0s autopkgtest [10:40:41]: starting date and time: 2024-10-30 10:40:41+0000 0s autopkgtest [10:40:41]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [10:40:41]: host juju-7f2275-prod-proposed-migration-environment-14; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.36hk9j2p/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:setuptools --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=setuptools/75.2.0-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-14@lcy02-22.secgroup --name adt-plucky-amd64-tombo-20241030-104040-juju-7f2275-prod-proposed-migration-environment-14-dd590128-0415-440d-8ad5-14b03a34185c --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-14 --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/ 46s autopkgtest [10:41:27]: testbed dpkg architecture: amd64 46s autopkgtest [10:41:27]: testbed apt version: 2.9.8 46s autopkgtest [10:41:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 46s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 46s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [2840 B] 46s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 46s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [213 kB] 46s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [30.5 kB] 46s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [66.9 kB] 46s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [25.6 kB] 46s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 46s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [84.3 kB] 46s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [258 kB] 46s Fetched 794 kB in 0s (4322 kB/s) 46s Reading package lists... 48s Reading package lists... 48s Building dependency tree... 48s Reading state information... 49s Calculating upgrade... 49s The following NEW packages will be installed: 49s python3-jaraco.text 49s The following packages will be upgraded: 49s python3-pkg-resources python3-setuptools 49s 2 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 49s Need to get 802 kB of archives. 49s After this operation, 12.3 kB of additional disk space will be used. 49s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jaraco.text all 4.0.0-1 [11.5 kB] 49s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-pkg-resources all 75.2.0-1 [134 kB] 49s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-setuptools all 75.2.0-1 [657 kB] 49s Fetched 802 kB in 0s (24.1 MB/s) 49s Selecting previously unselected package python3-jaraco.text. 50s (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 ... 75315 files and directories currently installed.) 50s Preparing to unpack .../python3-jaraco.text_4.0.0-1_all.deb ... 50s Unpacking python3-jaraco.text (4.0.0-1) ... 50s Preparing to unpack .../python3-pkg-resources_75.2.0-1_all.deb ... 50s Unpacking python3-pkg-resources (75.2.0-1) over (74.1.2-1) ... 50s Preparing to unpack .../python3-setuptools_75.2.0-1_all.deb ... 50s Unpacking python3-setuptools (75.2.0-1) over (74.1.2-1) ... 50s Setting up python3-pkg-resources (75.2.0-1) ... 50s Setting up python3-jaraco.text (4.0.0-1) ... 50s Setting up python3-setuptools (75.2.0-1) ... 51s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 52s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 52s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 52s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 52s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 53s Reading package lists... 53s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Calculating upgrade... 54s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s autopkgtest [10:41:37]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 56s autopkgtest [10:41:37]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 57s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (dsc) [2291 B] 57s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (tar) [22.3 MB] 57s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (diff) [7100 B] 57s gpgv: Signature made Wed Apr 10 17:15:32 2024 UTC 57s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 57s gpgv: Can't check signature: No public key 57s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6build1.dsc: no acceptable signature found 57s autopkgtest [10:41:38]: testing package tombo version 1.5.1-6build1 57s autopkgtest [10:41:38]: build not needed 58s autopkgtest [10:41:39]: test run-unit-test: preparing testbed 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 59s Starting pkgProblemResolver with broken count: 0 59s Starting 2 pkgProblemResolver with broken count: 0 59s Done 59s The following additional packages will be installed: 59s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 59s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 59s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 59s python3-decorator python3-h5py python3-h5py-serial python3-mappy 59s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 59s tombo-doc 59s Suggested packages: 59s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 59s gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 59s Recommended packages: 59s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 59s python3-rpy2 60s The following NEW packages will be installed: 60s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 60s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 60s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 60s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 60s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 60s tombo-doc 60s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 60s Need to get 62.9 MB/62.9 MB of archives. 60s After this operation, 202 MB of additional disk space will be used. 60s Get:1 /tmp/autopkgtest.e1Q5G6/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 60s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-lato all 2.015-1 [2781 kB] 60s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 60s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 60s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 60s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 60s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-7ubuntu1 [909 kB] 60s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 60s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 60s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB] 60s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 60s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 60s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-3 [157 kB] 60s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 60s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 60s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 60s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 60s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 60s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.11.0-5ubuntu1 [1107 kB] 60s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 60s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mappy amd64 2.27+dfsg-1 [150 kB] 60s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tqdm all 4.66.5-1 [91.4 kB] 60s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-rtd-theme-common all 2.0.0+dfsg-2 [1012 kB] 60s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-3 [16.9 MB] 60s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 tombo amd64 1.5.1-6build1 [450 kB] 60s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 60s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 tombo-doc all 1.5.1-6build1 [21.7 MB] 61s Fetched 62.9 MB in 1s (80.7 MB/s) 61s Selecting previously unselected package fonts-lato. 61s (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 ... 75324 files and directories currently installed.) 61s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 61s Unpacking fonts-lato (2.015-1) ... 61s Selecting previously unselected package fonts-font-awesome. 61s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 61s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 61s Selecting previously unselected package fonts-mathjax. 61s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 61s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 61s Selecting previously unselected package libaec0:amd64. 61s Preparing to unpack .../03-libaec0_1.1.3-1_amd64.deb ... 61s Unpacking libaec0:amd64 (1.1.3-1) ... 61s Selecting previously unselected package libblas3:amd64. 61s Preparing to unpack .../04-libblas3_3.12.0-3build2_amd64.deb ... 61s Unpacking libblas3:amd64 (3.12.0-3build2) ... 61s Selecting previously unselected package libgfortran5:amd64. 61s Preparing to unpack .../05-libgfortran5_14.2.0-7ubuntu1_amd64.deb ... 61s Unpacking libgfortran5:amd64 (14.2.0-7ubuntu1) ... 61s Selecting previously unselected package libsz2:amd64. 61s Preparing to unpack .../06-libsz2_1.1.3-1_amd64.deb ... 61s Unpacking libsz2:amd64 (1.1.3-1) ... 61s Selecting previously unselected package libhdf5-103-1t64:amd64. 61s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ... 61s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 61s Selecting previously unselected package libhdf5-hl-100t64:amd64. 61s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_amd64.deb ... 61s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 61s Selecting previously unselected package libjs-jquery. 61s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 61s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 61s Selecting previously unselected package libjs-underscore. 61s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 61s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 61s Selecting previously unselected package libjs-sphinxdoc. 61s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-3_all.deb ... 61s Unpacking libjs-sphinxdoc (7.4.7-3) ... 61s Selecting previously unselected package liblapack3:amd64. 61s Preparing to unpack .../12-liblapack3_3.12.0-3build2_amd64.deb ... 61s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 62s Selecting previously unselected package liblbfgsb0:amd64. 62s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 62s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 62s Selecting previously unselected package liblzf1:amd64. 62s Preparing to unpack .../14-liblzf1_3.6-4_amd64.deb ... 62s Unpacking liblzf1:amd64 (3.6-4) ... 62s Selecting previously unselected package python3-decorator. 62s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 62s Unpacking python3-decorator (5.1.1-5) ... 62s Selecting previously unselected package python3-numpy. 62s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 62s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 62s Selecting previously unselected package python3-h5py-serial. 62s Preparing to unpack .../17-python3-h5py-serial_3.11.0-5ubuntu1_amd64.deb ... 62s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 62s Selecting previously unselected package python3-h5py. 62s Preparing to unpack .../18-python3-h5py_3.11.0-5ubuntu1_all.deb ... 