0s autopkgtest [09:49:01]: starting date and time: 2024-10-30 09:49:01+0000 0s autopkgtest [09:49:01]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [09:49:01]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4jhajalz/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-2@bos03-arm64-5.secgroup --name adt-plucky-arm64-tombo-20241030-094901-juju-7f2275-prod-proposed-migration-environment-2-12964161-7681-43fc-b7c8-7cc6c1647e0d --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 89s autopkgtest [09:50:30]: testbed dpkg architecture: arm64 89s autopkgtest [09:50:30]: testbed apt version: 2.9.8 89s autopkgtest [09:50:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 91s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 91s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [28.1 kB] 91s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [212 kB] 92s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 92s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [2840 B] 92s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [59.3 kB] 92s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 92s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [249 kB] 92s Fetched 682 kB in 1s (736 kB/s) 92s Reading package lists... 95s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s Calculating upgrade... 98s The following NEW packages will be installed: 98s python3-jaraco.text 98s The following packages will be upgraded: 98s libkeyutils1 python3-pkg-resources python3-setuptools 98s 3 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 98s Need to get 812 kB of archives. 98s After this operation, 13.3 kB of additional disk space will be used. 98s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libkeyutils1 arm64 1.6.3-4ubuntu2 [10.2 kB] 98s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jaraco.text all 4.0.0-1 [11.5 kB] 98s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-pkg-resources all 75.2.0-1 [134 kB] 98s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-setuptools all 75.2.0-1 [657 kB] 99s Fetched 812 kB in 1s (1490 kB/s) 99s (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 ... 79697 files and directories currently installed.) 99s Preparing to unpack .../libkeyutils1_1.6.3-4ubuntu2_arm64.deb ... 99s Unpacking libkeyutils1:arm64 (1.6.3-4ubuntu2) over (1.6.3-3build1) ... 99s Selecting previously unselected package python3-jaraco.text. 100s Preparing to unpack .../python3-jaraco.text_4.0.0-1_all.deb ... 100s Unpacking python3-jaraco.text (4.0.0-1) ... 100s Preparing to unpack .../python3-pkg-resources_75.2.0-1_all.deb ... 100s Unpacking python3-pkg-resources (75.2.0-1) over (74.1.2-1) ... 100s Preparing to unpack .../python3-setuptools_75.2.0-1_all.deb ... 100s Unpacking python3-setuptools (75.2.0-1) over (74.1.2-1) ... 100s Setting up python3-pkg-resources (75.2.0-1) ... 101s Setting up libkeyutils1:arm64 (1.6.3-4ubuntu2) ... 101s Setting up python3-jaraco.text (4.0.0-1) ... 101s Setting up python3-setuptools (75.2.0-1) ... 102s Processing triggers for libc-bin (2.40-1ubuntu3) ... 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 104s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 104s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 104s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 105s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 106s Reading package lists... 106s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s Calculating upgrade... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s autopkgtest [09:50:55]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 114s autopkgtest [09:50:55]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 118s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (dsc) [2291 B] 118s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (tar) [22.3 MB] 118s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (diff) [7100 B] 118s gpgv: Signature made Wed Apr 10 17:15:32 2024 UTC 118s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 118s gpgv: Can't check signature: No public key 118s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6build1.dsc: no acceptable signature found 119s autopkgtest [09:51:00]: testing package tombo version 1.5.1-6build1 119s autopkgtest [09:51:00]: build not needed 121s autopkgtest [09:51:02]: test run-unit-test: preparing testbed 122s Reading package lists... 123s Building dependency tree... 123s Reading state information... 123s Starting pkgProblemResolver with broken count: 0 124s Starting 2 pkgProblemResolver with broken count: 0 124s Done 124s The following additional packages will be installed: 124s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 124s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 124s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 124s python3-decorator python3-h5py python3-h5py-serial python3-mappy 124s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 124s tombo-doc 124s Suggested packages: 124s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 124s gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 124s Recommended packages: 124s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 124s python3-rpy2 124s The following NEW packages will be installed: 124s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 124s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 124s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 124s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 124s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 124s tombo-doc 124s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 124s Need to get 60.4 MB/60.4 MB of archives. 124s After this operation, 193 MB of additional disk space will be used. 124s Get:1 /tmp/autopkgtest.sDj5sW/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 125s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB] 125s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 125s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 125s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 125s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 125s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-7ubuntu1 [438 kB] 125s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 125s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 125s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 125s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 125s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 125s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-3 [157 kB] 125s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 125s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 125s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 125s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 125s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 126s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-5ubuntu1 [1064 kB] 126s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 126s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mappy arm64 2.27+dfsg-1 [167 kB] 126s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.66.5-1 [91.4 kB] 126s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 2.0.0+dfsg-2 [1012 kB] 126s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-3 [16.3 MB] 126s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 tombo arm64 1.5.1-6build1 [446 kB] 126s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 126s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 tombo-doc all 1.5.1-6build1 [21.7 MB] 127s Fetched 60.4 MB in 2s (24.2 MB/s) 127s Selecting previously unselected package fonts-lato. 127s (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 ... 79706 files and directories currently installed.) 127s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 127s Unpacking fonts-lato (2.015-1) ... 128s Selecting previously unselected package fonts-font-awesome. 128s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 128s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 128s Selecting previously unselected package fonts-mathjax. 128s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 128s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 128s Selecting previously unselected package libaec0:arm64. 128s Preparing to unpack .../03-libaec0_1.1.3-1_arm64.deb ... 128s Unpacking libaec0:arm64 (1.1.3-1) ... 128s Selecting previously unselected package libblas3:arm64. 128s Preparing to unpack .../04-libblas3_3.12.0-3build2_arm64.deb ... 128s Unpacking libblas3:arm64 (3.12.0-3build2) ... 128s Selecting previously unselected package libgfortran5:arm64. 128s Preparing to unpack .../05-libgfortran5_14.2.0-7ubuntu1_arm64.deb ... 128s Unpacking libgfortran5:arm64 (14.2.0-7ubuntu1) ... 128s Selecting previously unselected package libsz2:arm64. 128s Preparing to unpack .../06-libsz2_1.1.3-1_arm64.deb ... 128s Unpacking libsz2:arm64 (1.1.3-1) ... 128s Selecting previously unselected package libhdf5-103-1t64:arm64. 128s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 128s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 128s Selecting previously unselected package libhdf5-hl-100t64:arm64. 128s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 128s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 128s Selecting previously unselected package libjs-jquery. 128s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 128s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 128s Selecting previously unselected package libjs-underscore. 128s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 128s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 128s Selecting previously unselected package libjs-sphinxdoc. 128s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-3_all.deb ... 128s Unpacking libjs-sphinxdoc (7.4.7-3) ... 128s Selecting previously unselected package liblapack3:arm64. 128s Preparing to unpack .../12-liblapack3_3.12.0-3build2_arm64.deb ... 128s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 128s Selecting previously unselected package liblbfgsb0:arm64. 129s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 129s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 129s Selecting previously unselected package liblzf1:arm64. 