000 67s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 67s FAST5 subgroup(s) (under /Analyses/[--basecall- 67s group]/) containing basecalls and created within 67s [--corrected-group] containing re-squiggle results. 67s Default: ['BaseCalled_template'] 67s 67s Miscellaneous Arguments: 67s --quiet, -q Don't print status information. 67s --help, -h Print this help message and exit 67s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 67s FAST5_BASEDIRS 67s [FAST5_BASEDIRS ...] 67s --statistics-file-basename 67s STATISTICS_FILE_BASENAME 67s --control-fast5-basedirs 67s CONTROL_FAST5_BASEDIRS 67s [CONTROL_FAST5_BASEDIRS ...] 67s [--sample-only-estimates] 67s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 67s [--dna] [--rna] 67s [--fishers-method-context FISHERS_METHOD_CONTEXT] 67s [--minimum-test-reads MINIMUM_TEST_READS] 67s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 67s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 67s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 67s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 67s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 67s [--processes PROCESSES] 67s [--corrected-group CORRECTED_GROUP] 67s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 67s [--quiet] [--help] 67s 67s Required Argument: 67s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 67s Directories containing fast5 files. 67s --statistics-file-basename STATISTICS_FILE_BASENAME 67s File base name to save base by base statistics from 67s testing. Filenames will be [--statistics-file- 67s basename].[--alternate-bases]?.tombo.stats 67s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 67s Set of directories containing fast5 files for control 67s reads, containing only canonical nucleotides. 67s 67s Model Prior Arguments: 67s --sample-only-estimates 67s Only use canonical sample to estimate expected signal 67s level and spread. Default: Use canonical model to 67s improve estimtates (esp. for low coverage regions) 67s using baysian posterior estimates. 67s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 67s Prior weights (one each for mean and spread) applied 67s to canonical base model for estimating posterior model 67s parameters for sample comparison. Default: [5, 40] 67s --dna Explicitly select canonical DNA model. Default: 67s Automatically determine from FAST5s 67s --rna Explicitly select canonical RNA model. Default: 67s Automatically determine from FAST5s 67s 67s Significance Test Arguments: 67s --fishers-method-context FISHERS_METHOD_CONTEXT 67s Number of context bases up and downstream over which 67s to compute Fisher's method combined p-values. Note: 67s Not applicable for alternative model likelihood ratio 67s tests. Default: 1. 67s --minimum-test-reads MINIMUM_TEST_READS 67s Number of reads required at a position to perform 67s significance testing or contribute to model 67s estimation. Default: 1 67s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 67s P-value threshold when computing fraction of 67s significant reads at each genomic position. If two 67s values are provided, statistics between these values 67s are not considered. Default thresholds: DNA:0.15-0.5 , 67s RNA:0.05-0.4 67s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 67s Dampen fraction modified estimates for low coverage 67s sites. Two parameters are unmodified and modified 67s pseudo read counts. This is equivalent to a beta prior 67s on the fraction estimate. Set to "0 0" to disable 67s dampened fraction estimation. Default: [2, 0] 67s 67s Output Argument: 67s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 67s Base for binary files containing per-read statistics 67s from statistical testing. Filenames will be [--per- 67s read-statistics-basename].[--alternate- 67s bases]?.tombo.per_read_stats 67s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 67s Number of the most significant sites to store for 67s faster access. If a longer list of most significant 67s sites is required the list must be re-computed from 67s all batches. Very large values can increase RAM usage. 67s Default: 100000 67s 67s Multiprocessing Arguments: 67s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 67s Size of regions over which to multiprocesses statistic 67s computation. For very deep samples a smaller value is 67s recommmended in order to control memory consumption. 67s Default: 10000 67s --processes PROCESSES 67s Number of processes. Default: 1 67s 67s FAST5 Data Arguments: 67s --corrected-group CORRECTED_GROUP 67s FAST5 group created by resquiggle command. Default: 67s RawGenomeCorrected_000 67s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 67s FAST5 subgroup(s) (under /Analyses/[--basecall- 67s group]/) containing basecalls and created within 67s [--corrected-group] containing re-squiggle results. 67s Default: ['BaseCalled_template'] 67s 67s Miscellaneous Arguments: 67s --quiet, -q Don't print status information. 67s --help, -h Print this help message and exit 67s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 67s FAST5_BASEDIRS 67s [FAST5_BASEDIRS ...] 67s --statistics-file-basename 67s STATISTICS_FILE_BASENAME 67s --alternate-fast5-basedirs 67s ALTERNATE_FAST5_BASEDIRS 67s [ALTERNATE_FAST5_BASEDIRS ...] 67s [--fishers-method-context FISHERS_METHOD_CONTEXT] 67s [--minimum-test-reads MINIMUM_TEST_READS] 67s [--statistic-type {ks,u,t}] 67s [--store-p-value] 67s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 67s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 67s [--processes PROCESSES] 67s [--corrected-group CORRECTED_GROUP] 67s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 67s [--quiet] [--help] 67s 67s Required Argument: 67s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 67s Directories containing fast5 files. 67s --statistics-file-basename STATISTICS_FILE_BASENAME 67s File base name to save base by base statistics from 67s testing. Filenames will be [--statistics-file- 67s basename].[--alternate-bases]?.tombo.stats 67s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 67s Set of directories containing fast5 files for 67s alternate set of reads. 67s 67s Significance Test Arguments: 67s --fishers-method-context FISHERS_METHOD_CONTEXT 67s Number of context bases up and downstream over which 67s to compute Fisher's method combined p-values. Note: 67s Not applicable for alternative model likelihood ratio 67s tests. Default: 1. 67s --minimum-test-reads MINIMUM_TEST_READS 67s Number of reads required at a position to perform 67s significance testing or contribute to model 67s estimation. Default: 50 67s --statistic-type {ks,u,t} 67s Type of statistical test to apply. Default: "ks" 67s --store-p-value Store p-value instead of effect-size statistic. 67s Statistics are D-statistic (KS-test), deviation from 67s even common language effect size (u-test), and Cohen's 67s D (t-test). 