62s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 62s Selecting previously unselected package python3-mappy. 62s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1_amd64.deb ... 62s Unpacking python3-mappy (2.27+dfsg-1) ... 62s Selecting previously unselected package python3-tqdm. 62s Preparing to unpack .../20-python3-tqdm_4.66.5-1_all.deb ... 62s Unpacking python3-tqdm (4.66.5-1) ... 62s Selecting previously unselected package sphinx-rtd-theme-common. 62s Preparing to unpack .../21-sphinx-rtd-theme-common_2.0.0+dfsg-2_all.deb ... 62s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-2) ... 62s Selecting previously unselected package python3-scipy. 62s Preparing to unpack .../22-python3-scipy_1.13.1-3_amd64.deb ... 62s Unpacking python3-scipy (1.13.1-3) ... 63s Selecting previously unselected package tombo. 63s Preparing to unpack .../23-tombo_1.5.1-6build1_amd64.deb ... 63s Unpacking tombo (1.5.1-6build1) ... 63s Selecting previously unselected package libjs-mathjax. 63s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 63s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 63s Selecting previously unselected package tombo-doc. 63s Preparing to unpack .../25-tombo-doc_1.5.1-6build1_all.deb ... 63s Unpacking tombo-doc (1.5.1-6build1) ... 63s Selecting previously unselected package autopkgtest-satdep. 63s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 63s Unpacking autopkgtest-satdep (0) ... 63s Setting up fonts-lato (2.015-1) ... 63s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 63s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 63s Setting up python3-tqdm (4.66.5-1) ... 64s Setting up python3-mappy (2.27+dfsg-1) ... 64s Setting up libaec0:amd64 (1.1.3-1) ... 64s Setting up python3-decorator (5.1.1-5) ... 64s Setting up libblas3:amd64 (3.12.0-3build2) ... 64s 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 64s Setting up liblzf1:amd64 (3.6-4) ... 64s Setting up libgfortran5:amd64 (14.2.0-7ubuntu1) ... 64s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 64s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 64s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-2) ... 64s Setting up libsz2:amd64 (1.1.3-1) ... 64s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 64s Setting up liblapack3:amd64 (3.12.0-3build2) ... 64s 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 64s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 66s Setting up libjs-sphinxdoc (7.4.7-3) ... 66s Setting up tombo-doc (1.5.1-6build1) ... 66s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 66s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 66s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 66s Setting up python3-scipy (1.13.1-3) ... 69s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 69s Setting up python3-h5py (3.11.0-5ubuntu1) ... 69s Setting up tombo (1.5.1-6build1) ... 69s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 69s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 69s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 69s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 69s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 69s re.match('\+', fastq_rec[2]) is None): 69s Setting up autopkgtest-satdep (0) ... 69s Processing triggers for man-db (2.12.1-3) ... 70s Processing triggers for libc-bin (2.40-1ubuntu3) ... 72s (Reading database ... 82526 files and directories currently installed.) 72s Removing autopkgtest-satdep (0) ... 72s autopkgtest [10:41:53]: test run-unit-test: [----------------------- 72s ********* Testing help commands ********** 73s usage: tombo [-h] [-v] 73s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 73s ... 73s 73s ********** Tombo ********* 73s 73s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 73s 73s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 73s 73s Tombo command groups (additional help available within each command group): 73s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 73s preprocess Pre-process nanopore reads for Tombo processing. 73s filter Apply filter to Tombo index file for specified criterion. 73s detect_modifications Perform statistical testing to detect non-standard nucleotides. 73s text_output Output Tombo results in text files. 73s build_model Create canonical and alternative base Tombo models. 73s plot Save plots to visualize raw nanopore signal or testing results. 73s 73s options: 73s -h, --help show this help message and exit 73s -v, --version show Tombo version and exit. 73s usage: tombo resquiggle [--dna] [--rna] 73s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 73s [--q-score Q_SCORE] 73s [--signal-matching-score SIGNAL_MATCHING_SCORE] 73s [--processes PROCESSES] 73s [--corrected-group CORRECTED_GROUP] 73s [--basecall-group BASECALL_GROUP] 73s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 73s [--overwrite] 73s [--failed-reads-filename FAILED_READS_FILENAME] 73s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 73s [--print-advanced-arguments] [--quiet] [--help] 73s fast5s_basedir reference 73s 73s Required Arguments: 73s fast5s_basedir Directory containing fast5 files. All files ending in 73s "fast5" found recursively within this base directory 73s will be processed. 73s reference Reference genome/transcriptome FASTA file or minimap2 73s index (with "map-ont" preset) for mapping. 73s 73s Model Parameters: 73s --dna Explicitly select canonical DNA model. Default: 73s Automatically determine from FAST5s 73s --rna Explicitly select canonical RNA model. Default: 73s Automatically determine from FAST5s 73s 73s Read Filtering Argument: 73s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 73s Filter reads based on observations per base percentile 73s thresholds. Format thresholds as "percentile:thresh 73s [pctl2:thresh2 ...]". For example to filter reads with 73s 99th pctl > 200 obs/base or max > 5k obs/base use 73s "99:200 100:5000". 73s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 73s Default: 0.000000 73s --signal-matching-score SIGNAL_MATCHING_SCORE 73s Observed to expected signal matching score (higher 73s score indicates poor matching). Sample type defaults: 73s RNA : 2 || DNA : 1.1 73s 73s Multiprocessing Arguments: 73s --processes PROCESSES 73s Number of processes. Default: 1 73s 73s FAST5 Data Arguments: 73s --corrected-group CORRECTED_GROUP 73s FAST5 group created by resquiggle command. Default: 73s RawGenomeCorrected_000 73s --basecall-group BASECALL_GROUP 73s FAST5 group obtain original basecalls (under Analyses 73s group). Default: Basecall_1D_000 73s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 73s FAST5 subgroup(s) (under /Analyses/[--basecall- 73s group]/) containing basecalls and created within 73s [--corrected-group] containing re-squiggle results. 73s Default: ['BaseCalled_template'] 73s --overwrite Overwrite previous corrected group in FAST5 files. 73s Note: only effects --corrected-group or --new- 73s corrected-group. 73s 73s Input/Output Arguments: 73s --failed-reads-filename FAILED_READS_FILENAME 73s Output failed read filenames with assoicated error. 73s Default: Do not store failed reads. 73s --num-most-common-errors NUM_MOST_COMMON_ERRORS 73s Dynamically show this many most common errors so far 73s through run. Default: 0; Just show progress 73s 73s Advanced Arguments: 73s --print-advanced-arguments 73s Print advanced re-squiggle arguments and exit. 73s 73s Miscellaneous Arguments: 73s --quiet, -q Don't print status information. 73s --help, -h Print this help message and exit 73s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 73s --fastq-filenames 73s FASTQ_FILENAMES 73s [FASTQ_FILENAMES ...] 73s [--basecall-group BASECALL_GROUP] 73s [--basecall-subgroup BASECALL_SUBGROUP] 73s [--overwrite] 73s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 73s [--processes PROCESSES] 73s [--quiet] [--help] 73s 73s Required Arguments: 73s --fast5-basedir FAST5_BASEDIR 73s Directory containing fast5 files. 73s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 73s FASTQ filenames containing basecalls to be added to 73s raw FAST5 files. 73s 73s FAST5 Data Arguments: 73s --basecall-group BASECALL_GROUP 73s FAST5 group obtain original basecalls (under Analyses 73s group). Default: Basecall_1D_000 73s --basecall-subgroup BASECALL_SUBGROUP 73s FAST5 subgroup (under /Analyses/[--basecall-group]/) 73s under which to store basecalls from FASTQs. Default: 73s BaseCalled_template 73s --overwrite Overwrite previous corrected group in FAST5 files. 73s Note: only effects --corrected-group or --new- 73s corrected-group. 73s 73s Sequencing Summary Argument: 73s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 73s Sequencing summary filenames produced by albacore. 73s These can make annotation of raw FAST5 files with 73s FASTQ sequence much faster. 73s 73s Multiprocessing Argument: 73s --processes PROCESSES 73s Number of processes. Default: 1 73s 73s Miscellaneous Arguments: 73s --quiet, -q Don't print status information. 73s --help, -h Print this help message and exit 73s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 73s [FAST5_BASEDIRS ...] 73s [--corrected-group CORRECTED_GROUP] 73s [--quiet] [--help] 73s 73s Required Argument: 73s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 73s Directories containing fast5 files. 73s 73s FAST5 Data Argument: 73s --corrected-group CORRECTED_GROUP 73s FAST5 group created by resquiggle command. Default: 73s RawGenomeCorrected_000 73s 73s Miscellaneous Arguments: 73s --quiet, -q Don't print status information. 73s --help, -h Print this help message and exit 73s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 73s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 73s [--corrected-group CORRECTED_GROUP] [--quiet] 73s [--help] 73s 73s Required Argument: 73s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 73s Directories containing fast5 files. 73s 73s Read Filtering Argument: 73s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 73s Filter reads based on observations per base percentile 73s thresholds. Format thresholds as "percentile:thresh 73s [pctl2:thresh2 ...]". For example to filter reads with 73s 99th pctl > 200 obs/base or max > 5k obs/base use 73s "99:200 100:5000". 73s 73s FAST5 Data Argument: 73s --corrected-group CORRECTED_GROUP 73s FAST5 group created by resquiggle command. Default: 73s RawGenomeCorrected_000 73s 73s Miscellaneous Arguments: 73s --quiet, -q Don't print status information. 73s --help, -h Print this help message and exit 73s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 73s [FAST5_BASEDIRS ...] 73s [--percent-to-filter PERCENT_TO_FILTER] 73s [--corrected-group CORRECTED_GROUP] 73s [--quiet] [--help] 73s 73s Required Arguments: 73s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 73s Directories containing fast5 files. 