129s Preparing to unpack .../14-liblzf1_3.6-4_arm64.deb ... 129s Unpacking liblzf1:arm64 (3.6-4) ... 129s Selecting previously unselected package python3-decorator. 129s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 129s Unpacking python3-decorator (5.1.1-5) ... 129s Selecting previously unselected package python3-numpy. 129s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 129s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 129s Selecting previously unselected package python3-h5py-serial. 129s Preparing to unpack .../17-python3-h5py-serial_3.11.0-5ubuntu1_arm64.deb ... 129s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 129s Selecting previously unselected package python3-h5py. 129s Preparing to unpack .../18-python3-h5py_3.11.0-5ubuntu1_all.deb ... 129s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 129s Selecting previously unselected package python3-mappy. 129s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1_arm64.deb ... 129s Unpacking python3-mappy (2.27+dfsg-1) ... 129s Selecting previously unselected package python3-tqdm. 129s Preparing to unpack .../20-python3-tqdm_4.66.5-1_all.deb ... 129s Unpacking python3-tqdm (4.66.5-1) ... 129s Selecting previously unselected package sphinx-rtd-theme-common. 129s Preparing to unpack .../21-sphinx-rtd-theme-common_2.0.0+dfsg-2_all.deb ... 129s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-2) ... 129s Selecting previously unselected package python3-scipy. 129s Preparing to unpack .../22-python3-scipy_1.13.1-3_arm64.deb ... 129s Unpacking python3-scipy (1.13.1-3) ... 130s Selecting previously unselected package tombo. 130s Preparing to unpack .../23-tombo_1.5.1-6build1_arm64.deb ... 130s Unpacking tombo (1.5.1-6build1) ... 130s Selecting previously unselected package libjs-mathjax. 130s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 130s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 130s Selecting previously unselected package tombo-doc. 130s Preparing to unpack .../25-tombo-doc_1.5.1-6build1_all.deb ... 130s Unpacking tombo-doc (1.5.1-6build1) ... 130s Selecting previously unselected package autopkgtest-satdep. 130s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 130s Unpacking autopkgtest-satdep (0) ... 131s Setting up fonts-lato (2.015-1) ... 131s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 131s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 131s Setting up python3-tqdm (4.66.5-1) ... 131s Setting up python3-mappy (2.27+dfsg-1) ... 131s Setting up libaec0:arm64 (1.1.3-1) ... 131s Setting up python3-decorator (5.1.1-5) ... 131s Setting up libblas3:arm64 (3.12.0-3build2) ... 131s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 131s Setting up liblzf1:arm64 (3.6-4) ... 131s Setting up libgfortran5:arm64 (14.2.0-7ubuntu1) ... 131s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 131s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 131s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-2) ... 131s Setting up libsz2:arm64 (1.1.3-1) ... 131s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 131s Setting up liblapack3:arm64 (3.12.0-3build2) ... 131s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 131s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 133s Setting up libjs-sphinxdoc (7.4.7-3) ... 133s Setting up tombo-doc (1.5.1-6build1) ... 133s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 133s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 133s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 133s Setting up python3-scipy (1.13.1-3) ... 137s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 137s Setting up python3-h5py (3.11.0-5ubuntu1) ... 137s Setting up tombo (1.5.1-6build1) ... 138s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 138s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 138s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 138s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 138s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 138s re.match('\+', fastq_rec[2]) is None): 138s Setting up autopkgtest-satdep (0) ... 138s Processing triggers for man-db (2.12.1-3) ... 139s Processing triggers for libc-bin (2.40-1ubuntu3) ... 143s (Reading database ... 86908 files and directories currently installed.) 143s Removing autopkgtest-satdep (0) ... 144s autopkgtest [09:51:25]: test run-unit-test: [----------------------- 145s ********* Testing help commands ********** 145s usage: tombo [-h] [-v] 145s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 145s ... 145s 145s ********** Tombo ********* 145s 145s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 145s 145s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 145s 145s Tombo command groups (additional help available within each command group): 145s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 145s preprocess Pre-process nanopore reads for Tombo processing. 145s filter Apply filter to Tombo index file for specified criterion. 145s detect_modifications Perform statistical testing to detect non-standard nucleotides. 145s text_output Output Tombo results in text files. 145s build_model Create canonical and alternative base Tombo models. 145s plot Save plots to visualize raw nanopore signal or testing results. 145s 145s options: 145s -h, --help show this help message and exit 145s -v, --version show Tombo version and exit. 145s usage: tombo resquiggle [--dna] [--rna] 145s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 145s [--q-score Q_SCORE] 145s [--signal-matching-score SIGNAL_MATCHING_SCORE] 145s [--processes PROCESSES] 145s [--corrected-group CORRECTED_GROUP] 145s [--basecall-group BASECALL_GROUP] 145s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 145s [--overwrite] 145s [--failed-reads-filename FAILED_READS_FILENAME] 145s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 145s [--print-advanced-arguments] [--quiet] [--help] 145s fast5s_basedir reference 145s 145s Required Arguments: 145s fast5s_basedir Directory containing fast5 files. All files ending in 145s "fast5" found recursively within this base directory 145s will be processed. 145s reference Reference genome/transcriptome FASTA file or minimap2 145s index (with "map-ont" preset) for mapping. 145s 145s Model Parameters: 145s --dna Explicitly select canonical DNA model. Default: 145s Automatically determine from FAST5s 145s --rna Explicitly select canonical RNA model. Default: 145s Automatically determine from FAST5s 145s 145s Read Filtering Argument: 145s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 145s Filter reads based on observations per base percentile 145s thresholds. Format thresholds as "percentile:thresh 145s [pctl2:thresh2 ...]". For example to filter reads with 145s 99th pctl > 200 obs/base or max > 5k obs/base use 145s "99:200 100:5000". 145s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 145s Default: 0.000000 145s --signal-matching-score SIGNAL_MATCHING_SCORE 145s Observed to expected signal matching score (higher 145s score indicates poor matching). Sample type defaults: 145s RNA : 2 || DNA : 1.1 145s 145s Multiprocessing Arguments: 145s --processes PROCESSES 145s Number of processes. Default: 1 145s 145s FAST5 Data Arguments: 145s --corrected-group CORRECTED_GROUP 145s FAST5 group created by resquiggle command. Default: 145s RawGenomeCorrected_000 145s --basecall-group BASECALL_GROUP 145s FAST5 group obtain original basecalls (under Analyses 145s group). Default: Basecall_1D_000 145s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 145s FAST5 subgroup(s) (under /Analyses/[--basecall- 145s group]/) containing basecalls and created within 145s [--corrected-group] containing re-squiggle results. 145s Default: ['BaseCalled_template'] 145s --overwrite Overwrite previous corrected group in FAST5 files. 145s Note: only effects --corrected-group or --new- 145s corrected-group. 145s 145s Input/Output Arguments: 145s --failed-reads-filename FAILED_READS_FILENAME 145s Output failed read filenames with assoicated error. 145s Default: Do not store failed reads. 145s --num-most-common-errors NUM_MOST_COMMON_ERRORS 145s Dynamically show this many most common errors so far 145s through run. Default: 0; Just show progress 145s 145s Advanced Arguments: 145s --print-advanced-arguments 145s Print advanced re-squiggle arguments and exit. 145s 145s Miscellaneous Arguments: 145s --quiet, -q Don't print status information. 145s --help, -h Print this help message and exit 145s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 145s --fastq-filenames 145s FASTQ_FILENAMES 145s [FASTQ_FILENAMES ...] 145s [--basecall-group BASECALL_GROUP] 145s [--basecall-subgroup BASECALL_SUBGROUP] 145s [--overwrite] 145s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 145s [--processes PROCESSES] 145s [--quiet] [--help] 145s 145s Required Arguments: 145s --fast5-basedir FAST5_BASEDIR 145s Directory containing fast5 files. 145s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 145s FASTQ filenames containing basecalls to be added to 145s raw FAST5 files. 145s 145s FAST5 Data Arguments: 145s --basecall-group BASECALL_GROUP 145s FAST5 group obtain original basecalls (under Analyses 145s group). Default: Basecall_1D_000 145s --basecall-subgroup BASECALL_SUBGROUP 145s FAST5 subgroup (under /Analyses/[--basecall-group]/) 145s under which to store basecalls from FASTQs. Default: 145s BaseCalled_template 145s --overwrite Overwrite previous corrected group in FAST5 files. 145s Note: only effects --corrected-group or --new- 145s corrected-group. 145s 145s Sequencing Summary Argument: 145s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 145s Sequencing summary filenames produced by albacore. 145s These can make annotation of raw FAST5 files with 145s FASTQ sequence much faster. 145s 145s Multiprocessing Argument: 145s --processes PROCESSES 145s Number of processes. Default: 1 145s 145s Miscellaneous Arguments: 145s --quiet, -q Don't print status information. 145s --help, -h Print this help message and exit 145s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 145s [FAST5_BASEDIRS ...] 