67s 67s Output Argument: 67s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 67s Number of the most significant sites to store for 67s faster access. If a longer list of most significant 67s sites is required the list must be re-computed from 67s all batches. Very large values can increase RAM usage. 67s Default: 100000 67s 67s Multiprocessing Arguments: 67s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 67s Size of regions over which to multiprocesses statistic 67s computation. For very deep samples a smaller value is 67s recommmended in order to control memory consumption. 67s Default: 10000 67s --processes PROCESSES 67s Number of processes. Default: 1 67s 67s FAST5 Data Arguments: 67s --corrected-group CORRECTED_GROUP 67s FAST5 group created by resquiggle command. Default: 67s RawGenomeCorrected_000 67s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 67s FAST5 subgroup(s) (under /Analyses/[--basecall- 67s group]/) containing basecalls and created within 67s [--corrected-group] containing re-squiggle results. 67s Default: ['BaseCalled_template'] 67s 67s Miscellaneous Arguments: 67s --quiet, -q Don't print status information. 67s --help, -h Print this help message and exit 67s usage: tombo detect_modifications aggregate_per_read_stats 67s --per-read-statistics-filename 67s PER_READ_STATISTICS_FILENAME 67s --statistics-filename 67s STATISTICS_FILENAME 67s --single-read-threshold 67s SINGLE_READ_THRESHOLD 67s [SINGLE_READ_THRESHOLD ...] 67s [--minimum-test-reads MINIMUM_TEST_READS] 67s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 67s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 67s [--processes PROCESSES] 67s [--corrected-group CORRECTED_GROUP] 67s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 67s [--quiet] [--help] 67s 67s Required Argument: 67s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 67s Binary file containing per-read statistics from 67s statistical testing. 67s --statistics-filename STATISTICS_FILENAME 67s File to save/load genomic base anchored statistics. 67s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 67s P-value or log likelihood ratio threshold when 67s computing fraction of significant reads at each 67s genomic position. If two values are provided, 67s statistics between these values are not considered. 67s 67s Significance Test Arguments: 67s --minimum-test-reads MINIMUM_TEST_READS 67s Number of reads required at a position to perform 67s significance testing or contribute to model 67s estimation. Default: 1 67s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 67s Dampen fraction modified estimates for low coverage 67s sites. Two parameters are unmodified and modified 67s pseudo read counts. This is equivalent to a beta prior 67s on the fraction estimate. Set to "0 0" to disable 67s dampened fraction estimation. Default: [2, 0] 67s 67s Output Argument: 67s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 67s Number of the most significant sites to store for 67s faster access. If a longer list of most significant 67s sites is required the list must be re-computed from 67s all batches. Very large values can increase RAM usage. 67s Default: 100000 67s 67s Multiprocessing Arguments: 67s --processes PROCESSES 67s Number of processes. Default: 1 67s 67s FAST5 Data Arguments: 67s --corrected-group CORRECTED_GROUP 67s FAST5 group created by resquiggle command. Default: 67s RawGenomeCorrected_000 67s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 67s FAST5 subgroup(s) (under /Analyses/[--basecall- 67s group]/) containing basecalls and created within 67s [--corrected-group] containing re-squiggle results. 67s Default: ['BaseCalled_template'] 67s 67s Miscellaneous Arguments: 67s --quiet, -q Don't print status information. 67s --help, -h Print this help message and exit 67s usage: tombo text_output browser_files 67s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 67s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 67s [--statistics-filename STATISTICS_FILENAME] 67s [--genome-fasta GENOME_FASTA] 67s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 67s [--browser-file-basename BROWSER_FILE_BASENAME] 67s [--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} ...]] 67s [--corrected-group CORRECTED_GROUP] 67s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 67s [--quiet] [--help] 67s 67s Data Arguments: 67s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 67s Directories containing fast5 files. 67s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 67s Set of directories containing fast5 files for control 67s reads, containing only canonical nucleotides. 67s --statistics-filename STATISTICS_FILENAME 67s File to save/load genomic base anchored statistics. 67s 67s Statistic Motif Filter Arguments: 67s --genome-fasta GENOME_FASTA 67s FASTA file used to re-squiggle. For faster sequence 67s access. 67s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 67s Ground truth, motif centered, modified base 67s descriptions for output filtering. Format descriptions 67s as: "motif:mod_pos:name". The mod_pos indicates the 67s modified base within the motif (1-based index). 67s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 67s output for identification of E. coli dam and dcm 67s methylation. 67s 67s Output Arguments: 67s --browser-file-basename BROWSER_FILE_BASENAME 67s Basename for output browser files. Two files (plus and 67s minus strand) will be produced for each --file-types 67s supplied. Filenames formatted as "[browser-file- 67s basename].[file- 67s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 67s Default: tombo_results 67s --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} ...] 67s Data types of genome browser files to produce. 67s Produced coverage files are in bedGraph format, while 67s all other file types will be in wiggle format 67s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 67s Default: "coverage" 67s 67s FAST5 Data Arguments: 67s --corrected-group CORRECTED_GROUP 67s FAST5 group created by resquiggle command. Default: 67s RawGenomeCorrected_000 67s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 67s FAST5 subgroup(s) (under /Analyses/[--basecall- 67s group]/) containing basecalls and created within 67s [--corrected-group] containing re-squiggle results. 67s Default: ['BaseCalled_template'] 67s 67s Miscellaneous Arguments: 67s --quiet, -q Don't print status information. 67s --help, -h Print this help message and exit 67s usage: tombo text_output signif_sequence_context --statistics-filename 67s STATISTICS_FILENAME 67s [--genome-fasta GENOME_FASTA] 67s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 67s [--num-regions NUM_REGIONS] 67s [--num-bases NUM_BASES] 67s [--sequences-filename SEQUENCES_FILENAME] 67s [--corrected-group CORRECTED_GROUP] 67s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 67s [--quiet] [--help] 67s 67s Required Argument: 67s --statistics-filename STATISTICS_FILENAME 67s File to save/load genomic base anchored statistics. 