73s 73s Read Filtering Argument: 73s --percent-to-filter PERCENT_TO_FILTER 73s Percentage of all reads to filter. Reads are randomly 73s selected weighted according to the approximate 73s coverage at the mapped genomic location. This can be 73s useful in modeling and testing. Default: 10.000000 73s 73s FAST5 Data Arguments: 73s --corrected-group CORRECTED_GROUP 73s FAST5 group created by resquiggle command. Default: 73s RawGenomeCorrected_000 73s 73s Miscellaneous Arguments: 73s --quiet, -q Don't print status information. 73s --help, -h Print this help message and exit 73s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 73s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 73s [--corrected-group CORRECTED_GROUP] 73s [--basecall-group BASECALL_GROUP] [--quiet] 73s [--help] 73s 73s Required Arguments: 73s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 73s Directories containing fast5 files. 73s 73s Read Filtering Argument: 73s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 73s Default: 7.000000 73s 73s FAST5 Data Arguments: 73s --corrected-group CORRECTED_GROUP 73s FAST5 group created by resquiggle command. Default: 73s RawGenomeCorrected_000 73s --basecall-group BASECALL_GROUP 73s FAST5 group obtain original basecalls (under Analyses 73s group). Default: Basecall_1D_000 73s 73s Miscellaneous Arguments: 73s --quiet, -q Don't print status information. 73s --help, -h Print this help message and exit 73s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 73s [FAST5_BASEDIRS ...] 73s --signal-matching-score 73s SIGNAL_MATCHING_SCORE 73s [--corrected-group CORRECTED_GROUP] 73s [--quiet] [--help] 73s 73s Required Arguments: 73s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 73s Directories containing fast5 files. 73s --signal-matching-score SIGNAL_MATCHING_SCORE 73s Observed to expected signal matching score (higher 73s score indicates poor matching). Sample type defaults: 73s RNA : 2 || DNA : 1.1 73s 73s FAST5 Data Arguments: 73s --corrected-group CORRECTED_GROUP 73s FAST5 group created by resquiggle command. Default: 73s RawGenomeCorrected_000 73s 73s Miscellaneous Arguments: 73s --quiet, -q Don't print status information. 73s --help, -h Print this help message and exit 73s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 73s [FAST5_BASEDIRS ...] 73s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 73s [--include-partial-overlap] 73s [--corrected-group CORRECTED_GROUP] 73s [--quiet] [--help] 73s 73s Required Arguments: 73s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 73s Directories containing fast5 files. 73s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 73s Filter out reads not falling completely within include 73s regions. Omit start and end coordinates to include an 73s entire chromosome/sequence record. Format regions as 73s "chrm[:start-end] [chrm2[:start2-end2] ...]". 73s 73s Filter Argument: 73s --include-partial-overlap 73s Include reads that partially overlap the specified 73s region. Default: Only include reads completely 73s contained in a specified region 73s 73s FAST5 Data Argument: 73s --corrected-group CORRECTED_GROUP 73s FAST5 group created by resquiggle command. Default: 73s RawGenomeCorrected_000 73s 73s Miscellaneous Arguments: 73s --quiet, -q Don't print status information. 73s --help, -h Print this help message and exit 73s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 73s [FAST5_BASEDIRS ...] 73s --statistics-file-basename 73s STATISTICS_FILE_BASENAME [--dna] 73s [--rna] 73s [--fishers-method-context FISHERS_METHOD_CONTEXT] 73s [--minimum-test-reads MINIMUM_TEST_READS] 73s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 73s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 73s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 73s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 73s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 73s [--processes PROCESSES] 73s [--corrected-group CORRECTED_GROUP] 73s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 73s [--quiet] [--help] 73s 73s Required Argument: 73s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 73s Directories containing fast5 files. 73s --statistics-file-basename STATISTICS_FILE_BASENAME 73s File base name to save base by base statistics from 73s testing. Filenames will be [--statistics-file- 73s basename].[--alternate-bases]?.tombo.stats 73s 73s Comparison Model Arguments: 73s --dna Explicitly select canonical DNA model. Default: 73s Automatically determine from FAST5s 73s --rna Explicitly select canonical RNA model. Default: 73s Automatically determine from FAST5s 73s 73s Significance Test Arguments: 73s --fishers-method-context FISHERS_METHOD_CONTEXT 73s Number of context bases up and downstream over which 73s to compute Fisher's method combined p-values. Note: 73s Not applicable for alternative model likelihood ratio 73s tests. Default: 1. 73s --minimum-test-reads MINIMUM_TEST_READS 73s Number of reads required at a position to perform 73s significance testing or contribute to model 73s estimation. Default: 1 73s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 73s P-value threshold when computing fraction of 73s significant reads at each genomic position. If two 73s values are provided, statistics between these values 73s are not considered. Default thresholds: DNA:0.15-0.5 , 73s RNA:0.05-0.4 73s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 73s Dampen fraction modified estimates for low coverage 73s sites. Two parameters are unmodified and modified 73s pseudo read counts. This is equivalent to a beta prior 73s on the fraction estimate. Set to "0 0" to disable 73s dampened fraction estimation. Default: [2, 0] 73s 73s Output Argument: 73s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 73s Base for binary files containing per-read statistics 73s from statistical testing. Filenames will be [--per- 73s read-statistics-basename].[--alternate- 73s bases]?.tombo.per_read_stats 73s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 73s Number of the most significant sites to store for 73s faster access. If a longer list of most significant 73s sites is required the list must be re-computed from 73s all batches. Very large values can increase RAM usage. 73s Default: 100000 73s 73s Multiprocessing Arguments: 73s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 73s Size of regions over which to multiprocesses statistic 73s computation. For very deep samples a smaller value is 73s recommmended in order to control memory consumption. 73s Default: 10000 73s --processes PROCESSES 73s Number of processes. Default: 1 73s 73s FAST5 Data Arguments: 73s --corrected-group CORRECTED_GROUP 73s FAST5 group created by resquiggle command. Default: 73s RawGenomeCorrected_000 73s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 73s FAST5 subgroup(s) (under /Analyses/[--basecall- 73s group]/) containing basecalls and created within 73s [--corrected-group] containing re-squiggle results. 73s Default: ['BaseCalled_template'] 73s 73s Miscellaneous Arguments: 73s --quiet, -q Don't print status information. 73s --help, -h Print this help message and exit 73s usage: tombo detect_modifications alternative_model 73s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 73s [--statistics-file-basename STATISTICS_FILE_BASENAME] 73s [--alternate-bases {5mC,6mA,dam,CpG,dcm} [{5mC,6mA,dam,CpG,dcm} ...]] 73s [--print-available-models] 73s [--dna] [--rna] 73s [--minimum-test-reads MINIMUM_TEST_READS] 73s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 73s [--standard-log-likelihood-ratio] 73s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 73s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 73s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 73s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 73s [--processes PROCESSES] 73s [--corrected-group CORRECTED_GROUP] 73s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 73s [--quiet] [--help] 73s 73s Required Argument: 73s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 73s Directories containing fast5 files. 73s --statistics-file-basename STATISTICS_FILE_BASENAME 73s File base name to save base by base statistics from 73s testing. Filenames will be [--statistics-file- 73s basename].[--alternate-bases]?.tombo.stats 73s --alternate-bases {5mC,6mA,dam,CpG,dcm} [{5mC,6mA,dam,CpG,dcm} ...] 73s Default non-standard base model for testing (not 73s required if user created --alternate-model-filenames 73s is provided). 73s 73s Comparison Arguments: 73s --print-available-models 73s Print available alternative models and exit. 73s --dna Explicitly select canonical DNA model. Default: 73s Automatically determine from FAST5s 73s --rna Explicitly select canonical RNA model. Default: 73s Automatically determine from FAST5s 73s 73s Significance Test Arguments: 73s --minimum-test-reads MINIMUM_TEST_READS 73s Number of reads required at a position to perform 73s significance testing or contribute to model 73s estimation. Default: 1 73s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 73s Log likelihood ratio threshold when computing fraction 73s of significant reads at each genomic position. If two 73s values are provided, statistics between these values 73s are not considered. Default thresholds: DNA:-1.5-2.5 , 73s RNA:-2.5-2.5 73s --standard-log-likelihood-ratio 73s Use a standard log likelihood ratio (LLR) statistic. 73s Default is to use an outlier-robust LLR-like 73s statistic. Detail in full online documentation. 73s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 73s Dampen fraction modified estimates for low coverage 73s sites. Two parameters are unmodified and modified 73s pseudo read counts. This is equivalent to a beta prior 73s on the fraction estimate. Set to "0 0" to disable 73s dampened fraction estimation. Default: [2, 0] 73s 73s Output Argument: 73s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 73s Base for binary files containing per-read statistics 73s from statistical testing. Filenames will be [--per- 73s read-statistics-basename].[--alternate- 73s bases]?.tombo.per_read_stats 73s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 73s Number of the most significant sites to store for 73s faster access. If a longer list of most significant 73s sites is required the list must be re-computed from 73s all batches. Very large values can increase RAM usage. 73s Default: 100000 73s 73s Multiprocessing Arguments: 73s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 73s Size of regions over which to multiprocesses statistic 73s computation. For very deep samples a smaller value is 73s recommmended in order to control memory consumption. 73s Default: 10000 73s --processes PROCESSES 73s Number of processes. Default: 1 73s 73s FAST5 Data Arguments: 73s --corrected-group CORRECTED_GROUP 73s FAST5 group created by resquiggle command. Default: 73s RawGenomeCorrected_000 73s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 73s FAST5 subgroup(s) (under /Analyses/[--basecall- 73s group]/) containing basecalls and created within 73s [--corrected-group] containing re-squiggle results. 73s Default: ['BaseCalled_template'] 73s 73s Miscellaneous Arguments: 73s --quiet, -q Don't print status information. 