145s [--corrected-group CORRECTED_GROUP] 145s [--quiet] [--help] 145s 145s Required Argument: 145s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 145s Directories containing fast5 files. 145s 145s FAST5 Data Argument: 145s --corrected-group CORRECTED_GROUP 145s FAST5 group created by resquiggle command. Default: 145s RawGenomeCorrected_000 145s 145s Miscellaneous Arguments: 145s --quiet, -q Don't print status information. 145s --help, -h Print this help message and exit 145s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 145s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 145s [--corrected-group CORRECTED_GROUP] [--quiet] 145s [--help] 145s 145s Required Argument: 145s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 145s Directories containing fast5 files. 145s 145s Read Filtering Argument: 145s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 145s Filter reads based on observations per base percentile 145s thresholds. Format thresholds as "percentile:thresh 145s [pctl2:thresh2 ...]". For example to filter reads with 145s 99th pctl > 200 obs/base or max > 5k obs/base use 145s "99:200 100:5000". 145s 145s FAST5 Data Argument: 145s --corrected-group CORRECTED_GROUP 145s FAST5 group created by resquiggle command. Default: 145s RawGenomeCorrected_000 145s 145s Miscellaneous Arguments: 145s --quiet, -q Don't print status information. 145s --help, -h Print this help message and exit 145s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 145s [FAST5_BASEDIRS ...] 145s [--percent-to-filter PERCENT_TO_FILTER] 145s [--corrected-group CORRECTED_GROUP] 145s [--quiet] [--help] 145s 145s Required Arguments: 145s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 145s Directories containing fast5 files. 145s 145s Read Filtering Argument: 145s --percent-to-filter PERCENT_TO_FILTER 145s Percentage of all reads to filter. Reads are randomly 145s selected weighted according to the approximate 145s coverage at the mapped genomic location. This can be 145s useful in modeling and testing. Default: 10.000000 145s 145s FAST5 Data Arguments: 145s --corrected-group CORRECTED_GROUP 145s FAST5 group created by resquiggle command. Default: 145s RawGenomeCorrected_000 145s 145s Miscellaneous Arguments: 145s --quiet, -q Don't print status information. 145s --help, -h Print this help message and exit 145s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 145s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 145s [--corrected-group CORRECTED_GROUP] 145s [--basecall-group BASECALL_GROUP] [--quiet] 145s [--help] 145s 145s Required Arguments: 145s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 145s Directories containing fast5 files. 145s 145s Read Filtering Argument: 145s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 145s Default: 7.000000 145s 145s FAST5 Data Arguments: 145s --corrected-group CORRECTED_GROUP 145s FAST5 group created by resquiggle command. Default: 145s RawGenomeCorrected_000 145s --basecall-group BASECALL_GROUP 145s FAST5 group obtain original basecalls (under Analyses 145s group). Default: Basecall_1D_000 145s 145s Miscellaneous Arguments: 145s --quiet, -q Don't print status information. 145s --help, -h Print this help message and exit 145s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 145s [FAST5_BASEDIRS ...] 145s --signal-matching-score 145s SIGNAL_MATCHING_SCORE 145s [--corrected-group CORRECTED_GROUP] 145s [--quiet] [--help] 145s 145s Required Arguments: 145s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 145s Directories containing fast5 files. 145s --signal-matching-score SIGNAL_MATCHING_SCORE 145s Observed to expected signal matching score (higher 145s score indicates poor matching). Sample type defaults: 145s RNA : 2 || DNA : 1.1 145s 145s FAST5 Data Arguments: 145s --corrected-group CORRECTED_GROUP 145s FAST5 group created by resquiggle command. Default: 145s RawGenomeCorrected_000 145s 145s Miscellaneous Arguments: 145s --quiet, -q Don't print status information. 145s --help, -h Print this help message and exit 146s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 146s [FAST5_BASEDIRS ...] 146s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 146s [--include-partial-overlap] 146s [--corrected-group CORRECTED_GROUP] 146s [--quiet] [--help] 146s 146s Required Arguments: 146s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 146s Directories containing fast5 files. 146s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 146s Filter out reads not falling completely within include 146s regions. Omit start and end coordinates to include an 146s entire chromosome/sequence record. Format regions as 146s "chrm[:start-end] [chrm2[:start2-end2] ...]". 146s 146s Filter Argument: 146s --include-partial-overlap 146s Include reads that partially overlap the specified 146s region. Default: Only include reads completely 146s contained in a specified region 146s 146s FAST5 Data Argument: 146s --corrected-group CORRECTED_GROUP 146s FAST5 group created by resquiggle command. Default: 146s RawGenomeCorrected_000 146s 146s Miscellaneous Arguments: 146s --quiet, -q Don't print status information. 146s --help, -h Print this help message and exit 146s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 146s [FAST5_BASEDIRS ...] 146s --statistics-file-basename 146s STATISTICS_FILE_BASENAME [--dna] 146s [--rna] 146s [--fishers-method-context FISHERS_METHOD_CONTEXT] 146s [--minimum-test-reads MINIMUM_TEST_READS] 146s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 146s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 146s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 146s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 146s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 146s [--processes PROCESSES] 146s [--corrected-group CORRECTED_GROUP] 146s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 146s [--quiet] [--help] 146s 146s Required Argument: 146s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 146s Directories containing fast5 files. 146s --statistics-file-basename STATISTICS_FILE_BASENAME 146s File base name to save base by base statistics from 146s testing. Filenames will be [--statistics-file- 146s basename].[--alternate-bases]?.tombo.stats 146s 146s Comparison Model Arguments: 146s --dna Explicitly select canonical DNA model. Default: 146s Automatically determine from FAST5s 146s --rna Explicitly select canonical RNA model. Default: 146s Automatically determine from FAST5s 146s 146s Significance Test Arguments: 146s --fishers-method-context FISHERS_METHOD_CONTEXT 146s Number of context bases up and downstream over which 146s to compute Fisher's method combined p-values. Note: 146s Not applicable for alternative model likelihood ratio 146s tests. Default: 1. 146s --minimum-test-reads MINIMUM_TEST_READS 146s Number of reads required at a position to perform 146s significance testing or contribute to model 146s estimation. Default: 1 146s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 146s P-value threshold when computing fraction of 146s significant reads at each genomic position. If two 146s values are provided, statistics between these values 146s are not considered. Default thresholds: DNA:0.15-0.5 , 146s RNA:0.05-0.4 146s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 146s Dampen fraction modified estimates for low coverage 146s sites. Two parameters are unmodified and modified 146s pseudo read counts. This is equivalent to a beta prior 146s on the fraction estimate. Set to "0 0" to disable 146s dampened fraction estimation. Default: [2, 0] 146s 146s Output Argument: 146s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 146s Base for binary files containing per-read statistics 146s from statistical testing. Filenames will be [--per- 146s read-statistics-basename].[--alternate- 146s bases]?.tombo.per_read_stats 146s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 146s Number of the most significant sites to store for 146s faster access. If a longer list of most significant 146s sites is required the list must be re-computed from 146s all batches. Very large values can increase RAM usage. 146s Default: 100000 146s 146s Multiprocessing Arguments: 146s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 146s Size of regions over which to multiprocesses statistic 146s computation. For very deep samples a smaller value is 146s recommmended in order to control memory consumption. 146s Default: 10000 146s --processes PROCESSES 146s Number of processes. Default: 1 146s 146s FAST5 Data Arguments: 146s --corrected-group CORRECTED_GROUP 146s FAST5 group created by resquiggle command. Default: 146s RawGenomeCorrected_000 146s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 146s FAST5 subgroup(s) (under /Analyses/[--basecall- 146s group]/) containing basecalls and created within 146s [--corrected-group] containing re-squiggle results. 146s Default: ['BaseCalled_template'] 146s 146s Miscellaneous Arguments: 146s --quiet, -q Don't print status information. 146s --help, -h Print this help message and exit 146s usage: tombo detect_modifications alternative_model 146s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 146s [--statistics-file-basename STATISTICS_FILE_BASENAME] 146s [--alternate-bases {dcm,dam,CpG,6mA,5mC} [{dcm,dam,CpG,6mA,5mC} ...]] 146s [--print-available-models] 146s [--dna] [--rna] 146s [--minimum-test-reads MINIMUM_TEST_READS] 146s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 146s [--standard-log-likelihood-ratio] 146s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 146s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 146s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 146s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 146s [--processes PROCESSES] 146s [--corrected-group CORRECTED_GROUP] 146s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 146s [--quiet] [--help] 146s 146s Required Argument: 146s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 146s Directories containing fast5 files. 