67s 67s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 67s --genome-fasta GENOME_FASTA 67s FASTA file used to re-squiggle. For faster sequence 67s access. 67s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 67s Directories containing fast5 files. 67s 67s Region Selection Arguments: 67s --num-regions NUM_REGIONS 67s Number of regions to plot. Default: 100 67s --num-bases NUM_BASES 67s Number of bases to plot/output. Default: 15 67s 67s Output Arguments: 67s --sequences-filename SEQUENCES_FILENAME 67s File for sequences from selected regions. Sequences 67s will be stored in FASTA format. Default: 67s tombo_results.significant_regions.fasta. 67s 67s FAST5 Data Arguments: 67s --corrected-group CORRECTED_GROUP 67s FAST5 group created by resquiggle command. Default: 67s RawGenomeCorrected_000 67s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 67s FAST5 subgroup(s) (under /Analyses/[--basecall- 67s group]/) containing basecalls and created within 67s [--corrected-group] containing re-squiggle results. 67s Default: ['BaseCalled_template'] 67s 67s Miscellaneous Arguments: 67s --quiet, -q Don't print status information. 67s --help, -h Print this help message and exit 68s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 68s [FAST5_BASEDIRS ...] 68s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 68s [--plot-standard-model] 68s [--plot-alternate-model {5mC,dcm,dam,6mA,CpG}] 68s [--overplot-threshold OVERPLOT_THRESHOLD] 68s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 68s [--num-regions NUM_REGIONS] 68s [--num-bases NUM_BASES] 68s [--pdf-filename PDF_FILENAME] 68s [--corrected-group CORRECTED_GROUP] 68s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 68s [--quiet] [--help] 68s 68s Required Argument: 68s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 68s Directories containing fast5 files. 68s 68s Comparison Arguments: 68s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 68s Set of directories containing fast5 files for control 68s reads, containing only canonical nucleotides. 68s --plot-standard-model 68s Add default standard model distribution to the plot. 68s --plot-alternate-model {5mC,dcm,dam,6mA,CpG} 68s Add alternative model distribution to the plot. 68s 68s Overplotting Arguments: 68s --overplot-threshold OVERPLOT_THRESHOLD 68s Coverage level to trigger alternative plot type 68s instead of raw signal. Default: 50 68s --overplot-type {Downsample,Boxplot,Quantile,Density} 68s Plot type for regions with higher coverage. Default: 68s Downsample 68s 68s Plotting Region Arguments: 68s --num-regions NUM_REGIONS 68s Number of regions to plot. Default: 10 68s --num-bases NUM_BASES 68s Number of bases to plot/output. Default: 21 68s 68s Output Argument: 68s --pdf-filename PDF_FILENAME 68s PDF filename to store plot(s). Default: 68s tombo_results.max_coverage.pdf 68s 68s FAST5 Data Arguments: 68s --corrected-group CORRECTED_GROUP 68s FAST5 group created by resquiggle command. Default: 68s RawGenomeCorrected_000 68s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 68s FAST5 subgroup(s) (under /Analyses/[--basecall- 68s group]/) containing basecalls and created within 68s [--corrected-group] containing re-squiggle results. 68s Default: ['BaseCalled_template'] 68s 68s Miscellaneous Arguments: 68s --quiet, -q Don't print status information. 68s --help, -h Print this help message and exit 68s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 68s [FAST5_BASEDIRS ...] --genome-locations 68s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 68s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 68s [--plot-standard-model] 68s [--plot-alternate-model {dam,CpG,6mA,5mC,dcm}] 68s [--overplot-threshold OVERPLOT_THRESHOLD] 68s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 68s [--num-bases NUM_BASES] 68s [--pdf-filename PDF_FILENAME] 68s [--corrected-group CORRECTED_GROUP] 68s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 68s [--quiet] [--help] 68s 68s Required Arguments: 68s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 68s Directories containing fast5 files. 68s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 68s Genomic locations at which to plot signal. Format 68s locations as "chrm:position[:strand] 68s [chrm2:position2[:strand2] ...]" (strand not 68s applicable for all applications) 68s 68s Comparison Arguments: 68s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 68s Set of directories containing fast5 files for control 68s reads, containing only canonical nucleotides. 68s --plot-standard-model 68s Add default standard model distribution to the plot. 68s --plot-alternate-model {dam,CpG,6mA,5mC,dcm} 68s Add alternative model distribution to the plot. 68s 68s Overplotting Arguments: 68s --overplot-threshold OVERPLOT_THRESHOLD 68s Coverage level to trigger alternative plot type 68s instead of raw signal. Default: 50 68s --overplot-type {Downsample,Boxplot,Quantile,Density} 68s Plot type for regions with higher coverage. Default: 68s Downsample 68s 68s Plotting Region Argument: 68s --num-bases NUM_BASES 68s Number of bases to plot/output. Default: 21 68s 68s Output Argument: 68s --pdf-filename PDF_FILENAME 68s PDF filename to store plot(s). Default: 68s tombo_results.genome_locations.pdf 68s 68s FAST5 Data Arguments: 68s --corrected-group CORRECTED_GROUP 68s FAST5 group created by resquiggle command. Default: 68s RawGenomeCorrected_000 68s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 68s FAST5 subgroup(s) (under /Analyses/[--basecall- 68s group]/) containing basecalls and created within 68s [--corrected-group] containing re-squiggle results. 68s Default: ['BaseCalled_template'] 68s 68s Miscellaneous Arguments: 68s --quiet, -q Don't print status information. 68s --help, -h Print this help message and exit 68s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 68s [FAST5_BASEDIRS ...] --motif MOTIF 68s --genome-fasta GENOME_FASTA 68s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 68s [--plot-standard-model] 68s [--plot-alternate-model {CpG,5mC,6mA,dam,dcm}] 68s [--overplot-threshold OVERPLOT_THRESHOLD] 68s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 68s [--num-regions NUM_REGIONS] 68s [--num-bases NUM_BASES] [--deepest-coverage] 68s [--pdf-filename PDF_FILENAME] 68s [--corrected-group CORRECTED_GROUP] 68s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 68s [--quiet] [--help] 68s 68s Required Arguments: 68s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 68s Directories containing fast5 files. 68s --motif MOTIF Motif of interest at which to plot signal and 68s statsitics. Supports IUPAC single letter codes (use T 68s for RNA). 68s --genome-fasta GENOME_FASTA 68s FASTA file used to re-squiggle. For faster sequence 68s access. 68s 68s Comparison Arguments: 68s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 68s Set of directories containing fast5 files for control 68s reads, containing only canonical nucleotides. 