73s --help, -h Print this help message and exit 74s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 74s FAST5_BASEDIRS 74s [FAST5_BASEDIRS ...] 74s --statistics-file-basename 74s STATISTICS_FILE_BASENAME 74s --control-fast5-basedirs 74s CONTROL_FAST5_BASEDIRS 74s [CONTROL_FAST5_BASEDIRS ...] 74s [--sample-only-estimates] 74s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 74s [--dna] [--rna] 74s [--fishers-method-context FISHERS_METHOD_CONTEXT] 74s [--minimum-test-reads MINIMUM_TEST_READS] 74s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 74s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 74s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 74s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 74s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 74s [--processes PROCESSES] 74s [--corrected-group CORRECTED_GROUP] 74s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 74s [--quiet] [--help] 74s 74s Required Argument: 74s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 74s Directories containing fast5 files. 74s --statistics-file-basename STATISTICS_FILE_BASENAME 74s File base name to save base by base statistics from 74s testing. Filenames will be [--statistics-file- 74s basename].[--alternate-bases]?.tombo.stats 74s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 74s Set of directories containing fast5 files for control 74s reads, containing only canonical nucleotides. 74s 74s Model Prior Arguments: 74s --sample-only-estimates 74s Only use canonical sample to estimate expected signal 74s level and spread. Default: Use canonical model to 74s improve estimtates (esp. for low coverage regions) 74s using baysian posterior estimates. 74s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 74s Prior weights (one each for mean and spread) applied 74s to canonical base model for estimating posterior model 74s parameters for sample comparison. Default: [5, 40] 74s --dna Explicitly select canonical DNA model. Default: 74s Automatically determine from FAST5s 74s --rna Explicitly select canonical RNA model. Default: 74s Automatically determine from FAST5s 74s 74s Significance Test Arguments: 74s --fishers-method-context FISHERS_METHOD_CONTEXT 74s Number of context bases up and downstream over which 74s to compute Fisher's method combined p-values. Note: 74s Not applicable for alternative model likelihood ratio 74s tests. Default: 1. 74s --minimum-test-reads MINIMUM_TEST_READS 74s Number of reads required at a position to perform 74s significance testing or contribute to model 74s estimation. Default: 1 74s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 74s P-value threshold when computing fraction of 74s significant reads at each genomic position. If two 74s values are provided, statistics between these values 74s are not considered. Default thresholds: DNA:0.15-0.5 , 74s RNA:0.05-0.4 74s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 74s Dampen fraction modified estimates for low coverage 74s sites. Two parameters are unmodified and modified 74s pseudo read counts. This is equivalent to a beta prior 74s on the fraction estimate. Set to "0 0" to disable 74s dampened fraction estimation. Default: [2, 0] 74s 74s Output Argument: 74s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 74s Base for binary files containing per-read statistics 74s from statistical testing. Filenames will be [--per- 74s read-statistics-basename].[--alternate- 74s bases]?.tombo.per_read_stats 74s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 74s Number of the most significant sites to store for 74s faster access. If a longer list of most significant 74s sites is required the list must be re-computed from 74s all batches. Very large values can increase RAM usage. 74s Default: 100000 74s 74s Multiprocessing Arguments: 74s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 74s Size of regions over which to multiprocesses statistic 74s computation. For very deep samples a smaller value is 74s recommmended in order to control memory consumption. 74s Default: 10000 74s --processes PROCESSES 74s Number of processes. Default: 1 74s 74s FAST5 Data Arguments: 74s --corrected-group CORRECTED_GROUP 74s FAST5 group created by resquiggle command. Default: 74s RawGenomeCorrected_000 74s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 74s FAST5 subgroup(s) (under /Analyses/[--basecall- 74s group]/) containing basecalls and created within 74s [--corrected-group] containing re-squiggle results. 74s Default: ['BaseCalled_template'] 74s 74s Miscellaneous Arguments: 74s --quiet, -q Don't print status information. 74s --help, -h Print this help message and exit 74s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 74s FAST5_BASEDIRS 74s [FAST5_BASEDIRS ...] 74s --statistics-file-basename 74s STATISTICS_FILE_BASENAME 74s --alternate-fast5-basedirs 74s ALTERNATE_FAST5_BASEDIRS 74s [ALTERNATE_FAST5_BASEDIRS ...] 74s [--fishers-method-context FISHERS_METHOD_CONTEXT] 74s [--minimum-test-reads MINIMUM_TEST_READS] 74s [--statistic-type {ks,u,t}] 74s [--store-p-value] 74s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 74s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 74s [--processes PROCESSES] 74s [--corrected-group CORRECTED_GROUP] 74s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 74s [--quiet] [--help] 74s 74s Required Argument: 74s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 74s Directories containing fast5 files. 74s --statistics-file-basename STATISTICS_FILE_BASENAME 74s File base name to save base by base statistics from 74s testing. Filenames will be [--statistics-file- 74s basename].[--alternate-bases]?.tombo.stats 74s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 74s Set of directories containing fast5 files for 74s alternate set of reads. 74s 74s Significance Test Arguments: 74s --fishers-method-context FISHERS_METHOD_CONTEXT 74s Number of context bases up and downstream over which 74s to compute Fisher's method combined p-values. Note: 74s Not applicable for alternative model likelihood ratio 74s tests. Default: 1. 74s --minimum-test-reads MINIMUM_TEST_READS 74s Number of reads required at a position to perform 74s significance testing or contribute to model 74s estimation. Default: 50 74s --statistic-type {ks,u,t} 74s Type of statistical test to apply. Default: "ks" 74s --store-p-value Store p-value instead of effect-size statistic. 74s Statistics are D-statistic (KS-test), deviation from 74s even common language effect size (u-test), and Cohen's 74s D (t-test). 74s 74s Output Argument: 74s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 74s Number of the most significant sites to store for 74s faster access. If a longer list of most significant 74s sites is required the list must be re-computed from 74s all batches. Very large values can increase RAM usage. 74s Default: 100000 74s 74s Multiprocessing Arguments: 74s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 74s Size of regions over which to multiprocesses statistic 74s computation. For very deep samples a smaller value is 74s recommmended in order to control memory consumption. 74s Default: 10000 74s --processes PROCESSES 74s Number of processes. Default: 1 74s 74s FAST5 Data Arguments: 74s --corrected-group CORRECTED_GROUP 74s FAST5 group created by resquiggle command. Default: 74s RawGenomeCorrected_000 74s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 74s FAST5 subgroup(s) (under /Analyses/[--basecall- 74s group]/) containing basecalls and created within 74s [--corrected-group] containing re-squiggle results. 74s Default: ['BaseCalled_template'] 74s 74s Miscellaneous Arguments: 74s --quiet, -q Don't print status information. 74s --help, -h Print this help message and exit 74s usage: tombo detect_modifications aggregate_per_read_stats 74s --per-read-statistics-filename 74s PER_READ_STATISTICS_FILENAME 74s --statistics-filename 74s STATISTICS_FILENAME 74s --single-read-threshold 74s SINGLE_READ_THRESHOLD 74s [SINGLE_READ_THRESHOLD ...] 74s [--minimum-test-reads MINIMUM_TEST_READS] 74s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 74s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 74s [--processes PROCESSES] 74s [--corrected-group CORRECTED_GROUP] 74s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 74s [--quiet] [--help] 74s 74s Required Argument: 74s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 74s Binary file containing per-read statistics from 74s statistical testing. 74s --statistics-filename STATISTICS_FILENAME 74s File to save/load genomic base anchored statistics. 74s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 74s P-value or log likelihood ratio threshold when 74s computing fraction of significant reads at each 74s genomic position. If two values are provided, 74s statistics between these values are not considered. 74s 74s Significance Test Arguments: 74s --minimum-test-reads MINIMUM_TEST_READS 74s Number of reads required at a position to perform 74s significance testing or contribute to model 74s estimation. Default: 1 74s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 74s Dampen fraction modified estimates for low coverage 74s sites. Two parameters are unmodified and modified 74s pseudo read counts. This is equivalent to a beta prior 74s on the fraction estimate. Set to "0 0" to disable 74s dampened fraction estimation. Default: [2, 0] 74s 74s Output Argument: 74s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 74s Number of the most significant sites to store for 74s faster access. If a longer list of most significant 74s sites is required the list must be re-computed from 74s all batches. Very large values can increase RAM usage. 74s Default: 100000 74s 74s Multiprocessing Arguments: 74s --processes PROCESSES 74s Number of processes. Default: 1 74s 74s FAST5 Data Arguments: 74s --corrected-group CORRECTED_GROUP 74s FAST5 group created by resquiggle command. Default: 74s RawGenomeCorrected_000 74s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 74s FAST5 subgroup(s) (under /Analyses/[--basecall- 74s group]/) containing basecalls and created within 74s [--corrected-group] containing re-squiggle results. 74s Default: ['BaseCalled_template'] 74s 74s Miscellaneous Arguments: 74s --quiet, -q Don't print status information. 74s --help, -h Print this help message and exit 74s usage: tombo text_output browser_files 74s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 74s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 74s [--statistics-filename STATISTICS_FILENAME] 74s [--genome-fasta GENOME_FASTA] 74s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 74s [--browser-file-basename BROWSER_FILE_BASENAME] 74s [--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} ...]] 74s [--corrected-group CORRECTED_GROUP] 74s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 74s [--quiet] [--help] 74s 74s Data Arguments: 74s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 74s Directories containing fast5 files. 