146s --statistics-file-basename STATISTICS_FILE_BASENAME 146s File base name to save base by base statistics from 146s testing. Filenames will be [--statistics-file- 146s basename].[--alternate-bases]?.tombo.stats 146s --alternate-bases {dcm,dam,CpG,6mA,5mC} [{dcm,dam,CpG,6mA,5mC} ...] 146s Default non-standard base model for testing (not 146s required if user created --alternate-model-filenames 146s is provided). 146s 146s Comparison Arguments: 146s --print-available-models 146s Print available alternative models and exit. 146s --dna Explicitly select canonical DNA model. Default: 146s Automatically determine from FAST5s 146s --rna Explicitly select canonical RNA model. Default: 146s Automatically determine from FAST5s 146s 146s Significance Test Arguments: 146s --minimum-test-reads MINIMUM_TEST_READS 146s Number of reads required at a position to perform 146s significance testing or contribute to model 146s estimation. Default: 1 146s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 146s Log likelihood ratio threshold when computing fraction 146s of significant reads at each genomic position. If two 146s values are provided, statistics between these values 146s are not considered. Default thresholds: DNA:-1.5-2.5 , 146s RNA:-2.5-2.5 146s --standard-log-likelihood-ratio 146s Use a standard log likelihood ratio (LLR) statistic. 146s Default is to use an outlier-robust LLR-like 146s statistic. Detail in full online documentation. 146s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 146s Dampen fraction modified estimates for low coverage 146s sites. Two parameters are unmodified and modified 146s pseudo read counts. This is equivalent to a beta prior 146s on the fraction estimate. Set to "0 0" to disable 146s dampened fraction estimation. Default: [2, 0] 146s 146s Output Argument: 146s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 146s Base for binary files containing per-read statistics 146s from statistical testing. Filenames will be [--per- 146s read-statistics-basename].[--alternate- 146s bases]?.tombo.per_read_stats 146s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 146s Number of the most significant sites to store for 146s faster access. If a longer list of most significant 146s sites is required the list must be re-computed from 146s all batches. Very large values can increase RAM usage. 146s Default: 100000 146s 146s Multiprocessing Arguments: 146s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 146s Size of regions over which to multiprocesses statistic 146s computation. For very deep samples a smaller value is 146s recommmended in order to control memory consumption. 146s Default: 10000 146s --processes PROCESSES 146s Number of processes. Default: 1 146s 146s FAST5 Data Arguments: 146s --corrected-group CORRECTED_GROUP 146s FAST5 group created by resquiggle command. Default: 146s RawGenomeCorrected_000 146s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 146s FAST5 subgroup(s) (under /Analyses/[--basecall- 146s group]/) containing basecalls and created within 146s [--corrected-group] containing re-squiggle results. 146s Default: ['BaseCalled_template'] 146s 146s Miscellaneous Arguments: 146s --quiet, -q Don't print status information. 146s --help, -h Print this help message and exit 146s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 146s FAST5_BASEDIRS 146s [FAST5_BASEDIRS ...] 146s --statistics-file-basename 146s STATISTICS_FILE_BASENAME 146s --control-fast5-basedirs 146s CONTROL_FAST5_BASEDIRS 146s [CONTROL_FAST5_BASEDIRS ...] 146s [--sample-only-estimates] 146s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 146s [--dna] [--rna] 146s [--fishers-method-context FISHERS_METHOD_CONTEXT] 146s [--minimum-test-reads MINIMUM_TEST_READS] 146s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 146s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 146s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 146s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 146s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 146s [--processes PROCESSES] 146s [--corrected-group CORRECTED_GROUP] 146s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 146s [--quiet] [--help] 146s 146s Required Argument: 146s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 146s Directories containing fast5 files. 146s --statistics-file-basename STATISTICS_FILE_BASENAME 146s File base name to save base by base statistics from 146s testing. Filenames will be [--statistics-file- 146s basename].[--alternate-bases]?.tombo.stats 146s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 146s Set of directories containing fast5 files for control 146s reads, containing only canonical nucleotides. 146s 146s Model Prior Arguments: 146s --sample-only-estimates 146s Only use canonical sample to estimate expected signal 146s level and spread. Default: Use canonical model to 146s improve estimtates (esp. for low coverage regions) 146s using baysian posterior estimates. 146s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 146s Prior weights (one each for mean and spread) applied 146s to canonical base model for estimating posterior model 146s parameters for sample comparison. Default: [5, 40] 146s --dna Explicitly select canonical DNA model. Default: 146s Automatically determine from FAST5s 146s --rna Explicitly select canonical RNA model. Default: 146s Automatically determine from FAST5s 146s 146s Significance Test Arguments: 146s --fishers-method-context FISHERS_METHOD_CONTEXT 146s Number of context bases up and downstream over which 146s to compute Fisher's method combined p-values. Note: 146s Not applicable for alternative model likelihood ratio 146s tests. Default: 1. 146s --minimum-test-reads MINIMUM_TEST_READS 146s Number of reads required at a position to perform 146s significance testing or contribute to model 146s estimation. Default: 1 146s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 146s P-value threshold when computing fraction of 146s significant reads at each genomic position. If two 146s values are provided, statistics between these values 146s are not considered. Default thresholds: DNA:0.15-0.5 , 146s RNA:0.05-0.4 146s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 146s Dampen fraction modified estimates for low coverage 146s sites. Two parameters are unmodified and modified 146s pseudo read counts. This is equivalent to a beta prior 146s on the fraction estimate. Set to "0 0" to disable 146s dampened fraction estimation. Default: [2, 0] 146s 146s Output Argument: 146s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 146s Base for binary files containing per-read statistics 146s from statistical testing. Filenames will be [--per- 146s read-statistics-basename].[--alternate- 146s bases]?.tombo.per_read_stats 146s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 146s Number of the most significant sites to store for 146s faster access. If a longer list of most significant 146s sites is required the list must be re-computed from 146s all batches. Very large values can increase RAM usage. 146s Default: 100000 146s 146s Multiprocessing Arguments: 146s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 146s Size of regions over which to multiprocesses statistic 146s computation. For very deep samples a smaller value is 146s recommmended in order to control memory consumption. 146s Default: 10000 146s --processes PROCESSES 146s Number of processes. Default: 1 146s 146s FAST5 Data Arguments: 146s --corrected-group CORRECTED_GROUP 146s FAST5 group created by resquiggle command. Default: 146s RawGenomeCorrected_000 146s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 146s FAST5 subgroup(s) (under /Analyses/[--basecall- 146s group]/) containing basecalls and created within 146s [--corrected-group] containing re-squiggle results. 146s Default: ['BaseCalled_template'] 146s 146s Miscellaneous Arguments: 146s --quiet, -q Don't print status information. 146s --help, -h Print this help message and exit 146s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 146s FAST5_BASEDIRS 146s [FAST5_BASEDIRS ...] 146s --statistics-file-basename 146s STATISTICS_FILE_BASENAME 146s --alternate-fast5-basedirs 146s ALTERNATE_FAST5_BASEDIRS 146s [ALTERNATE_FAST5_BASEDIRS ...] 146s [--fishers-method-context FISHERS_METHOD_CONTEXT] 146s [--minimum-test-reads MINIMUM_TEST_READS] 146s [--statistic-type {ks,u,t}] 146s [--store-p-value] 146s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 146s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 146s [--processes PROCESSES] 146s [--corrected-group CORRECTED_GROUP] 146s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 146s [--quiet] [--help] 146s 146s Required Argument: 146s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 146s Directories containing fast5 files. 146s --statistics-file-basename STATISTICS_FILE_BASENAME 146s File base name to save base by base statistics from 146s testing. Filenames will be [--statistics-file- 146s basename].[--alternate-bases]?.tombo.stats 146s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 146s Set of directories containing fast5 files for 146s alternate set of reads. 146s 146s Significance Test Arguments: 146s --fishers-method-context FISHERS_METHOD_CONTEXT 146s Number of context bases up and downstream over which 146s to compute Fisher's method combined p-values. Note: 146s Not applicable for alternative model likelihood ratio 146s tests. Default: 1. 146s --minimum-test-reads MINIMUM_TEST_READS 146s Number of reads required at a position to perform 146s significance testing or contribute to model 146s estimation. Default: 50 146s --statistic-type {ks,u,t} 146s Type of statistical test to apply. Default: "ks" 146s --store-p-value Store p-value instead of effect-size statistic. 146s Statistics are D-statistic (KS-test), deviation from 146s even common language effect size (u-test), and Cohen's 146s D (t-test). 146s 146s Output Argument: 146s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 146s Number of the most significant sites to store for 146s faster access. If a longer list of most significant 146s sites is required the list must be re-computed from 146s all batches. Very large values can increase RAM usage. 