68s --plot-standard-model 68s Add default standard model distribution to the plot. 68s --plot-alternate-model {CpG,5mC,6mA,dam,dcm} 68s Add alternative model distribution to the plot. 68s 68s Overplotting Arguments: 68s --overplot-threshold OVERPLOT_THRESHOLD 68s Coverage level to trigger alternative plot type 68s instead of raw signal. Default: 50 68s --overplot-type {Downsample,Boxplot,Quantile,Density} 68s Plot type for regions with higher coverage. Default: 68s Downsample 68s 68s Plotting Region Arguments: 68s --num-regions NUM_REGIONS 68s Number of regions to plot. Default: 10 68s --num-bases NUM_BASES 68s Number of bases to plot/output. Default: 21 68s --deepest-coverage Plot the deepest coverage regions. 68s 68s Output Argument: 68s --pdf-filename PDF_FILENAME 68s PDF filename to store plot(s). Default: 68s tombo_results.motif_centered.pdf 68s 68s FAST5 Data Arguments: 68s --corrected-group CORRECTED_GROUP 68s FAST5 group created by resquiggle command. Default: 68s RawGenomeCorrected_000 68s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 68s FAST5 subgroup(s) (under /Analyses/[--basecall- 68s group]/) containing basecalls and created within 68s [--corrected-group] containing re-squiggle results. 68s Default: ['BaseCalled_template'] 68s 68s Miscellaneous Arguments: 68s --quiet, -q Don't print status information. 68s --help, -h Print this help message and exit 68s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 68s [FAST5_BASEDIRS ...] --control-fast5-basedirs 68s CONTROL_FAST5_BASEDIRS 68s [CONTROL_FAST5_BASEDIRS ...] 68s [--overplot-threshold OVERPLOT_THRESHOLD] 68s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 68s [--num-regions NUM_REGIONS] 68s [--num-bases NUM_BASES] 68s [--pdf-filename PDF_FILENAME] 68s [--sequences-filename SEQUENCES_FILENAME] 68s [--corrected-group CORRECTED_GROUP] 68s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 68s [--quiet] [--help] 68s 68s Required Arguments: 68s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 68s Directories containing fast5 files. 68s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 68s Set of directories containing fast5 files for control 68s reads, containing only canonical nucleotides. 68s 68s Overplotting Arguments: 68s --overplot-threshold OVERPLOT_THRESHOLD 68s Coverage level to trigger alternative plot type 68s instead of raw signal. Default: 50 68s --overplot-type {Downsample,Boxplot,Quantile,Density} 68s Plot type for regions with higher coverage. Default: 68s Downsample 68s 68s Plotting Region Arguments: 68s --num-regions NUM_REGIONS 68s Number of regions to plot. Default: 10 68s --num-bases NUM_BASES 68s Number of bases to plot/output. Default: 21 68s 68s Output Arguments: 68s --pdf-filename PDF_FILENAME 68s PDF filename to store plot(s). Default: 68s tombo_results.max_difference.pdf 68s --sequences-filename SEQUENCES_FILENAME 68s File for sequences from selected regions. Sequences 68s will be stored in FASTA format. Default: None. 68s 68s FAST5 Data Arguments: 68s --corrected-group CORRECTED_GROUP 68s FAST5 group created by resquiggle command. Default: 68s RawGenomeCorrected_000 68s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 68s FAST5 subgroup(s) (under /Analyses/[--basecall- 68s group]/) containing basecalls and created within 68s [--corrected-group] containing re-squiggle results. 68s Default: ['BaseCalled_template'] 68s 68s Miscellaneous Arguments: 68s --quiet, -q Don't print status information. 68s --help, -h Print this help message and exit 68s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 68s [FAST5_BASEDIRS ...] --statistics-filename 68s STATISTICS_FILENAME 68s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 68s [--plot-standard-model] 68s [--plot-alternate-model {dcm,5mC,CpG,6mA,dam}] 68s [--overplot-threshold OVERPLOT_THRESHOLD] 68s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 68s [--num-regions NUM_REGIONS] 68s [--num-bases NUM_BASES] 68s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 68s [--pdf-filename PDF_FILENAME] 68s [--sequences-filename SEQUENCES_FILENAME] 68s [--corrected-group CORRECTED_GROUP] 68s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 68s [--quiet] [--help] 68s 68s Required Arguments: 68s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 68s Directories containing fast5 files. 68s --statistics-filename STATISTICS_FILENAME 68s File to save/load genomic base anchored statistics. 68s 68s Comparison Arguments: 68s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 68s Set of directories containing fast5 files for control 68s reads, containing only canonical nucleotides. 68s --plot-standard-model 68s Add default standard model distribution to the plot. 68s --plot-alternate-model {dcm,5mC,CpG,6mA,dam} 68s Add alternative model distribution to the plot. 68s 68s Overplotting Arguments: 68s --overplot-threshold OVERPLOT_THRESHOLD 68s Coverage level to trigger alternative plot type 68s instead of raw signal. Default: 50 68s --overplot-type {Downsample,Boxplot,Quantile,Density} 68s Plot type for regions with higher coverage. Default: 68s Downsample 68s 68s Plotting Region Arguments: 68s --num-regions NUM_REGIONS 68s Number of regions to plot. Default: 10 68s --num-bases NUM_BASES 68s Number of bases to plot/output. Default: 21 68s 68s Statistical Argument: 68s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 68s Dampen fraction modified estimates for low coverage 68s sites. Two parameters are unmodified and modified 68s pseudo read counts. This is equivalent to a beta prior 68s on the fraction estimate. Set to "0 0" to disable 68s dampened fraction estimation. Default: [2, 0] 68s 68s Output Arguments: 68s --pdf-filename PDF_FILENAME 68s PDF filename to store plot(s). Default: 68s tombo_results.significant_difference.pdf 68s --sequences-filename SEQUENCES_FILENAME 68s File for sequences from selected regions. Sequences 68s will be stored in FASTA format. Default: None. 68s 68s FAST5 Data Arguments: 68s --corrected-group CORRECTED_GROUP 68s FAST5 group created by resquiggle command. Default: 68s RawGenomeCorrected_000 68s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 68s FAST5 subgroup(s) (under /Analyses/[--basecall- 68s group]/) containing basecalls and created within 68s [--corrected-group] containing re-squiggle results. 68s Default: ['BaseCalled_template'] 68s 68s Miscellaneous Arguments: 68s --quiet, -q Don't print status information. 