74s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 74s Set of directories containing fast5 files for control 74s reads, containing only canonical nucleotides. 74s --statistics-filename STATISTICS_FILENAME 74s File to save/load genomic base anchored statistics. 74s 74s Statistic Motif Filter Arguments: 74s --genome-fasta GENOME_FASTA 74s FASTA file used to re-squiggle. For faster sequence 74s access. 74s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 74s Ground truth, motif centered, modified base 74s descriptions for output filtering. Format descriptions 74s as: "motif:mod_pos:name". The mod_pos indicates the 74s modified base within the motif (1-based index). 74s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 74s output for identification of E. coli dam and dcm 74s methylation. 74s 74s Output Arguments: 74s --browser-file-basename BROWSER_FILE_BASENAME 74s Basename for output browser files. Two files (plus and 74s minus strand) will be produced for each --file-types 74s supplied. Filenames formatted as "[browser-file- 74s basename].[file- 74s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 74s Default: tombo_results 74s --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} ...] 74s Data types of genome browser files to produce. 74s Produced coverage files are in bedGraph format, while 74s all other file types will be in wiggle format 74s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 74s Default: "coverage" 74s 74s FAST5 Data Arguments: 74s --corrected-group CORRECTED_GROUP 74s FAST5 group created by resquiggle command. Default: 74s RawGenomeCorrected_000 74s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 74s FAST5 subgroup(s) (under /Analyses/[--basecall- 74s group]/) containing basecalls and created within 74s [--corrected-group] containing re-squiggle results. 74s Default: ['BaseCalled_template'] 74s 74s Miscellaneous Arguments: 74s --quiet, -q Don't print status information. 74s --help, -h Print this help message and exit 74s usage: tombo text_output signif_sequence_context --statistics-filename 74s STATISTICS_FILENAME 74s [--genome-fasta GENOME_FASTA] 74s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 74s [--num-regions NUM_REGIONS] 74s [--num-bases NUM_BASES] 74s [--sequences-filename SEQUENCES_FILENAME] 74s [--corrected-group CORRECTED_GROUP] 74s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 74s [--quiet] [--help] 74s 74s Required Argument: 74s --statistics-filename STATISTICS_FILENAME 74s File to save/load genomic base anchored statistics. 74s 74s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 74s --genome-fasta GENOME_FASTA 74s FASTA file used to re-squiggle. For faster sequence 74s access. 74s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 74s Directories containing fast5 files. 74s 74s Region Selection Arguments: 74s --num-regions NUM_REGIONS 74s Number of regions to plot. Default: 100 74s --num-bases NUM_BASES 74s Number of bases to plot/output. Default: 15 74s 74s Output Arguments: 74s --sequences-filename SEQUENCES_FILENAME 74s File for sequences from selected regions. Sequences 74s will be stored in FASTA format. Default: 74s tombo_results.significant_regions.fasta. 74s 74s FAST5 Data Arguments: 74s --corrected-group CORRECTED_GROUP 74s FAST5 group created by resquiggle command. Default: 74s RawGenomeCorrected_000 74s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 74s FAST5 subgroup(s) (under /Analyses/[--basecall- 74s group]/) containing basecalls and created within 74s [--corrected-group] containing re-squiggle results. 74s Default: ['BaseCalled_template'] 74s 74s Miscellaneous Arguments: 74s --quiet, -q Don't print status information. 74s --help, -h Print this help message and exit 74s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 74s [FAST5_BASEDIRS ...] 74s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 74s [--plot-standard-model] 74s [--plot-alternate-model {5mC,dam,dcm,6mA,CpG}] 74s [--overplot-threshold OVERPLOT_THRESHOLD] 74s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 74s [--num-regions NUM_REGIONS] 74s [--num-bases NUM_BASES] 74s [--pdf-filename PDF_FILENAME] 74s [--corrected-group CORRECTED_GROUP] 74s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 74s [--quiet] [--help] 74s 74s Required Argument: 74s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 74s Directories containing fast5 files. 74s 74s Comparison Arguments: 74s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 74s Set of directories containing fast5 files for control 74s reads, containing only canonical nucleotides. 74s --plot-standard-model 74s Add default standard model distribution to the plot. 74s --plot-alternate-model {5mC,dam,dcm,6mA,CpG} 74s Add alternative model distribution to the plot. 74s 74s Overplotting Arguments: 74s --overplot-threshold OVERPLOT_THRESHOLD 74s Coverage level to trigger alternative plot type 74s instead of raw signal. Default: 50 74s --overplot-type {Downsample,Boxplot,Quantile,Density} 74s Plot type for regions with higher coverage. Default: 74s Downsample 74s 74s Plotting Region Arguments: 74s --num-regions NUM_REGIONS 74s Number of regions to plot. Default: 10 74s --num-bases NUM_BASES 74s Number of bases to plot/output. Default: 21 74s 74s Output Argument: 74s --pdf-filename PDF_FILENAME 74s PDF filename to store plot(s). Default: 74s tombo_results.max_coverage.pdf 74s 74s FAST5 Data Arguments: 74s --corrected-group CORRECTED_GROUP 74s FAST5 group created by resquiggle command. Default: 74s RawGenomeCorrected_000 74s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 74s FAST5 subgroup(s) (under /Analyses/[--basecall- 74s group]/) containing basecalls and created within 74s [--corrected-group] containing re-squiggle results. 74s Default: ['BaseCalled_template'] 74s 74s Miscellaneous Arguments: 74s --quiet, -q Don't print status information. 74s --help, -h Print this help message and exit 74s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 74s [FAST5_BASEDIRS ...] --genome-locations 74s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 74s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 74s [--plot-standard-model] 74s [--plot-alternate-model {dam,5mC,6mA,dcm,CpG}] 74s [--overplot-threshold OVERPLOT_THRESHOLD] 74s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 74s [--num-bases NUM_BASES] 74s [--pdf-filename PDF_FILENAME] 74s [--corrected-group CORRECTED_GROUP] 74s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 74s [--quiet] [--help] 74s 74s Required Arguments: 74s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 74s Directories containing fast5 files. 74s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 74s Genomic locations at which to plot signal. Format 74s locations as "chrm:position[:strand] 74s [chrm2:position2[:strand2] ...]" (strand not 74s applicable for all applications) 74s 74s Comparison Arguments: 74s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 74s Set of directories containing fast5 files for control 74s reads, containing only canonical nucleotides. 74s --plot-standard-model 74s Add default standard model distribution to the plot. 74s --plot-alternate-model {dam,5mC,6mA,dcm,CpG} 74s Add alternative model distribution to the plot. 74s 74s Overplotting Arguments: 74s --overplot-threshold OVERPLOT_THRESHOLD 74s Coverage level to trigger alternative plot type 74s instead of raw signal. Default: 50 74s --overplot-type {Downsample,Boxplot,Quantile,Density} 74s Plot type for regions with higher coverage. Default: 74s Downsample 74s 74s Plotting Region Argument: 74s --num-bases NUM_BASES 74s Number of bases to plot/output. Default: 21 74s 74s Output Argument: 74s --pdf-filename PDF_FILENAME 74s PDF filename to store plot(s). Default: 74s tombo_results.genome_locations.pdf 74s 74s FAST5 Data Arguments: 74s --corrected-group CORRECTED_GROUP 74s FAST5 group created by resquiggle command. Default: 74s RawGenomeCorrected_000 74s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 74s FAST5 subgroup(s) (under /Analyses/[--basecall- 74s group]/) containing basecalls and created within 74s [--corrected-group] containing re-squiggle results. 74s Default: ['BaseCalled_template'] 74s 74s Miscellaneous Arguments: 74s --quiet, -q Don't print status information. 74s --help, -h Print this help message and exit 74s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 74s [FAST5_BASEDIRS ...] --motif MOTIF 74s --genome-fasta GENOME_FASTA 74s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 74s [--plot-standard-model] 74s [--plot-alternate-model {5mC,dam,dcm,CpG,6mA}] 74s [--overplot-threshold OVERPLOT_THRESHOLD] 74s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 74s [--num-regions NUM_REGIONS] 74s [--num-bases NUM_BASES] [--deepest-coverage] 74s [--pdf-filename PDF_FILENAME] 74s [--corrected-group CORRECTED_GROUP] 74s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 74s [--quiet] [--help] 74s 74s Required Arguments: 74s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 74s Directories containing fast5 files. 74s --motif MOTIF Motif of interest at which to plot signal and 74s statsitics. Supports IUPAC single letter codes (use T 74s for RNA). 74s --genome-fasta GENOME_FASTA 74s FASTA file used to re-squiggle. For faster sequence 74s access. 74s 74s Comparison Arguments: 74s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 74s Set of directories containing fast5 files for control 74s reads, containing only canonical nucleotides. 74s --plot-standard-model 74s Add default standard model distribution to the plot. 74s --plot-alternate-model {5mC,dam,dcm,CpG,6mA} 74s Add alternative model distribution to the plot. 74s 74s Overplotting Arguments: 74s --overplot-threshold OVERPLOT_THRESHOLD 74s Coverage level to trigger alternative plot type 74s instead of raw signal. Default: 50 74s --overplot-type {Downsample,Boxplot,Quantile,Density} 74s Plot type for regions with higher coverage. Default: 74s Downsample 74s 74s Plotting Region Arguments: 74s --num-regions NUM_REGIONS 74s Number of regions to plot. Default: 10 74s --num-bases NUM_BASES 74s Number of bases to plot/output. Default: 21 74s --deepest-coverage Plot the deepest coverage regions. 74s 74s Output Argument: 74s --pdf-filename PDF_FILENAME 74s PDF filename to store plot(s). Default: 74s tombo_results.motif_centered.pdf 74s 74s FAST5 Data Arguments: 74s --corrected-group CORRECTED_GROUP 74s FAST5 group created by resquiggle command. Default: 74s RawGenomeCorrected_000 74s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 74s FAST5 subgroup(s) (under /Analyses/[--basecall- 74s group]/) containing basecalls and created within 74s [--corrected-group] containing re-squiggle results. 74s Default: ['BaseCalled_template'] 74s 74s Miscellaneous Arguments: 74s --quiet, -q Don't print status information. 74s --help, -h Print this help message and exit 74s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 74s [FAST5_BASEDIRS ...] --control-fast5-basedirs 74s CONTROL_FAST5_BASEDIRS 74s [CONTROL_FAST5_BASEDIRS ...] 