146s Default: 100000 146s 146s Multiprocessing Arguments: 146s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 146s Size of regions over which to multiprocesses statistic 146s computation. For very deep samples a smaller value is 146s recommmended in order to control memory consumption. 146s Default: 10000 146s --processes PROCESSES 146s Number of processes. Default: 1 146s 146s FAST5 Data Arguments: 146s --corrected-group CORRECTED_GROUP 146s FAST5 group created by resquiggle command. Default: 146s RawGenomeCorrected_000 146s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 146s FAST5 subgroup(s) (under /Analyses/[--basecall- 146s group]/) containing basecalls and created within 146s [--corrected-group] containing re-squiggle results. 146s Default: ['BaseCalled_template'] 146s 146s Miscellaneous Arguments: 146s --quiet, -q Don't print status information. 146s --help, -h Print this help message and exit 146s usage: tombo detect_modifications aggregate_per_read_stats 146s --per-read-statistics-filename 146s PER_READ_STATISTICS_FILENAME 146s --statistics-filename 146s STATISTICS_FILENAME 146s --single-read-threshold 146s SINGLE_READ_THRESHOLD 146s [SINGLE_READ_THRESHOLD ...] 146s [--minimum-test-reads MINIMUM_TEST_READS] 146s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 146s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 146s [--processes PROCESSES] 146s [--corrected-group CORRECTED_GROUP] 146s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 146s [--quiet] [--help] 146s 146s Required Argument: 146s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 146s Binary file containing per-read statistics from 146s statistical testing. 146s --statistics-filename STATISTICS_FILENAME 146s File to save/load genomic base anchored statistics. 146s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 146s P-value or log likelihood ratio threshold when 146s computing fraction of significant reads at each 146s genomic position. If two values are provided, 146s statistics between these values are not considered. 146s 146s Significance Test Arguments: 146s --minimum-test-reads MINIMUM_TEST_READS 146s Number of reads required at a position to perform 146s significance testing or contribute to model 146s estimation. Default: 1 146s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 146s Dampen fraction modified estimates for low coverage 146s sites. Two parameters are unmodified and modified 146s pseudo read counts. This is equivalent to a beta prior 146s on the fraction estimate. Set to "0 0" to disable 146s dampened fraction estimation. Default: [2, 0] 146s 146s Output Argument: 146s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 146s Number of the most significant sites to store for 146s faster access. If a longer list of most significant 146s sites is required the list must be re-computed from 146s all batches. Very large values can increase RAM usage. 146s Default: 100000 146s 146s Multiprocessing Arguments: 146s --processes PROCESSES 146s Number of processes. Default: 1 146s 146s FAST5 Data Arguments: 146s --corrected-group CORRECTED_GROUP 146s FAST5 group created by resquiggle command. Default: 146s RawGenomeCorrected_000 146s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 146s FAST5 subgroup(s) (under /Analyses/[--basecall- 146s group]/) containing basecalls and created within 146s [--corrected-group] containing re-squiggle results. 146s Default: ['BaseCalled_template'] 146s 146s Miscellaneous Arguments: 146s --quiet, -q Don't print status information. 146s --help, -h Print this help message and exit 146s usage: tombo text_output browser_files 146s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 146s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 146s [--statistics-filename STATISTICS_FILENAME] 146s [--genome-fasta GENOME_FASTA] 146s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 146s [--browser-file-basename BROWSER_FILE_BASENAME] 146s [--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} ...]] 146s [--corrected-group CORRECTED_GROUP] 146s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 146s [--quiet] [--help] 146s 146s Data Arguments: 146s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 146s Directories containing fast5 files. 146s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 146s Set of directories containing fast5 files for control 146s reads, containing only canonical nucleotides. 146s --statistics-filename STATISTICS_FILENAME 146s File to save/load genomic base anchored statistics. 146s 146s Statistic Motif Filter Arguments: 146s --genome-fasta GENOME_FASTA 146s FASTA file used to re-squiggle. For faster sequence 146s access. 146s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 146s Ground truth, motif centered, modified base 146s descriptions for output filtering. Format descriptions 146s as: "motif:mod_pos:name". The mod_pos indicates the 146s modified base within the motif (1-based index). 146s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 146s output for identification of E. coli dam and dcm 146s methylation. 146s 146s Output Arguments: 146s --browser-file-basename BROWSER_FILE_BASENAME 146s Basename for output browser files. Two files (plus and 146s minus strand) will be produced for each --file-types 146s supplied. Filenames formatted as "[browser-file- 146s basename].[file- 146s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 146s Default: tombo_results 146s --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} ...] 146s Data types of genome browser files to produce. 146s Produced coverage files are in bedGraph format, while 146s all other file types will be in wiggle format 146s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 146s Default: "coverage" 146s 146s FAST5 Data Arguments: 146s --corrected-group CORRECTED_GROUP 146s FAST5 group created by resquiggle command. Default: 146s RawGenomeCorrected_000 146s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 146s FAST5 subgroup(s) (under /Analyses/[--basecall- 146s group]/) containing basecalls and created within 146s [--corrected-group] containing re-squiggle results. 146s Default: ['BaseCalled_template'] 146s 146s Miscellaneous Arguments: 146s --quiet, -q Don't print status information. 146s --help, -h Print this help message and exit 146s usage: tombo text_output signif_sequence_context --statistics-filename 146s STATISTICS_FILENAME 146s [--genome-fasta GENOME_FASTA] 146s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 146s [--num-regions NUM_REGIONS] 146s [--num-bases NUM_BASES] 146s [--sequences-filename SEQUENCES_FILENAME] 146s [--corrected-group CORRECTED_GROUP] 146s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 146s [--quiet] [--help] 146s 146s Required Argument: 146s --statistics-filename STATISTICS_FILENAME 146s File to save/load genomic base anchored statistics. 146s 146s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 146s --genome-fasta GENOME_FASTA 146s FASTA file used to re-squiggle. For faster sequence 146s access. 146s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 146s Directories containing fast5 files. 146s 146s Region Selection Arguments: 146s --num-regions NUM_REGIONS 146s Number of regions to plot. Default: 100 146s --num-bases NUM_BASES 146s Number of bases to plot/output. Default: 15 146s 146s Output Arguments: 146s --sequences-filename SEQUENCES_FILENAME 146s File for sequences from selected regions. Sequences 146s will be stored in FASTA format. Default: 146s tombo_results.significant_regions.fasta. 146s 146s FAST5 Data Arguments: 146s --corrected-group CORRECTED_GROUP 146s FAST5 group created by resquiggle command. Default: 146s RawGenomeCorrected_000 146s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 146s FAST5 subgroup(s) (under /Analyses/[--basecall- 146s group]/) containing basecalls and created within 146s [--corrected-group] containing re-squiggle results. 146s Default: ['BaseCalled_template'] 146s 146s Miscellaneous Arguments: 146s --quiet, -q Don't print status information. 146s --help, -h Print this help message and exit 147s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 147s [FAST5_BASEDIRS ...] 147s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 147s [--plot-standard-model] 147s [--plot-alternate-model {6mA,5mC,dam,dcm,CpG}] 147s [--overplot-threshold OVERPLOT_THRESHOLD] 147s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 147s [--num-regions NUM_REGIONS] 147s [--num-bases NUM_BASES] 147s [--pdf-filename PDF_FILENAME] 147s [--corrected-group CORRECTED_GROUP] 147s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 147s [--quiet] [--help] 147s 147s Required Argument: 147s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 147s Directories containing fast5 files. 147s 147s Comparison Arguments: 147s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 147s Set of directories containing fast5 files for control 147s reads, containing only canonical nucleotides. 147s --plot-standard-model 147s Add default standard model distribution to the plot. 147s --plot-alternate-model {6mA,5mC,dam,dcm,CpG} 147s Add alternative model distribution to the plot. 147s 147s Overplotting Arguments: 147s --overplot-threshold OVERPLOT_THRESHOLD 147s Coverage level to trigger alternative plot type 147s instead of raw signal. Default: 50 147s --overplot-type {Downsample,Boxplot,Quantile,Density} 147s Plot type for regions with higher coverage. Default: 147s Downsample 147s 147s Plotting Region Arguments: 147s --num-regions NUM_REGIONS 147s Number of regions to plot. Default: 10 147s --num-bases NUM_BASES 147s Number of bases to plot/output. Default: 21 147s 147s Output Argument: 147s --pdf-filename PDF_FILENAME 147s PDF filename to store plot(s). Default: 147s tombo_results.max_coverage.pdf 147s 147s FAST5 Data Arguments: 147s --corrected-group CORRECTED_GROUP 147s FAST5 group created by resquiggle command. Default: 147s RawGenomeCorrected_000 147s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 147s FAST5 subgroup(s) (under /Analyses/[--basecall- 147s group]/) containing basecalls and created within 147s [--corrected-group] containing re-squiggle results. 