68s --help, -h Print this help message and exit 68s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 68s [FAST5_BASEDIRS ...] --motif MOTIF 68s --statistics-filename STATISTICS_FILENAME 68s --genome-fasta GENOME_FASTA 68s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 68s [--plot-standard-model] 68s [--plot-alternate-model {CpG,5mC,6mA,dcm,dam}] 68s [--overplot-threshold OVERPLOT_THRESHOLD] 68s [--num-regions NUM_REGIONS] 68s [--num-context NUM_CONTEXT] 68s [--num-statistics NUM_STATISTICS] 68s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 68s [--pdf-filename PDF_FILENAME] 68s [--corrected-group CORRECTED_GROUP] 68s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 68s [--quiet] [--help] 68s 68s Required Arguments: 68s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 68s Directories containing fast5 files. 68s --motif MOTIF Motif of interest at which to plot signal and 68s statsitics. Supports IUPAC single letter codes (use T 68s for RNA). 68s --statistics-filename STATISTICS_FILENAME 68s File to save/load genomic base anchored statistics. 68s --genome-fasta GENOME_FASTA 68s FASTA file used to re-squiggle. For faster sequence 68s access. 68s 68s Comparison Arguments: 68s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 68s Set of directories containing fast5 files for control 68s reads, containing only canonical nucleotides. 68s --plot-standard-model 68s Add default standard model distribution to the plot. 68s --plot-alternate-model {CpG,5mC,6mA,dcm,dam} 68s Add alternative model distribution to the plot. 68s 68s Overplotting Argument: 68s --overplot-threshold OVERPLOT_THRESHOLD 68s Coverage level to trigger alternative plot type 68s instead of raw signal. Default: 50 68s 68s Plotting Region Arguments: 68s --num-regions NUM_REGIONS 68s Number of regions to plot. Default: 3 68s --num-context NUM_CONTEXT 68s Number of context bases around motif. Default: 5 68s --num-statistics NUM_STATISTICS 68s Number of motif centered regions to include in 68s statistic distributions. Default: 200 68s 68s Statistical Argument: 68s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 68s Dampen fraction modified estimates for low coverage 68s sites. Two parameters are unmodified and modified 68s pseudo read counts. This is equivalent to a beta prior 68s on the fraction estimate. Set to "0 0" to disable 68s dampened fraction estimation. Default: [2, 0] 68s 68s Output Argument: 68s --pdf-filename PDF_FILENAME 68s PDF filename to store plot(s). Default: 68s tombo_results.motif_statistics.pdf 68s 68s FAST5 Data Arguments: 68s --corrected-group CORRECTED_GROUP 68s FAST5 group created by resquiggle command. Default: 68s RawGenomeCorrected_000 68s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 68s FAST5 subgroup(s) (under /Analyses/[--basecall- 68s group]/) containing basecalls and created within 68s [--corrected-group] containing re-squiggle results. 68s Default: ['BaseCalled_template'] 68s 68s Miscellaneous Arguments: 68s --quiet, -q Don't print status information. 68s --help, -h Print this help message and exit 68s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 68s [GENOME_LOCATIONS ...] 68s --per-read-statistics-filename 68s PER_READ_STATISTICS_FILENAME 68s [--genome-fasta GENOME_FASTA] 68s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 68s [--num-reads NUM_READS] [--num-bases NUM_BASES] 68s [--box-center] [--pdf-filename PDF_FILENAME] 68s [--corrected-group CORRECTED_GROUP] 68s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 68s [--quiet] [--help] 68s 68s Required Arguments: 68s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 68s Genomic locations at which to plot signal. Format 68s locations as "chrm:position[:strand] 68s [chrm2:position2[:strand2] ...]" (strand not 68s applicable for all applications) 68s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 68s Binary file containing per-read statistics from 68s statistical testing. 68s 68s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 68s --genome-fasta GENOME_FASTA 68s FASTA file used to re-squiggle. For faster sequence 68s access. 68s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 68s Directories containing fast5 files. 68s 68s Plotting Region Arguments: 68s --num-reads NUM_READS 68s Number of reads to plot. Default: 100 68s --num-bases NUM_BASES 68s Number of bases to plot/output. Default: 51 68s --box-center Plot a box around the central base. 68s 68s Output Argument: 68s --pdf-filename PDF_FILENAME 68s PDF filename to store plot(s). Default: 68s tombo_results.per_read_stats.pdf 68s 68s FAST5 Data Arguments: 68s --corrected-group CORRECTED_GROUP 68s FAST5 group created by resquiggle command. Default: 68s RawGenomeCorrected_000 68s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 68s FAST5 subgroup(s) (under /Analyses/[--basecall- 68s group]/) containing basecalls and created within 68s [--corrected-group] containing re-squiggle results. 68s Default: ['BaseCalled_template'] 68s 68s Miscellaneous Arguments: 68s --quiet, -q Don't print status information. 68s --help, -h Print this help message and exit 68s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 68s [STATISTICS_FILENAMES ...] 68s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 68s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 68s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 68s [--genome-fasta GENOME_FASTA] 68s [--pdf-filename PDF_FILENAME] 68s [--statistics-per-block STATISTICS_PER_BLOCK] 68s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 68s [--quiet] [--help] 68s 68s Required Argument: 68s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 68s Files to load genomic base anchored statistics. 68s 68s Ground Truth Arguments (provide bed files or motifs): 68s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 68s Modification description and bed format files 68s containing single base locations of ground truth 68s modified sites. Bed files should contain 6 fields 68s including strand. Format descriptions as 68s "mod_name:locs.bed". Example: "CpG 68s bisulfite":bisulfite_locs.bed 68s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 68s Bed format files containing single base locations of 68s ground truth unmodified sites. Bed files should 68s contain 6 fields including strand. 68s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 68s Ground truth, motif centered, modified base 68s descriptions for computing ROC and PR curves. Each 68s statistics file is associated with a set of motif 68s descriptions. Format descriptions as: 68s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 68s mod_pos indicates the alternate-base within the motif 68s (1-based index). Example: CCWGG:2:"dcm 68s 5mC"::GATC:2:"dam 6mA" would assess the performance of 68s a single Tombo statistics file for identification of 68s E. coli dam and dcm methylation. 68s --genome-fasta GENOME_FASTA 68s FASTA file used to re-squiggle. For faster sequence 68s access. 68s 68s Output Arguments: 68s --pdf-filename PDF_FILENAME 68s PDF filename to store plot(s). Default: 68s tombo_results.roc.pdf 68s 68s Down-sampling Arguments: 68s --statistics-per-block STATISTICS_PER_BLOCK 68s Number of randomly selected per-read, per-base 68s statistics to extract from each genomic block for 68s plotting. Default: Include all stats 68s --total-statistics-limit TOTAL_STATISTICS_LIMIT 68s Total per-read statistics to be extracted for 68s plotting. Avoids memory overflow for large runs. 68s Default: 5000000 68s 68s Miscellaneous Arguments: 68s --quiet, -q Don't print status information. 