74s [--overplot-threshold OVERPLOT_THRESHOLD] 74s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 74s [--num-regions NUM_REGIONS] 74s [--num-bases NUM_BASES] 74s [--pdf-filename PDF_FILENAME] 74s [--sequences-filename SEQUENCES_FILENAME] 74s [--corrected-group CORRECTED_GROUP] 74s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 74s [--quiet] [--help] 74s 74s Required Arguments: 74s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 74s Directories containing fast5 files. 74s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 74s Set of directories containing fast5 files for control 74s reads, containing only canonical nucleotides. 74s 74s Overplotting Arguments: 74s --overplot-threshold OVERPLOT_THRESHOLD 74s Coverage level to trigger alternative plot type 74s instead of raw signal. Default: 50 74s --overplot-type {Downsample,Boxplot,Quantile,Density} 74s Plot type for regions with higher coverage. Default: 74s Downsample 74s 74s Plotting Region Arguments: 74s --num-regions NUM_REGIONS 74s Number of regions to plot. Default: 10 74s --num-bases NUM_BASES 74s Number of bases to plot/output. Default: 21 74s 74s Output Arguments: 74s --pdf-filename PDF_FILENAME 74s PDF filename to store plot(s). Default: 74s tombo_results.max_difference.pdf 74s --sequences-filename SEQUENCES_FILENAME 74s File for sequences from selected regions. Sequences 74s will be stored in FASTA format. Default: None. 74s 74s FAST5 Data Arguments: 74s --corrected-group CORRECTED_GROUP 74s FAST5 group created by resquiggle command. Default: 74s RawGenomeCorrected_000 74s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 74s FAST5 subgroup(s) (under /Analyses/[--basecall- 74s group]/) containing basecalls and created within 74s [--corrected-group] containing re-squiggle results. 74s Default: ['BaseCalled_template'] 74s 74s Miscellaneous Arguments: 74s --quiet, -q Don't print status information. 74s --help, -h Print this help message and exit 74s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 74s [FAST5_BASEDIRS ...] --statistics-filename 74s STATISTICS_FILENAME 74s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 74s [--plot-standard-model] 74s [--plot-alternate-model {6mA,dam,dcm,CpG,5mC}] 74s [--overplot-threshold OVERPLOT_THRESHOLD] 74s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 74s [--num-regions NUM_REGIONS] 74s [--num-bases NUM_BASES] 74s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 74s [--pdf-filename PDF_FILENAME] 74s [--sequences-filename SEQUENCES_FILENAME] 74s [--corrected-group CORRECTED_GROUP] 74s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 74s [--quiet] [--help] 74s 74s Required Arguments: 74s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 74s Directories containing fast5 files. 74s --statistics-filename STATISTICS_FILENAME 74s File to save/load genomic base anchored statistics. 74s 74s Comparison Arguments: 74s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 74s Set of directories containing fast5 files for control 74s reads, containing only canonical nucleotides. 74s --plot-standard-model 74s Add default standard model distribution to the plot. 74s --plot-alternate-model {6mA,dam,dcm,CpG,5mC} 74s Add alternative model distribution to the plot. 74s 74s Overplotting Arguments: 74s --overplot-threshold OVERPLOT_THRESHOLD 74s Coverage level to trigger alternative plot type 74s instead of raw signal. Default: 50 74s --overplot-type {Downsample,Boxplot,Quantile,Density} 74s Plot type for regions with higher coverage. Default: 74s Downsample 74s 74s Plotting Region Arguments: 74s --num-regions NUM_REGIONS 74s Number of regions to plot. Default: 10 74s --num-bases NUM_BASES 74s Number of bases to plot/output. Default: 21 74s 74s Statistical Argument: 74s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 74s Dampen fraction modified estimates for low coverage 74s sites. Two parameters are unmodified and modified 74s pseudo read counts. This is equivalent to a beta prior 74s on the fraction estimate. Set to "0 0" to disable 74s dampened fraction estimation. Default: [2, 0] 74s 74s Output Arguments: 74s --pdf-filename PDF_FILENAME 74s PDF filename to store plot(s). Default: 74s tombo_results.significant_difference.pdf 74s --sequences-filename SEQUENCES_FILENAME 74s File for sequences from selected regions. Sequences 74s will be stored in FASTA format. Default: None. 74s 74s FAST5 Data Arguments: 74s --corrected-group CORRECTED_GROUP 74s FAST5 group created by resquiggle command. Default: 74s RawGenomeCorrected_000 74s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 74s FAST5 subgroup(s) (under /Analyses/[--basecall- 74s group]/) containing basecalls and created within 74s [--corrected-group] containing re-squiggle results. 74s Default: ['BaseCalled_template'] 74s 74s Miscellaneous Arguments: 74s --quiet, -q Don't print status information. 74s --help, -h Print this help message and exit 74s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 74s [FAST5_BASEDIRS ...] --motif MOTIF 74s --statistics-filename STATISTICS_FILENAME 74s --genome-fasta GENOME_FASTA 74s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 74s [--plot-standard-model] 74s [--plot-alternate-model {dam,dcm,6mA,CpG,5mC}] 74s [--overplot-threshold OVERPLOT_THRESHOLD] 74s [--num-regions NUM_REGIONS] 74s [--num-context NUM_CONTEXT] 74s [--num-statistics NUM_STATISTICS] 74s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 74s [--pdf-filename PDF_FILENAME] 74s [--corrected-group CORRECTED_GROUP] 74s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 74s [--quiet] [--help] 74s 74s Required Arguments: 74s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 74s Directories containing fast5 files. 74s --motif MOTIF Motif of interest at which to plot signal and 74s statsitics. Supports IUPAC single letter codes (use T 74s for RNA). 74s --statistics-filename STATISTICS_FILENAME 74s File to save/load genomic base anchored statistics. 74s --genome-fasta GENOME_FASTA 74s FASTA file used to re-squiggle. For faster sequence 74s access. 74s 74s Comparison Arguments: 74s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 74s Set of directories containing fast5 files for control 74s reads, containing only canonical nucleotides. 74s --plot-standard-model 74s Add default standard model distribution to the plot. 74s --plot-alternate-model {dam,dcm,6mA,CpG,5mC} 74s Add alternative model distribution to the plot. 74s 74s Overplotting Argument: 74s --overplot-threshold OVERPLOT_THRESHOLD 74s Coverage level to trigger alternative plot type 74s instead of raw signal. Default: 50 74s 74s Plotting Region Arguments: 74s --num-regions NUM_REGIONS 74s Number of regions to plot. Default: 3 74s --num-context NUM_CONTEXT 74s Number of context bases around motif. Default: 5 74s --num-statistics NUM_STATISTICS 74s Number of motif centered regions to include in 74s statistic distributions. Default: 200 74s 74s Statistical Argument: 74s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 74s Dampen fraction modified estimates for low coverage 74s sites. Two parameters are unmodified and modified 74s pseudo read counts. This is equivalent to a beta prior 74s on the fraction estimate. Set to "0 0" to disable 74s dampened fraction estimation. Default: [2, 0] 74s 74s Output Argument: 74s --pdf-filename PDF_FILENAME 74s PDF filename to store plot(s). Default: 74s tombo_results.motif_statistics.pdf 74s 74s FAST5 Data Arguments: 74s --corrected-group CORRECTED_GROUP 74s FAST5 group created by resquiggle command. Default: 74s RawGenomeCorrected_000 74s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 74s FAST5 subgroup(s) (under /Analyses/[--basecall- 74s group]/) containing basecalls and created within 74s [--corrected-group] containing re-squiggle results. 74s Default: ['BaseCalled_template'] 74s 74s Miscellaneous Arguments: 74s --quiet, -q Don't print status information. 74s --help, -h Print this help message and exit 75s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 75s [GENOME_LOCATIONS ...] 75s --per-read-statistics-filename 75s PER_READ_STATISTICS_FILENAME 75s [--genome-fasta GENOME_FASTA] 75s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 75s [--num-reads NUM_READS] [--num-bases NUM_BASES] 75s [--box-center] [--pdf-filename PDF_FILENAME] 75s [--corrected-group CORRECTED_GROUP] 75s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 75s [--quiet] [--help] 75s 75s Required Arguments: 75s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 75s Genomic locations at which to plot signal. Format 75s locations as "chrm:position[:strand] 75s [chrm2:position2[:strand2] ...]" (strand not 75s applicable for all applications) 75s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 75s Binary file containing per-read statistics from 75s statistical testing. 75s 75s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 75s --genome-fasta GENOME_FASTA 75s FASTA file used to re-squiggle. For faster sequence 75s access. 75s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 75s Directories containing fast5 files. 75s 75s Plotting Region Arguments: 75s --num-reads NUM_READS 75s Number of reads to plot. Default: 100 75s --num-bases NUM_BASES 75s Number of bases to plot/output. Default: 51 75s --box-center Plot a box around the central base. 75s 75s Output Argument: 75s --pdf-filename PDF_FILENAME 75s PDF filename to store plot(s). Default: 75s tombo_results.per_read_stats.pdf 75s 75s FAST5 Data Arguments: 75s --corrected-group CORRECTED_GROUP 75s FAST5 group created by resquiggle command. Default: 75s RawGenomeCorrected_000 75s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 75s FAST5 subgroup(s) (under /Analyses/[--basecall- 75s group]/) containing basecalls and created within 75s [--corrected-group] containing re-squiggle results. 75s Default: ['BaseCalled_template'] 75s 75s Miscellaneous Arguments: 75s --quiet, -q Don't print status information. 75s --help, -h Print this help message and exit 75s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 75s [STATISTICS_FILENAMES ...] 75s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 75s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 75s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 75s [--genome-fasta GENOME_FASTA] 75s [--pdf-filename PDF_FILENAME] 75s [--statistics-per-block STATISTICS_PER_BLOCK] 75s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 75s [--quiet] [--help] 75s 75s Required Argument: 75s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 75s Files to load genomic base anchored statistics. 75s 75s Ground Truth Arguments (provide bed files or motifs): 75s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 75s Modification description and bed format files 75s containing single base locations of ground truth 75s modified sites. Bed files should contain 6 fields 75s including strand. Format descriptions as 75s "mod_name:locs.bed". Example: "CpG 75s bisulfite":bisulfite_locs.bed 75s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 75s Bed format files containing single base locations of 75s ground truth unmodified sites. Bed files should 75s contain 6 fields including strand. 