147s Default: ['BaseCalled_template'] 147s 147s Miscellaneous Arguments: 147s --quiet, -q Don't print status information. 147s --help, -h Print this help message and exit 147s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 147s [FAST5_BASEDIRS ...] --genome-locations 147s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 147s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 147s [--plot-standard-model] 147s [--plot-alternate-model {dam,5mC,6mA,dcm,CpG}] 147s [--overplot-threshold OVERPLOT_THRESHOLD] 147s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 147s [--num-bases NUM_BASES] 147s [--pdf-filename PDF_FILENAME] 147s [--corrected-group CORRECTED_GROUP] 147s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 147s [--quiet] [--help] 147s 147s Required Arguments: 147s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 147s Directories containing fast5 files. 147s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 147s Genomic locations at which to plot signal. Format 147s locations as "chrm:position[:strand] 147s [chrm2:position2[:strand2] ...]" (strand not 147s applicable for all applications) 147s 147s Comparison Arguments: 147s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 147s Set of directories containing fast5 files for control 147s reads, containing only canonical nucleotides. 147s --plot-standard-model 147s Add default standard model distribution to the plot. 147s --plot-alternate-model {dam,5mC,6mA,dcm,CpG} 147s Add alternative model distribution to the plot. 147s 147s Overplotting Arguments: 147s --overplot-threshold OVERPLOT_THRESHOLD 147s Coverage level to trigger alternative plot type 147s instead of raw signal. Default: 50 147s --overplot-type {Downsample,Boxplot,Quantile,Density} 147s Plot type for regions with higher coverage. Default: 147s Downsample 147s 147s Plotting Region Argument: 147s --num-bases NUM_BASES 147s Number of bases to plot/output. Default: 21 147s 147s Output Argument: 147s --pdf-filename PDF_FILENAME 147s PDF filename to store plot(s). Default: 147s tombo_results.genome_locations.pdf 147s 147s FAST5 Data Arguments: 147s --corrected-group CORRECTED_GROUP 147s FAST5 group created by resquiggle command. Default: 147s RawGenomeCorrected_000 147s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 147s FAST5 subgroup(s) (under /Analyses/[--basecall- 147s group]/) containing basecalls and created within 147s [--corrected-group] containing re-squiggle results. 147s Default: ['BaseCalled_template'] 147s 147s Miscellaneous Arguments: 147s --quiet, -q Don't print status information. 147s --help, -h Print this help message and exit 147s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 147s [FAST5_BASEDIRS ...] --motif MOTIF 147s --genome-fasta GENOME_FASTA 147s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 147s [--plot-standard-model] 147s [--plot-alternate-model {6mA,CpG,5mC,dcm,dam}] 147s [--overplot-threshold OVERPLOT_THRESHOLD] 147s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 147s [--num-regions NUM_REGIONS] 147s [--num-bases NUM_BASES] [--deepest-coverage] 147s [--pdf-filename PDF_FILENAME] 147s [--corrected-group CORRECTED_GROUP] 147s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 147s [--quiet] [--help] 147s 147s Required Arguments: 147s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 147s Directories containing fast5 files. 147s --motif MOTIF Motif of interest at which to plot signal and 147s statsitics. Supports IUPAC single letter codes (use T 147s for RNA). 147s --genome-fasta GENOME_FASTA 147s FASTA file used to re-squiggle. For faster sequence 147s access. 147s 147s Comparison Arguments: 147s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 147s Set of directories containing fast5 files for control 147s reads, containing only canonical nucleotides. 147s --plot-standard-model 147s Add default standard model distribution to the plot. 147s --plot-alternate-model {6mA,CpG,5mC,dcm,dam} 147s Add alternative model distribution to the plot. 147s 147s Overplotting Arguments: 147s --overplot-threshold OVERPLOT_THRESHOLD 147s Coverage level to trigger alternative plot type 147s instead of raw signal. Default: 50 147s --overplot-type {Downsample,Boxplot,Quantile,Density} 147s Plot type for regions with higher coverage. Default: 147s Downsample 147s 147s Plotting Region Arguments: 147s --num-regions NUM_REGIONS 147s Number of regions to plot. Default: 10 147s --num-bases NUM_BASES 147s Number of bases to plot/output. Default: 21 147s --deepest-coverage Plot the deepest coverage regions. 147s 147s Output Argument: 147s --pdf-filename PDF_FILENAME 147s PDF filename to store plot(s). Default: 147s tombo_results.motif_centered.pdf 147s 147s FAST5 Data Arguments: 147s --corrected-group CORRECTED_GROUP 147s FAST5 group created by resquiggle command. Default: 147s RawGenomeCorrected_000 147s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 147s FAST5 subgroup(s) (under /Analyses/[--basecall- 147s group]/) containing basecalls and created within 147s [--corrected-group] containing re-squiggle results. 147s Default: ['BaseCalled_template'] 147s 147s Miscellaneous Arguments: 147s --quiet, -q Don't print status information. 147s --help, -h Print this help message and exit 147s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 147s [FAST5_BASEDIRS ...] --control-fast5-basedirs 147s CONTROL_FAST5_BASEDIRS 147s [CONTROL_FAST5_BASEDIRS ...] 147s [--overplot-threshold OVERPLOT_THRESHOLD] 147s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 147s [--num-regions NUM_REGIONS] 147s [--num-bases NUM_BASES] 147s [--pdf-filename PDF_FILENAME] 147s [--sequences-filename SEQUENCES_FILENAME] 147s [--corrected-group CORRECTED_GROUP] 147s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 147s [--quiet] [--help] 147s 147s Required Arguments: 147s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 147s Directories containing fast5 files. 147s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 147s Set of directories containing fast5 files for control 147s reads, containing only canonical nucleotides. 147s 147s Overplotting Arguments: 147s --overplot-threshold OVERPLOT_THRESHOLD 147s Coverage level to trigger alternative plot type 147s instead of raw signal. Default: 50 147s --overplot-type {Downsample,Boxplot,Quantile,Density} 147s Plot type for regions with higher coverage. Default: 147s Downsample 147s 147s Plotting Region Arguments: 147s --num-regions NUM_REGIONS 147s Number of regions to plot. Default: 10 147s --num-bases NUM_BASES 147s Number of bases to plot/output. Default: 21 147s 147s Output Arguments: 147s --pdf-filename PDF_FILENAME 147s PDF filename to store plot(s). Default: 147s tombo_results.max_difference.pdf 147s --sequences-filename SEQUENCES_FILENAME 147s File for sequences from selected regions. Sequences 147s will be stored in FASTA format. Default: None. 147s 147s FAST5 Data Arguments: 147s --corrected-group CORRECTED_GROUP 147s FAST5 group created by resquiggle command. Default: 147s RawGenomeCorrected_000 147s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 147s FAST5 subgroup(s) (under /Analyses/[--basecall- 147s group]/) containing basecalls and created within 147s [--corrected-group] containing re-squiggle results. 147s Default: ['BaseCalled_template'] 147s 147s Miscellaneous Arguments: 147s --quiet, -q Don't print status information. 147s --help, -h Print this help message and exit 147s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 147s [FAST5_BASEDIRS ...] --statistics-filename 147s STATISTICS_FILENAME 147s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 147s [--plot-standard-model] 147s [--plot-alternate-model {dam,CpG,dcm,5mC,6mA}] 147s [--overplot-threshold OVERPLOT_THRESHOLD] 147s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 147s [--num-regions NUM_REGIONS] 147s [--num-bases NUM_BASES] 147s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 147s [--pdf-filename PDF_FILENAME] 147s [--sequences-filename SEQUENCES_FILENAME] 147s [--corrected-group CORRECTED_GROUP] 147s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 147s [--quiet] [--help] 147s 147s Required Arguments: 147s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 147s Directories containing fast5 files. 147s --statistics-filename STATISTICS_FILENAME 147s File to save/load genomic base anchored statistics. 147s 147s Comparison Arguments: 147s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 147s Set of directories containing fast5 files for control 147s reads, containing only canonical nucleotides. 147s --plot-standard-model 147s Add default standard model distribution to the plot. 147s --plot-alternate-model {dam,CpG,dcm,5mC,6mA} 147s Add alternative model distribution to the plot. 147s 147s Overplotting Arguments: 147s --overplot-threshold OVERPLOT_THRESHOLD 147s Coverage level to trigger alternative plot type 147s instead of raw signal. Default: 50 147s --overplot-type {Downsample,Boxplot,Quantile,Density} 147s Plot type for regions with higher coverage. Default: 147s Downsample 147s 147s Plotting Region Arguments: 147s --num-regions NUM_REGIONS 147s Number of regions to plot. Default: 10 147s --num-bases NUM_BASES 147s Number of bases to plot/output. Default: 21 147s 147s Statistical Argument: 147s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 147s Dampen fraction modified estimates for low coverage 147s sites. Two parameters are unmodified and modified 147s pseudo read counts. This is equivalent to a beta prior 147s on the fraction estimate. Set to "0 0" to disable 147s dampened fraction estimation. Default: [2, 0] 147s 147s Output Arguments: 147s --pdf-filename PDF_FILENAME 147s PDF filename to store plot(s). Default: 147s tombo_results.significant_difference.pdf 147s --sequences-filename SEQUENCES_FILENAME 147s File for sequences from selected regions. Sequences 147s will be stored in FASTA format. Default: None. 147s 147s FAST5 Data Arguments: 147s --corrected-group CORRECTED_GROUP 147s FAST5 group created by resquiggle command. Default: 147s RawGenomeCorrected_000 147s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 147s FAST5 subgroup(s) (under /Analyses/[--basecall- 147s group]/) containing basecalls and created within 147s [--corrected-group] containing re-squiggle results. 