68s --help, -h Print this help message and exit 68s usage: tombo plot per_read_roc --per-read-statistics-filenames 68s PER_READ_STATISTICS_FILENAMES 68s [PER_READ_STATISTICS_FILENAMES ...] 68s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 68s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 68s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 68s [--genome-fasta GENOME_FASTA] 68s [--statistics-per-block STATISTICS_PER_BLOCK] 68s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 68s [--pdf-filename PDF_FILENAME] [--quiet] 68s [--help] 68s 68s Required Argument: 68s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 68s Binary files containing per-read statistics from 68s statistical testing. 68s 68s Ground Truth Arguments (provide bed files or motifs): 68s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 68s Modification description and bed format files 68s containing single base locations of ground truth 68s modified sites. Bed files should contain 6 fields 68s including strand. Format descriptions as 68s "mod_name:locs.bed". Example: "CpG 68s bisulfite":bisulfite_locs.bed 68s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 68s Bed format files containing single base locations of 68s ground truth unmodified sites. Bed files should 68s contain 6 fields including strand. 68s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 68s Ground truth, motif centered, modified base 68s descriptions for computing ROC and PR curves. Each 68s statistics file is associated with a set of motif 68s descriptions. Format descriptions as: 68s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 68s mod_pos indicates the alternate-base within the motif 68s (1-based index). Example: CCWGG:2:"dcm 68s 5mC"::GATC:2:"dam 6mA" would assess the performance of 68s a single Tombo statistics file for identification of 68s E. coli dam and dcm methylation. 68s --genome-fasta GENOME_FASTA 68s FASTA file used to re-squiggle. For faster sequence 68s access. 68s 68s Down-sampling Arguments: 68s --statistics-per-block STATISTICS_PER_BLOCK 68s Number of randomly selected per-read, per-base 68s statistics to extract from each genomic block for 68s plotting. Default: 100000 68s --total-statistics-limit TOTAL_STATISTICS_LIMIT 68s Total per-read statistics to be extracted for 68s plotting. Avoids memory overflow for large runs. 68s Default: 5000000 68s 68s Output Arguments: 68s --pdf-filename PDF_FILENAME 68s PDF filename to store plot(s). Default: 68s tombo_results.per_reads_roc.pdf 68s 68s Miscellaneous Arguments: 68s --quiet, -q Don't print status information. 68s --help, -h Print this help message and exit 68s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 68s [--upstream-bases {0,1,2,3,4}] 68s [--downstream-bases {0,1,2,3,4}] [--read-mean] 68s [--num-kmer-threshold NUM_KMER_THRESHOLD] 68s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 68s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 68s [--corrected-group CORRECTED_GROUP] 68s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 68s [--quiet] [--help] 68s 68s Required Argument: 68s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 68s Directories containing fast5 files. 68s 68s Data Processing Arguments: 68s --upstream-bases {0,1,2,3,4} 68s Upstream bases in k-mer. Default: 1 68s --downstream-bases {0,1,2,3,4} 68s Downstream bases in k-mer. Default: 2 68s --read-mean Plot k-mer means across whole reads as opposed to 68s individual k-mer event levels. 68s --num-kmer-threshold NUM_KMER_THRESHOLD 68s Observations of each k-mer required to include a read 68s in read level averages. Default: 1 68s 68s Plotting Region Arguments: 68s --num-reads NUM_READS 68s Number of reads to plot. Default: 100 68s 68s Output Arguments: 68s --pdf-filename PDF_FILENAME 68s PDF filename to store plot(s). Default: 68s tombo_results.kmer_distribution.pdf 68s --r-data-filename R_DATA_FILENAME 68s Filename to save R data structure. Default: Don't save 68s --dont-plot Don't plot result. Useful to produce only R data file. 68s 68s FAST5 Data Arguments: 68s --corrected-group CORRECTED_GROUP 68s FAST5 group created by resquiggle command. Default: 68s RawGenomeCorrected_000 68s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 68s FAST5 subgroup(s) (under /Analyses/[--basecall- 68s group]/) containing basecalls and created within 68s [--corrected-group] containing re-squiggle results. 68s Default: ['BaseCalled_template'] 68s 68s Miscellaneous Arguments: 68s --quiet, -q Don't print status information. 68s --help, -h Print this help message and exit 68s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 68s [FAST5_BASEDIRS ...] 68s --control-fast5-basedirs 68s CONTROL_FAST5_BASEDIRS 68s [CONTROL_FAST5_BASEDIRS ...] 68s --statistics-filename 68s STATISTICS_FILENAME 68s [--genome-fasta GENOME_FASTA] 68s [--processes PROCESSES] 68s [--num-regions NUM_REGIONS] 68s [--num-bases NUM_BASES] 68s [--slide-span SLIDE_SPAN] 68s [--pdf-filename PDF_FILENAME] 68s [--r-data-filename R_DATA_FILENAME] 68s [--corrected-group CORRECTED_GROUP] 68s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 68s [--quiet] [--help] 68s 68s Required Arguments: 68s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 68s Directories containing fast5 files. 68s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 68s Set of directories containing fast5 files for control 68s reads, containing only canonical nucleotides. 68s --statistics-filename STATISTICS_FILENAME 68s File to save/load genomic base anchored statistics. 68s 68s FASTA Sequence Argument: 68s --genome-fasta GENOME_FASTA 68s FASTA file used to re-squiggle. For faster sequence 68s access. 68s 68s Multiprocessing Argument: 68s --processes PROCESSES 68s Number of processes. Default: 1 68s 68s Plotting Region Arguments: 68s --num-regions NUM_REGIONS 68s Number of regions to plot. Default: 10 68s --num-bases NUM_BASES 68s Number of bases to plot/output. Default: 21 68s --slide-span SLIDE_SPAN 68s Number of bases offset over which to search when 68s computing distances for signal cluster plotting. 68s Default: 0 (exact position) 68s 68s Output Arguments: 68s --pdf-filename PDF_FILENAME 68s PDF filename to store plot(s). Default: 68s tombo_results.signal_clusters.pdf 68s --r-data-filename R_DATA_FILENAME 68s Filename to save R data structure. Default: Don't save 68s 68s FAST5 Data Arguments: 68s --corrected-group CORRECTED_GROUP 68s FAST5 group created by resquiggle command. Default: 68s RawGenomeCorrected_000 68s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 68s FAST5 subgroup(s) (under /Analyses/[--basecall- 68s group]/) containing basecalls and created within 68s [--corrected-group] containing re-squiggle results. 