75s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 75s Ground truth, motif centered, modified base 75s descriptions for computing ROC and PR curves. Each 75s statistics file is associated with a set of motif 75s descriptions. Format descriptions as: 75s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 75s mod_pos indicates the alternate-base within the motif 75s (1-based index). Example: CCWGG:2:"dcm 75s 5mC"::GATC:2:"dam 6mA" would assess the performance of 75s a single Tombo statistics file for identification of 75s E. coli dam and dcm methylation. 75s --genome-fasta GENOME_FASTA 75s FASTA file used to re-squiggle. For faster sequence 75s access. 75s 75s Output Arguments: 75s --pdf-filename PDF_FILENAME 75s PDF filename to store plot(s). Default: 75s tombo_results.roc.pdf 75s 75s Down-sampling Arguments: 75s --statistics-per-block STATISTICS_PER_BLOCK 75s Number of randomly selected per-read, per-base 75s statistics to extract from each genomic block for 75s plotting. Default: Include all stats 75s --total-statistics-limit TOTAL_STATISTICS_LIMIT 75s Total per-read statistics to be extracted for 75s plotting. Avoids memory overflow for large runs. 75s Default: 5000000 75s 75s Miscellaneous Arguments: 75s --quiet, -q Don't print status information. 75s --help, -h Print this help message and exit 75s usage: tombo plot per_read_roc --per-read-statistics-filenames 75s PER_READ_STATISTICS_FILENAMES 75s [PER_READ_STATISTICS_FILENAMES ...] 75s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 75s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 75s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 75s [--genome-fasta GENOME_FASTA] 75s [--statistics-per-block STATISTICS_PER_BLOCK] 75s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 75s [--pdf-filename PDF_FILENAME] [--quiet] 75s [--help] 75s 75s Required Argument: 75s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 75s Binary files containing per-read statistics from 75s statistical testing. 75s 75s Ground Truth Arguments (provide bed files or motifs): 75s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 75s Modification description and bed format files 75s containing single base locations of ground truth 75s modified sites. Bed files should contain 6 fields 75s including strand. Format descriptions as 75s "mod_name:locs.bed". Example: "CpG 75s bisulfite":bisulfite_locs.bed 75s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 75s Bed format files containing single base locations of 75s ground truth unmodified sites. Bed files should 75s contain 6 fields including strand. 75s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 75s Ground truth, motif centered, modified base 75s descriptions for computing ROC and PR curves. Each 75s statistics file is associated with a set of motif 75s descriptions. Format descriptions as: 75s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 75s mod_pos indicates the alternate-base within the motif 75s (1-based index). Example: CCWGG:2:"dcm 75s 5mC"::GATC:2:"dam 6mA" would assess the performance of 75s a single Tombo statistics file for identification of 75s E. coli dam and dcm methylation. 75s --genome-fasta GENOME_FASTA 75s FASTA file used to re-squiggle. For faster sequence 75s access. 75s 75s Down-sampling Arguments: 75s --statistics-per-block STATISTICS_PER_BLOCK 75s Number of randomly selected per-read, per-base 75s statistics to extract from each genomic block for 75s plotting. Default: 100000 75s --total-statistics-limit TOTAL_STATISTICS_LIMIT 75s Total per-read statistics to be extracted for 75s plotting. Avoids memory overflow for large runs. 75s Default: 5000000 75s 75s Output Arguments: 75s --pdf-filename PDF_FILENAME 75s PDF filename to store plot(s). Default: 75s tombo_results.per_reads_roc.pdf 75s 75s Miscellaneous Arguments: 75s --quiet, -q Don't print status information. 75s --help, -h Print this help message and exit 75s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 75s [--upstream-bases {0,1,2,3,4}] 75s [--downstream-bases {0,1,2,3,4}] [--read-mean] 75s [--num-kmer-threshold NUM_KMER_THRESHOLD] 75s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 75s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 75s [--corrected-group CORRECTED_GROUP] 75s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 75s [--quiet] [--help] 75s 75s Required Argument: 75s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 75s Directories containing fast5 files. 75s 75s Data Processing Arguments: 75s --upstream-bases {0,1,2,3,4} 75s Upstream bases in k-mer. Default: 1 75s --downstream-bases {0,1,2,3,4} 75s Downstream bases in k-mer. Default: 2 75s --read-mean Plot k-mer means across whole reads as opposed to 75s individual k-mer event levels. 75s --num-kmer-threshold NUM_KMER_THRESHOLD 75s Observations of each k-mer required to include a read 75s in read level averages. Default: 1 75s 75s Plotting Region Arguments: 75s --num-reads NUM_READS 75s Number of reads to plot. Default: 100 75s 75s Output Arguments: 75s --pdf-filename PDF_FILENAME 75s PDF filename to store plot(s). Default: 75s tombo_results.kmer_distribution.pdf 75s --r-data-filename R_DATA_FILENAME 75s Filename to save R data structure. Default: Don't save 75s --dont-plot Don't plot result. Useful to produce only R data file. 75s 75s FAST5 Data Arguments: 75s --corrected-group CORRECTED_GROUP 75s FAST5 group created by resquiggle command. Default: 75s RawGenomeCorrected_000 75s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 75s FAST5 subgroup(s) (under /Analyses/[--basecall- 75s group]/) containing basecalls and created within 75s [--corrected-group] containing re-squiggle results. 75s Default: ['BaseCalled_template'] 75s 75s Miscellaneous Arguments: 75s --quiet, -q Don't print status information. 75s --help, -h Print this help message and exit 75s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 75s [FAST5_BASEDIRS ...] 75s --control-fast5-basedirs 75s CONTROL_FAST5_BASEDIRS 75s [CONTROL_FAST5_BASEDIRS ...] 75s --statistics-filename 75s STATISTICS_FILENAME 75s [--genome-fasta GENOME_FASTA] 75s [--processes PROCESSES] 75s [--num-regions NUM_REGIONS] 75s [--num-bases NUM_BASES] 75s [--slide-span SLIDE_SPAN] 75s [--pdf-filename PDF_FILENAME] 75s [--r-data-filename R_DATA_FILENAME] 75s [--corrected-group CORRECTED_GROUP] 75s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 75s [--quiet] [--help] 75s 75s Required Arguments: 75s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 75s Directories containing fast5 files. 75s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 75s Set of directories containing fast5 files for control 75s reads, containing only canonical nucleotides. 75s --statistics-filename STATISTICS_FILENAME 75s File to save/load genomic base anchored statistics. 75s 75s FASTA Sequence Argument: 75s --genome-fasta GENOME_FASTA 75s FASTA file used to re-squiggle. For faster sequence 75s access. 75s 75s Multiprocessing Argument: 75s --processes PROCESSES 75s Number of processes. Default: 1 75s 75s Plotting Region Arguments: 75s --num-regions NUM_REGIONS 75s Number of regions to plot. Default: 10 75s --num-bases NUM_BASES 75s Number of bases to plot/output. Default: 21 75s --slide-span SLIDE_SPAN 75s Number of bases offset over which to search when 75s computing distances for signal cluster plotting. 75s Default: 0 (exact position) 75s 75s Output Arguments: 75s --pdf-filename PDF_FILENAME 75s PDF filename to store plot(s). Default: 75s tombo_results.signal_clusters.pdf 75s --r-data-filename R_DATA_FILENAME 75s Filename to save R data structure. Default: Don't save 75s 75s FAST5 Data Arguments: 75s --corrected-group CORRECTED_GROUP 75s FAST5 group created by resquiggle command. Default: 75s RawGenomeCorrected_000 75s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 75s FAST5 subgroup(s) (under /Analyses/[--basecall- 75s group]/) containing basecalls and created within 75s [--corrected-group] containing re-squiggle results. 75s Default: ['BaseCalled_template'] 75s 75s Miscellaneous Arguments: 75s --quiet, -q Don't print status information. 75s --help, -h Print this help message and exit 75s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 75s 75s Required Arguments: 75s fast5s_basedir Directory containing fast5 files. All files ending in 75s "fast5" found recursively within this base directory will be 75s processed. 75s 75s Miscellaneous Arguments: 75s --quiet, -q Don't print status information. 75s --help, -h Print this help message and exit 75s usage: tombo build_model event_resquiggle 75s [--minimap2-executable MINIMAP2_EXECUTABLE] 75s [--minimap2-index MINIMAP2_INDEX] 75s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 75s [--graphmap-executable GRAPHMAP_EXECUTABLE] 75s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 75s [--normalization-type {median,pA,pA_raw,none}] 75s [--pore-model-filename PORE_MODEL_FILENAME] 75s [--outlier-threshold OUTLIER_THRESHOLD] 75s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 75s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 75s [--timeout TIMEOUT] 75s [--cpts-limit CPTS_LIMIT] 75s [--skip-index] [--overwrite] 75s [--failed-reads-filename FAILED_READS_FILENAME] 75s [--include-event-stdev] 75s [--corrected-group CORRECTED_GROUP] 75s [--basecall-group BASECALL_GROUP] 75s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 75s [--processes PROCESSES] 75s [--align-processes ALIGN_PROCESSES] 75s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 75s [--resquiggle-processes RESQUIGGLE_PROCESSES] 75s [--quiet] [--help] 75s fast5s_basedir reference_fasta 75s 75s Required Arguments: 75s fast5s_basedir Directory containing fast5 files. All files ending in 75s "fast5" found recursively within this base directory 75s will be processed. 75s reference_fasta Reference genome/transcriptome FASTA file for mapping. 75s 75s Mapper Arguments (One mapper is required): 75s --minimap2-executable MINIMAP2_EXECUTABLE 75s Path to minimap2 executable. 75s --minimap2-index MINIMAP2_INDEX 75s Path to minimap2 index (with map-ont preset) file 75s corresponding to the [genome_fasta] provided. 75s --bwa-mem-executable BWA_MEM_EXECUTABLE 75s Path to bwa-mem executable. 75s --graphmap-executable GRAPHMAP_EXECUTABLE 75s Path to graphmap executable. 75s --alignment-batch-size ALIGNMENT_BATCH_SIZE 75s Number of reads included in each alignment call. Note: 75s A new system mapping call is made for each batch 75s (including loading of the genome), so it is advised to 75s use larger values for larger genomes. Default: 1000 75s 75s Signal Processing Arguments: 75s --normalization-type {median,pA,pA_raw,none} 75s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 75s as in the ONT events (using offset, range and 75s digitization), "pA": k-mer-based correction for pA 75s drift as in nanopolish (requires [--pore-model- 75s filename]), "median": median and MAD from raw signal. 