147s Default: ['BaseCalled_template'] 147s 147s Miscellaneous Arguments: 147s --quiet, -q Don't print status information. 147s --help, -h Print this help message and exit 147s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 147s [FAST5_BASEDIRS ...] --motif MOTIF 147s --statistics-filename STATISTICS_FILENAME 147s --genome-fasta GENOME_FASTA 147s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 147s [--plot-standard-model] 147s [--plot-alternate-model {dam,dcm,5mC,6mA,CpG}] 147s [--overplot-threshold OVERPLOT_THRESHOLD] 147s [--num-regions NUM_REGIONS] 147s [--num-context NUM_CONTEXT] 147s [--num-statistics NUM_STATISTICS] 147s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 147s [--pdf-filename PDF_FILENAME] 147s [--corrected-group CORRECTED_GROUP] 147s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 147s [--quiet] [--help] 147s 147s Required Arguments: 147s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 147s Directories containing fast5 files. 147s --motif MOTIF Motif of interest at which to plot signal and 147s statsitics. Supports IUPAC single letter codes (use T 147s for RNA). 147s --statistics-filename STATISTICS_FILENAME 147s File to save/load genomic base anchored statistics. 147s --genome-fasta GENOME_FASTA 147s FASTA file used to re-squiggle. For faster sequence 147s access. 147s 147s Comparison Arguments: 147s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 147s Set of directories containing fast5 files for control 147s reads, containing only canonical nucleotides. 147s --plot-standard-model 147s Add default standard model distribution to the plot. 147s --plot-alternate-model {dam,dcm,5mC,6mA,CpG} 147s Add alternative model distribution to the plot. 147s 147s Overplotting Argument: 147s --overplot-threshold OVERPLOT_THRESHOLD 147s Coverage level to trigger alternative plot type 147s instead of raw signal. Default: 50 147s 147s Plotting Region Arguments: 147s --num-regions NUM_REGIONS 147s Number of regions to plot. Default: 3 147s --num-context NUM_CONTEXT 147s Number of context bases around motif. Default: 5 147s --num-statistics NUM_STATISTICS 147s Number of motif centered regions to include in 147s statistic distributions. Default: 200 147s 147s Statistical Argument: 147s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 147s Dampen fraction modified estimates for low coverage 147s sites. Two parameters are unmodified and modified 147s pseudo read counts. This is equivalent to a beta prior 147s on the fraction estimate. Set to "0 0" to disable 147s dampened fraction estimation. Default: [2, 0] 147s 147s Output Argument: 147s --pdf-filename PDF_FILENAME 147s PDF filename to store plot(s). Default: 147s tombo_results.motif_statistics.pdf 147s 147s FAST5 Data Arguments: 147s --corrected-group CORRECTED_GROUP 147s FAST5 group created by resquiggle command. Default: 147s RawGenomeCorrected_000 147s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 147s FAST5 subgroup(s) (under /Analyses/[--basecall- 147s group]/) containing basecalls and created within 147s [--corrected-group] containing re-squiggle results. 147s Default: ['BaseCalled_template'] 147s 147s Miscellaneous Arguments: 147s --quiet, -q Don't print status information. 147s --help, -h Print this help message and exit 147s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 147s [GENOME_LOCATIONS ...] 147s --per-read-statistics-filename 147s PER_READ_STATISTICS_FILENAME 147s [--genome-fasta GENOME_FASTA] 147s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 147s [--num-reads NUM_READS] [--num-bases NUM_BASES] 147s [--box-center] [--pdf-filename PDF_FILENAME] 147s [--corrected-group CORRECTED_GROUP] 147s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 147s [--quiet] [--help] 147s 147s Required Arguments: 147s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 147s Genomic locations at which to plot signal. Format 147s locations as "chrm:position[:strand] 147s [chrm2:position2[:strand2] ...]" (strand not 147s applicable for all applications) 147s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 147s Binary file containing per-read statistics from 147s statistical testing. 147s 147s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 147s --genome-fasta GENOME_FASTA 147s FASTA file used to re-squiggle. For faster sequence 147s access. 147s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 147s Directories containing fast5 files. 147s 147s Plotting Region Arguments: 147s --num-reads NUM_READS 147s Number of reads to plot. Default: 100 147s --num-bases NUM_BASES 147s Number of bases to plot/output. Default: 51 147s --box-center Plot a box around the central base. 147s 147s Output Argument: 147s --pdf-filename PDF_FILENAME 147s PDF filename to store plot(s). Default: 147s tombo_results.per_read_stats.pdf 147s 147s FAST5 Data Arguments: 147s --corrected-group CORRECTED_GROUP 147s FAST5 group created by resquiggle command. Default: 147s RawGenomeCorrected_000 147s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 147s FAST5 subgroup(s) (under /Analyses/[--basecall- 147s group]/) containing basecalls and created within 147s [--corrected-group] containing re-squiggle results. 147s Default: ['BaseCalled_template'] 147s 147s Miscellaneous Arguments: 147s --quiet, -q Don't print status information. 147s --help, -h Print this help message and exit 147s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 147s [STATISTICS_FILENAMES ...] 147s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 147s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 147s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 147s [--genome-fasta GENOME_FASTA] 147s [--pdf-filename PDF_FILENAME] 147s [--statistics-per-block STATISTICS_PER_BLOCK] 147s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 147s [--quiet] [--help] 147s 147s Required Argument: 147s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 147s Files to load genomic base anchored statistics. 147s 147s Ground Truth Arguments (provide bed files or motifs): 147s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 147s Modification description and bed format files 147s containing single base locations of ground truth 147s modified sites. Bed files should contain 6 fields 147s including strand. Format descriptions as 147s "mod_name:locs.bed". Example: "CpG 147s bisulfite":bisulfite_locs.bed 147s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 147s Bed format files containing single base locations of 147s ground truth unmodified sites. Bed files should 147s contain 6 fields including strand. 147s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 147s Ground truth, motif centered, modified base 147s descriptions for computing ROC and PR curves. Each 147s statistics file is associated with a set of motif 147s descriptions. Format descriptions as: 147s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 147s mod_pos indicates the alternate-base within the motif 147s (1-based index). Example: CCWGG:2:"dcm 147s 5mC"::GATC:2:"dam 6mA" would assess the performance of 147s a single Tombo statistics file for identification of 147s E. coli dam and dcm methylation. 147s --genome-fasta GENOME_FASTA 147s FASTA file used to re-squiggle. For faster sequence 147s access. 147s 147s Output Arguments: 147s --pdf-filename PDF_FILENAME 147s PDF filename to store plot(s). Default: 147s tombo_results.roc.pdf 147s 147s Down-sampling Arguments: 147s --statistics-per-block STATISTICS_PER_BLOCK 147s Number of randomly selected per-read, per-base 147s statistics to extract from each genomic block for 147s plotting. Default: Include all stats 147s --total-statistics-limit TOTAL_STATISTICS_LIMIT 147s Total per-read statistics to be extracted for 147s plotting. Avoids memory overflow for large runs. 147s Default: 5000000 147s 147s Miscellaneous Arguments: 147s --quiet, -q Don't print status information. 147s --help, -h Print this help message and exit 148s usage: tombo plot per_read_roc --per-read-statistics-filenames 148s PER_READ_STATISTICS_FILENAMES 148s [PER_READ_STATISTICS_FILENAMES ...] 148s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 148s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 148s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 148s [--genome-fasta GENOME_FASTA] 148s [--statistics-per-block STATISTICS_PER_BLOCK] 148s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 148s [--pdf-filename PDF_FILENAME] [--quiet] 148s [--help] 148s 148s Required Argument: 148s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 148s Binary files containing per-read statistics from 148s statistical testing. 148s 148s Ground Truth Arguments (provide bed files or motifs): 148s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 148s Modification description and bed format files 148s containing single base locations of ground truth 148s modified sites. Bed files should contain 6 fields 148s including strand. Format descriptions as 148s "mod_name:locs.bed". Example: "CpG 148s bisulfite":bisulfite_locs.bed 148s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 148s Bed format files containing single base locations of 148s ground truth unmodified sites. Bed files should 148s contain 6 fields including strand. 148s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 148s Ground truth, motif centered, modified base 148s descriptions for computing ROC and PR curves. Each 148s statistics file is associated with a set of motif 148s descriptions. Format descriptions as: 148s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 148s mod_pos indicates the alternate-base within the motif 148s (1-based index). Example: CCWGG:2:"dcm 148s 5mC"::GATC:2:"dam 6mA" would assess the performance of 148s a single Tombo statistics file for identification of 148s E. coli dam and dcm methylation. 148s --genome-fasta GENOME_FASTA 148s FASTA file used to re-squiggle. For faster sequence 148s access. 