68s Default: ['BaseCalled_template'] 68s 68s Miscellaneous Arguments: 68s --quiet, -q Don't print status information. 68s --help, -h Print this help message and exit 69s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 69s 69s Required Arguments: 69s fast5s_basedir Directory containing fast5 files. All files ending in 69s "fast5" found recursively within this base directory will be 69s processed. 69s 69s Miscellaneous Arguments: 69s --quiet, -q Don't print status information. 69s --help, -h Print this help message and exit 69s usage: tombo build_model event_resquiggle 69s [--minimap2-executable MINIMAP2_EXECUTABLE] 69s [--minimap2-index MINIMAP2_INDEX] 69s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 69s [--graphmap-executable GRAPHMAP_EXECUTABLE] 69s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 69s [--normalization-type {median,pA,pA_raw,none}] 69s [--pore-model-filename PORE_MODEL_FILENAME] 69s [--outlier-threshold OUTLIER_THRESHOLD] 69s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 69s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 69s [--timeout TIMEOUT] 69s [--cpts-limit CPTS_LIMIT] 69s [--skip-index] [--overwrite] 69s [--failed-reads-filename FAILED_READS_FILENAME] 69s [--include-event-stdev] 69s [--corrected-group CORRECTED_GROUP] 69s [--basecall-group BASECALL_GROUP] 69s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 69s [--processes PROCESSES] 69s [--align-processes ALIGN_PROCESSES] 69s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 69s [--resquiggle-processes RESQUIGGLE_PROCESSES] 69s [--quiet] [--help] 69s fast5s_basedir reference_fasta 69s 69s Required Arguments: 69s fast5s_basedir Directory containing fast5 files. All files ending in 69s "fast5" found recursively within this base directory 69s will be processed. 69s reference_fasta Reference genome/transcriptome FASTA file for mapping. 69s 69s Mapper Arguments (One mapper is required): 69s --minimap2-executable MINIMAP2_EXECUTABLE 69s Path to minimap2 executable. 69s --minimap2-index MINIMAP2_INDEX 69s Path to minimap2 index (with map-ont preset) file 69s corresponding to the [genome_fasta] provided. 69s --bwa-mem-executable BWA_MEM_EXECUTABLE 69s Path to bwa-mem executable. 69s --graphmap-executable GRAPHMAP_EXECUTABLE 69s Path to graphmap executable. 69s --alignment-batch-size ALIGNMENT_BATCH_SIZE 69s Number of reads included in each alignment call. Note: 69s A new system mapping call is made for each batch 69s (including loading of the genome), so it is advised to 69s use larger values for larger genomes. Default: 1000 69s 69s Signal Processing Arguments: 69s --normalization-type {median,pA,pA_raw,none} 69s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 69s as in the ONT events (using offset, range and 69s digitization), "pA": k-mer-based correction for pA 69s drift as in nanopolish (requires [--pore-model- 69s filename]), "median": median and MAD from raw signal. 69s Default: median 69s --pore-model-filename PORE_MODEL_FILENAME 69s File containing kmer model parameters (level_mean and 69s level_stdv) used in order to compute kmer-based 69s corrected pA values. E.g. https://github.com/jts/nanop 69s olish/blob/master/etc/r9- 69s models/template_median68pA.5mers.model 69s --outlier-threshold OUTLIER_THRESHOLD 69s Windosrize the signal at this number of scale values. 69s Negative value disables outlier clipping. Default: 69s 5.000000 69s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 69s Specify the 2 parameters for segmentation 1) running 69s neighboring windows width 2) minimum raw observations 69s per genomic base. Sample type defaults: RNA : 12 6 || 69s DNA : 5 3 69s 69s Read Filtering Arguments: 69s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 69s Filter reads based on observations per base percentile 69s thresholds. Format thresholds as "percentile:thresh 69s [pctl2:thresh2 ...]". For example to filter reads with 69s 99th pctl > 200 obs/base or max > 5k obs/base use 69s "99:200 100:5000". 69s --timeout TIMEOUT Timeout in seconds for processing a single read. 69s Default: No timeout. 69s --cpts-limit CPTS_LIMIT 69s Maximum number of changepoints to find within a single 69s indel group. Default: No limit. 69s 69s Input/Output Arguments: 69s --skip-index Skip creation of tombo index. This drastically slows 69s downstream tombo commands. Default stores tombo index 69s named ".[--fast5-basedir].[--corrected- 69s group].tombo.index" to be loaded automatically for 69s downstream commands. 69s --overwrite Overwrite previous corrected group in FAST5 files. 69s Note: only effects --corrected-group or --new- 69s corrected-group. 69s --failed-reads-filename FAILED_READS_FILENAME 69s Output failed read filenames with assoicated error. 69s Default: Do not store failed reads. 69s --include-event-stdev 69s Include corrected event standard deviation in output 69s FAST5 data. 69s 69s FAST5 Data Arguments: 69s --corrected-group CORRECTED_GROUP 69s FAST5 group created by resquiggle command. Default: 69s RawGenomeCorrected_000 69s --basecall-group BASECALL_GROUP 69s FAST5 group obtain original basecalls (under Analyses 69s group). Default: Basecall_1D_000 69s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 69s FAST5 subgroup(s) (under /Analyses/[--basecall- 69s group]/) containing basecalls and created within 69s [--corrected-group] containing re-squiggle results. 69s Default: ['BaseCalled_template'] 69s 69s Multiprocessing Arguments: 69s --processes PROCESSES 69s Number of processes. Default: 2 69s --align-processes ALIGN_PROCESSES 69s Number of processes to use for parsing and aligning 69s original basecalls. Each process will independently 69s load the genome into memory, so use caution with 69s larger genomes (e.g. human). Default: 1 69s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 69s Number of threads to use for aligner system call. 69s Default: [--processes] / (2 * [--align-processes)] 69s --resquiggle-processes RESQUIGGLE_PROCESSES 69s Number of processes to use for resquiggle algorithm. 69s Default: [--processes] / 2 69s 69s Miscellaneous Arguments: 69s --quiet, -q Don't print status information. 69s --help, -h Print this help message and exit 69s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 69s [FAST5_BASEDIRS ...] 69s --tombo-model-filename 69s TOMBO_MODEL_FILENAME 69s [--estimate-mean] 69s [--kmer-specific-sd] 69s [--upstream-bases {0,1,2,3,4}] 69s [--downstream-bases {0,1,2,3,4}] 69s [--minimum-test-reads MINIMUM_TEST_READS] 69s [--coverage-threshold COVERAGE_THRESHOLD] 69s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 69s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 69s [--processes PROCESSES] 69s [--corrected-group CORRECTED_GROUP] 69s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 69s [--quiet] [--help] 69s 69s Required Arguments: 69s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 69s Directories containing fast5 files. 