75s Default: median 75s --pore-model-filename PORE_MODEL_FILENAME 75s File containing kmer model parameters (level_mean and 75s level_stdv) used in order to compute kmer-based 75s corrected pA values. E.g. https://github.com/jts/nanop 75s olish/blob/master/etc/r9- 75s models/template_median68pA.5mers.model 75s --outlier-threshold OUTLIER_THRESHOLD 75s Windosrize the signal at this number of scale values. 75s Negative value disables outlier clipping. Default: 75s 5.000000 75s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 75s Specify the 2 parameters for segmentation 1) running 75s neighboring windows width 2) minimum raw observations 75s per genomic base. Sample type defaults: RNA : 12 6 || 75s DNA : 5 3 75s 75s Read Filtering Arguments: 75s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 75s Filter reads based on observations per base percentile 75s thresholds. Format thresholds as "percentile:thresh 75s [pctl2:thresh2 ...]". For example to filter reads with 75s 99th pctl > 200 obs/base or max > 5k obs/base use 75s "99:200 100:5000". 75s --timeout TIMEOUT Timeout in seconds for processing a single read. 75s Default: No timeout. 75s --cpts-limit CPTS_LIMIT 75s Maximum number of changepoints to find within a single 75s indel group. Default: No limit. 75s 75s Input/Output Arguments: 75s --skip-index Skip creation of tombo index. This drastically slows 75s downstream tombo commands. Default stores tombo index 75s named ".[--fast5-basedir].[--corrected- 75s group].tombo.index" to be loaded automatically for 75s downstream commands. 75s --overwrite Overwrite previous corrected group in FAST5 files. 75s Note: only effects --corrected-group or --new- 75s corrected-group. 75s --failed-reads-filename FAILED_READS_FILENAME 75s Output failed read filenames with assoicated error. 75s Default: Do not store failed reads. 75s --include-event-stdev 75s Include corrected event standard deviation in output 75s FAST5 data. 75s 75s FAST5 Data Arguments: 75s --corrected-group CORRECTED_GROUP 75s FAST5 group created by resquiggle command. Default: 75s RawGenomeCorrected_000 75s --basecall-group BASECALL_GROUP 75s FAST5 group obtain original basecalls (under Analyses 75s group). Default: Basecall_1D_000 75s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 75s FAST5 subgroup(s) (under /Analyses/[--basecall- 75s group]/) containing basecalls and created within 75s [--corrected-group] containing re-squiggle results. 75s Default: ['BaseCalled_template'] 75s 75s Multiprocessing Arguments: 75s --processes PROCESSES 75s Number of processes. Default: 2 75s --align-processes ALIGN_PROCESSES 75s Number of processes to use for parsing and aligning 75s original basecalls. Each process will independently 75s load the genome into memory, so use caution with 75s larger genomes (e.g. human). Default: 1 75s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 75s Number of threads to use for aligner system call. 75s Default: [--processes] / (2 * [--align-processes)] 75s --resquiggle-processes RESQUIGGLE_PROCESSES 75s Number of processes to use for resquiggle algorithm. 75s Default: [--processes] / 2 75s 75s Miscellaneous Arguments: 75s --quiet, -q Don't print status information. 75s --help, -h Print this help message and exit 75s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 75s [FAST5_BASEDIRS ...] 75s --tombo-model-filename 75s TOMBO_MODEL_FILENAME 75s [--estimate-mean] 75s [--kmer-specific-sd] 75s [--upstream-bases {0,1,2,3,4}] 75s [--downstream-bases {0,1,2,3,4}] 75s [--minimum-test-reads MINIMUM_TEST_READS] 75s [--coverage-threshold COVERAGE_THRESHOLD] 75s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 75s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 75s [--processes PROCESSES] 75s [--corrected-group CORRECTED_GROUP] 75s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 75s [--quiet] [--help] 75s 75s Required Arguments: 75s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 75s Directories containing fast5 files. 75s --tombo-model-filename TOMBO_MODEL_FILENAME 75s Filename to save Tombo model. 75s 75s Modeling Arguments: 75s --estimate-mean Use the mean instead of median for model level 75s estimation. Note: This can cause poor fits due to 75s outliers 75s --kmer-specific-sd Estimate standard deviation for each k-mers 75s individually. 75s --upstream-bases {0,1,2,3,4} 75s Upstream bases in k-mer. Default: 1 75s --downstream-bases {0,1,2,3,4} 75s Downstream bases in k-mer. Default: 2 75s 75s Filtering Arguments: 75s --minimum-test-reads MINIMUM_TEST_READS 75s Number of reads required at a position to perform 75s significance testing or contribute to model 75s estimation. Default: 10 75s --coverage-threshold COVERAGE_THRESHOLD 75s Maximum mean coverage per region when estimating k-mer 75s model (limits compute time for deep samples). Default: 75s 100 75s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 75s Number of each k-mer observations required in order to 75s produce a reference (genomic locations for standard 75s reference and per-read for alternative reference). 75s Default: 5 75s 75s Multiprocessing Arguments: 75s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 75s Size of regions over which to multiprocesses statistic 75s computation. For very deep samples a smaller value is 75s recommmended in order to control memory consumption. 75s Default: 10000 75s --processes PROCESSES 75s Number of processes. Default: 1 75s 75s FAST5 Data Arguments: 75s --corrected-group CORRECTED_GROUP 75s FAST5 group created by resquiggle command. Default: 75s RawGenomeCorrected_000 75s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 75s FAST5 subgroup(s) (under /Analyses/[--basecall- 75s group]/) containing basecalls and created within 75s [--corrected-group] containing re-squiggle results. 75s Default: ['BaseCalled_template'] 75s 75s Miscellaneous Arguments: 75s --quiet, -q Don't print status information. 75s --help, -h Print this help message and exit 75s usage: tombo build_model estimate_alt_reference --alternate-model-filename 75s ALTERNATE_MODEL_FILENAME 75s --alternate-model-name 75s ALTERNATE_MODEL_NAME 75s --alternate-model-base 75s {A,C,G,T} 75s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 75s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 75s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 75s [--control-density-filename CONTROL_DENSITY_FILENAME] 75s [--dna] [--rna] 75s [--tombo-model-filename TOMBO_MODEL_FILENAME] 75s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 75s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 75s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 75s [--save-density-basename SAVE_DENSITY_BASENAME] 75s [--processes PROCESSES] 75s [--corrected-group CORRECTED_GROUP] 75s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 75s [--quiet] [--help] 75s 75s Required Arguments: 75s --alternate-model-filename ALTERNATE_MODEL_FILENAME 75s Tombo model for alternative likelihood ratio 75s significance testing. 75s --alternate-model-name ALTERNATE_MODEL_NAME 75s A short name to associate with this alternate model 75s (e.g. 5mC, 6mA, etc.). This text will be included in 75s output filenames when this model is used for testing. 75s --alternate-model-base {A,C,G,T} 75s Non-standard base is an alternative to this base. 75s 75s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 75s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 75s Directories containing fast5 files. 75s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 75s Set of directories containing fast5 files for control 75s reads, containing only canonical nucleotides. 75s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 75s File containing k-mer level kernel density estimates 75s for the alternative sample saved using --save-density- 75s basename. 75s --control-density-filename CONTROL_DENSITY_FILENAME 75s File containing k-mer level kernel density estimates 75s for the control sample saved using --save-density- 75s basename. 75s 75s Standard Model Arguments: 75s --dna Explicitly select canonical DNA model. Default: 75s Automatically determine from FAST5s 75s --rna Explicitly select canonical RNA model. Default: 75s Automatically determine from FAST5s 75s --tombo-model-filename TOMBO_MODEL_FILENAME 75s Tombo model filename. If no file is provided, the 75s default DNA or RNA Tombo model will be used. 75s 75s Model Fitting Arguments: 75s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 75s When esitmating the alternative base incorporation 75s rate, this percent of k-mers are assumed to have 75s significantly shifted signal so the alternative 75s distribution minimally overlaps the standard base 75s distribution. Default: 5.000000 75s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 75s Bandwidth applied when performing Gaussian kernal 75s density esitmation on standard and alternative base 75s signal distributions. Default: 0.050000 75s 75s Filtering Argument: 75s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 75s Number of each k-mer observations required in order to 75s produce a reference (genomic locations for standard 75s reference and per-read for alternative reference). 75s Default: 1000 75s 75s Output Argument: 75s --save-density-basename SAVE_DENSITY_BASENAME 75s Basename to save alternative model estimation density 75s estimation information. See scripts/debug_est_alt.R 75s for info use example. Default: Don't save. 75s 75s Multiprocessing Arguments: 75s --processes PROCESSES 75s Number of processes. Default: 1 75s 75s FAST5 Data Arguments: 75s --corrected-group CORRECTED_GROUP 75s FAST5 group created by resquiggle command. Default: 75s RawGenomeCorrected_000 75s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 75s FAST5 subgroup(s) (under /Analyses/[--basecall- 75s group]/) containing basecalls and created within 75s [--corrected-group] containing re-squiggle results. 75s Default: ['BaseCalled_template'] 75s 75s Miscellaneous Arguments: 75s --quiet, -q Don't print status information. 75s --help, -h Print this help message and exit 75s This test only tests the help system 75s There is an extensive test in 75s 75s tombo/tests/shell_tests.sh 75s 75s but this requires to download larger data 75s sets which is not done for the moment. 76s autopkgtest [10:41:57]: test run-unit-test: -----------------------] 76s autopkgtest [10:41:57]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 76s run-unit-test PASS 76s autopkgtest [10:41:57]: @@@@@@@@@@@@@@@@@@@@ summary 76s run-unit-test PASS 88s nova [W] Skipping flock for amd64 88s Creating nova instance adt-plucky-amd64-tombo-20241030-104040-juju-7f2275-prod-proposed-migration-environment-14-dd590128-0415-440d-8ad5-14b03a34185c from image adt/ubuntu-plucky-amd64-server-20241029.img (UUID 38cf62dc-8d54-4e4f-bcab-db8084c89f55)...