69s --tombo-model-filename TOMBO_MODEL_FILENAME 69s Filename to save Tombo model. 69s 69s Modeling Arguments: 69s --estimate-mean Use the mean instead of median for model level 69s estimation. Note: This can cause poor fits due to 69s outliers 69s --kmer-specific-sd Estimate standard deviation for each k-mers 69s individually. 69s --upstream-bases {0,1,2,3,4} 69s Upstream bases in k-mer. Default: 1 69s --downstream-bases {0,1,2,3,4} 69s Downstream bases in k-mer. Default: 2 69s 69s Filtering Arguments: 69s --minimum-test-reads MINIMUM_TEST_READS 69s Number of reads required at a position to perform 69s significance testing or contribute to model 69s estimation. Default: 10 69s --coverage-threshold COVERAGE_THRESHOLD 69s Maximum mean coverage per region when estimating k-mer 69s model (limits compute time for deep samples). Default: 69s 100 69s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 69s Number of each k-mer observations required in order to 69s produce a reference (genomic locations for standard 69s reference and per-read for alternative reference). 69s Default: 5 69s 69s Multiprocessing Arguments: 69s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 69s Size of regions over which to multiprocesses statistic 69s computation. For very deep samples a smaller value is 69s recommmended in order to control memory consumption. 69s Default: 10000 69s --processes PROCESSES 69s Number of processes. Default: 1 69s 69s FAST5 Data Arguments: 69s --corrected-group CORRECTED_GROUP 69s FAST5 group created by resquiggle command. Default: 69s RawGenomeCorrected_000 69s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 69s FAST5 subgroup(s) (under /Analyses/[--basecall- 69s group]/) containing basecalls and created within 69s [--corrected-group] containing re-squiggle results. 69s Default: ['BaseCalled_template'] 69s 69s Miscellaneous Arguments: 69s --quiet, -q Don't print status information. 69s --help, -h Print this help message and exit 69s usage: tombo build_model estimate_alt_reference --alternate-model-filename 69s ALTERNATE_MODEL_FILENAME 69s --alternate-model-name 69s ALTERNATE_MODEL_NAME 69s --alternate-model-base 69s {A,C,G,T} 69s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 69s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 69s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 69s [--control-density-filename CONTROL_DENSITY_FILENAME] 69s [--dna] [--rna] 69s [--tombo-model-filename TOMBO_MODEL_FILENAME] 69s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 69s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 69s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 69s [--save-density-basename SAVE_DENSITY_BASENAME] 69s [--processes PROCESSES] 69s [--corrected-group CORRECTED_GROUP] 69s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 69s [--quiet] [--help] 69s 69s Required Arguments: 69s --alternate-model-filename ALTERNATE_MODEL_FILENAME 69s Tombo model for alternative likelihood ratio 69s significance testing. 69s --alternate-model-name ALTERNATE_MODEL_NAME 69s A short name to associate with this alternate model 69s (e.g. 5mC, 6mA, etc.). This text will be included in 69s output filenames when this model is used for testing. 69s --alternate-model-base {A,C,G,T} 69s Non-standard base is an alternative to this base. 69s 69s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 69s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 69s Directories containing fast5 files. 69s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 69s Set of directories containing fast5 files for control 69s reads, containing only canonical nucleotides. 69s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 69s File containing k-mer level kernel density estimates 69s for the alternative sample saved using --save-density- 69s basename. 69s --control-density-filename CONTROL_DENSITY_FILENAME 69s File containing k-mer level kernel density estimates 69s for the control sample saved using --save-density- 69s basename. 69s 69s Standard Model Arguments: 69s --dna Explicitly select canonical DNA model. Default: 69s Automatically determine from FAST5s 69s --rna Explicitly select canonical RNA model. Default: 69s Automatically determine from FAST5s 69s --tombo-model-filename TOMBO_MODEL_FILENAME 69s Tombo model filename. If no file is provided, the 69s default DNA or RNA Tombo model will be used. 69s 69s Model Fitting Arguments: 69s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 69s When esitmating the alternative base incorporation 69s rate, this percent of k-mers are assumed to have 69s significantly shifted signal so the alternative 69s distribution minimally overlaps the standard base 69s distribution. Default: 5.000000 69s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 69s Bandwidth applied when performing Gaussian kernal 69s density esitmation on standard and alternative base 69s signal distributions. Default: 0.050000 69s 69s Filtering Argument: 69s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 69s Number of each k-mer observations required in order to 69s produce a reference (genomic locations for standard 69s reference and per-read for alternative reference). 69s Default: 1000 69s 69s Output Argument: 69s --save-density-basename SAVE_DENSITY_BASENAME 69s Basename to save alternative model estimation density 69s estimation information. See scripts/debug_est_alt.R 69s for info use example. Default: Don't save. 69s 69s Multiprocessing Arguments: 69s --processes PROCESSES 69s Number of processes. Default: 1 69s 69s FAST5 Data Arguments: 69s --corrected-group CORRECTED_GROUP 69s FAST5 group created by resquiggle command. Default: 69s RawGenomeCorrected_000 69s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 69s FAST5 subgroup(s) (under /Analyses/[--basecall- 69s group]/) containing basecalls and created within 69s [--corrected-group] containing re-squiggle results. 69s Default: ['BaseCalled_template'] 69s 69s Miscellaneous Arguments: 69s --quiet, -q Don't print status information. 69s --help, -h Print this help message and exit 69s This test only tests the help system 69s There is an extensive test in 69s 69s tombo/tests/shell_tests.sh 69s 69s but this requires to download larger data 69s sets which is not done for the moment. 69s autopkgtest [12:13:10]: test run-unit-test: -----------------------] 69s run-unit-test PASS 69s autopkgtest [12:13:10]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 69s autopkgtest [12:13:10]: @@@@@@@@@@@@@@@@@@@@ summary 69s run-unit-test PASS 79s virt: nova [W] Skipping flock for amd64 79s virt: Creating nova instance adt-plucky-amd64-tombo-20241115-121201-juju-7f2275-prod-proposed-migration-environment-2-a2a2bbdb-f31b-4c2f-bfdc-7f342b6df3bc from image adt/ubuntu-plucky-amd64-server-20241115.img (UUID cc9375bb-1426-47d8-a5d8-f3536037532e)...