148s 148s Down-sampling Arguments: 148s --statistics-per-block STATISTICS_PER_BLOCK 148s Number of randomly selected per-read, per-base 148s statistics to extract from each genomic block for 148s plotting. Default: 100000 148s --total-statistics-limit TOTAL_STATISTICS_LIMIT 148s Total per-read statistics to be extracted for 148s plotting. Avoids memory overflow for large runs. 148s Default: 5000000 148s 148s Output Arguments: 148s --pdf-filename PDF_FILENAME 148s PDF filename to store plot(s). Default: 148s tombo_results.per_reads_roc.pdf 148s 148s Miscellaneous Arguments: 148s --quiet, -q Don't print status information. 148s --help, -h Print this help message and exit 148s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 148s [--upstream-bases {0,1,2,3,4}] 148s [--downstream-bases {0,1,2,3,4}] [--read-mean] 148s [--num-kmer-threshold NUM_KMER_THRESHOLD] 148s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 148s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 148s [--corrected-group CORRECTED_GROUP] 148s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 148s [--quiet] [--help] 148s 148s Required Argument: 148s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 148s Directories containing fast5 files. 148s 148s Data Processing Arguments: 148s --upstream-bases {0,1,2,3,4} 148s Upstream bases in k-mer. Default: 1 148s --downstream-bases {0,1,2,3,4} 148s Downstream bases in k-mer. Default: 2 148s --read-mean Plot k-mer means across whole reads as opposed to 148s individual k-mer event levels. 148s --num-kmer-threshold NUM_KMER_THRESHOLD 148s Observations of each k-mer required to include a read 148s in read level averages. Default: 1 148s 148s Plotting Region Arguments: 148s --num-reads NUM_READS 148s Number of reads to plot. Default: 100 148s 148s Output Arguments: 148s --pdf-filename PDF_FILENAME 148s PDF filename to store plot(s). Default: 148s tombo_results.kmer_distribution.pdf 148s --r-data-filename R_DATA_FILENAME 148s Filename to save R data structure. Default: Don't save 148s --dont-plot Don't plot result. Useful to produce only R data file. 148s 148s FAST5 Data Arguments: 148s --corrected-group CORRECTED_GROUP 148s FAST5 group created by resquiggle command. Default: 148s RawGenomeCorrected_000 148s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 148s FAST5 subgroup(s) (under /Analyses/[--basecall- 148s group]/) containing basecalls and created within 148s [--corrected-group] containing re-squiggle results. 148s Default: ['BaseCalled_template'] 148s 148s Miscellaneous Arguments: 148s --quiet, -q Don't print status information. 148s --help, -h Print this help message and exit 148s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 148s [FAST5_BASEDIRS ...] 148s --control-fast5-basedirs 148s CONTROL_FAST5_BASEDIRS 148s [CONTROL_FAST5_BASEDIRS ...] 148s --statistics-filename 148s STATISTICS_FILENAME 148s [--genome-fasta GENOME_FASTA] 148s [--processes PROCESSES] 148s [--num-regions NUM_REGIONS] 148s [--num-bases NUM_BASES] 148s [--slide-span SLIDE_SPAN] 148s [--pdf-filename PDF_FILENAME] 148s [--r-data-filename R_DATA_FILENAME] 148s [--corrected-group CORRECTED_GROUP] 148s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 148s [--quiet] [--help] 148s 148s Required Arguments: 148s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 148s Directories containing fast5 files. 148s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 148s Set of directories containing fast5 files for control 148s reads, containing only canonical nucleotides. 148s --statistics-filename STATISTICS_FILENAME 148s File to save/load genomic base anchored statistics. 148s 148s FASTA Sequence Argument: 148s --genome-fasta GENOME_FASTA 148s FASTA file used to re-squiggle. For faster sequence 148s access. 148s 148s Multiprocessing Argument: 148s --processes PROCESSES 148s Number of processes. Default: 1 148s 148s Plotting Region Arguments: 148s --num-regions NUM_REGIONS 148s Number of regions to plot. Default: 10 148s --num-bases NUM_BASES 148s Number of bases to plot/output. Default: 21 148s --slide-span SLIDE_SPAN 148s Number of bases offset over which to search when 148s computing distances for signal cluster plotting. 148s Default: 0 (exact position) 148s 148s Output Arguments: 148s --pdf-filename PDF_FILENAME 148s PDF filename to store plot(s). Default: 148s tombo_results.signal_clusters.pdf 148s --r-data-filename R_DATA_FILENAME 148s Filename to save R data structure. Default: Don't save 148s 148s FAST5 Data Arguments: 148s --corrected-group CORRECTED_GROUP 148s FAST5 group created by resquiggle command. Default: 148s RawGenomeCorrected_000 148s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 148s FAST5 subgroup(s) (under /Analyses/[--basecall- 148s group]/) containing basecalls and created within 148s [--corrected-group] containing re-squiggle results. 148s Default: ['BaseCalled_template'] 148s 148s Miscellaneous Arguments: 148s --quiet, -q Don't print status information. 148s --help, -h Print this help message and exit 148s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 148s 148s Required Arguments: 148s fast5s_basedir Directory containing fast5 files. All files ending in 148s "fast5" found recursively within this base directory will be 148s processed. 148s 148s Miscellaneous Arguments: 148s --quiet, -q Don't print status information. 148s --help, -h Print this help message and exit 148s usage: tombo build_model event_resquiggle 148s [--minimap2-executable MINIMAP2_EXECUTABLE] 148s [--minimap2-index MINIMAP2_INDEX] 148s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 148s [--graphmap-executable GRAPHMAP_EXECUTABLE] 148s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 148s [--normalization-type {median,pA,pA_raw,none}] 148s [--pore-model-filename PORE_MODEL_FILENAME] 148s [--outlier-threshold OUTLIER_THRESHOLD] 148s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 148s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 148s [--timeout TIMEOUT] 148s [--cpts-limit CPTS_LIMIT] 148s [--skip-index] [--overwrite] 148s [--failed-reads-filename FAILED_READS_FILENAME] 148s [--include-event-stdev] 148s [--corrected-group CORRECTED_GROUP] 148s [--basecall-group BASECALL_GROUP] 148s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 148s [--processes PROCESSES] 148s [--align-processes ALIGN_PROCESSES] 148s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 148s [--resquiggle-processes RESQUIGGLE_PROCESSES] 148s [--quiet] [--help] 148s fast5s_basedir reference_fasta 148s 148s Required Arguments: 148s fast5s_basedir Directory containing fast5 files. All files ending in 148s "fast5" found recursively within this base directory 148s will be processed. 148s reference_fasta Reference genome/transcriptome FASTA file for mapping. 148s 148s Mapper Arguments (One mapper is required): 148s --minimap2-executable MINIMAP2_EXECUTABLE 148s Path to minimap2 executable. 148s --minimap2-index MINIMAP2_INDEX 148s Path to minimap2 index (with map-ont preset) file 148s corresponding to the [genome_fasta] provided. 148s --bwa-mem-executable BWA_MEM_EXECUTABLE 148s Path to bwa-mem executable. 148s --graphmap-executable GRAPHMAP_EXECUTABLE 148s Path to graphmap executable. 148s --alignment-batch-size ALIGNMENT_BATCH_SIZE 148s Number of reads included in each alignment call. Note: 148s A new system mapping call is made for each batch 148s (including loading of the genome), so it is advised to 148s use larger values for larger genomes. Default: 1000 148s 148s Signal Processing Arguments: 148s --normalization-type {median,pA,pA_raw,none} 148s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 148s as in the ONT events (using offset, range and 148s digitization), "pA": k-mer-based correction for pA 148s drift as in nanopolish (requires [--pore-model- 148s filename]), "median": median and MAD from raw signal. 148s Default: median 148s --pore-model-filename PORE_MODEL_FILENAME 148s File containing kmer model parameters (level_mean and 148s level_stdv) used in order to compute kmer-based 148s corrected pA values. E.g. https://github.com/jts/nanop 148s olish/blob/master/etc/r9- 148s models/template_median68pA.5mers.model 148s --outlier-threshold OUTLIER_THRESHOLD 148s Windosrize the signal at this number of scale values. 148s Negative value disables outlier clipping. Default: 148s 5.000000 148s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 148s Specify the 2 parameters for segmentation 1) running 148s neighboring windows width 2) minimum raw observations 148s per genomic base. Sample type defaults: RNA : 12 6 || 148s DNA : 5 3 148s 148s Read Filtering Arguments: 148s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 148s Filter reads based on observations per base percentile 148s thresholds. Format thresholds as "percentile:thresh 148s [pctl2:thresh2 ...]". For example to filter reads with 148s 99th pctl > 200 obs/base or max > 5k obs/base use 148s "99:200 100:5000". 148s --timeout TIMEOUT Timeout in seconds for processing a single read. 148s Default: No timeout. 148s --cpts-limit CPTS_LIMIT 148s Maximum number of changepoints to find within a single 148s indel group. Default: No limit. 148s 148s Input/Output Arguments: 148s --skip-index Skip creation of tombo index. This drastically slows 148s downstream tombo commands. Default stores tombo index 148s named ".[--fast5-basedir].[--corrected- 148s group].tombo.index" to be loaded automatically for 148s downstream commands. 148s --overwrite Overwrite previous corrected group in FAST5 files. 148s Note: only effects --corrected-group or --new- 148s corrected-group. 148s --failed-reads-filename FAILED_READS_FILENAME 148s Output failed read filenames with assoicated error. 148s Default: Do not store failed reads. 148s --include-event-stdev 148s Include corrected event standard deviation in output 148s FAST5 data. 148s 148s FAST5 Data Arguments: 148s --corrected-group CORRECTED_GROUP 148s FAST5 group created by resquiggle command. Default: 148s RawGenomeCorrected_000 148s --basecall-group BASECALL_GROUP 148s FAST5 group obtain original basecalls (under Analyses 148s group). Default: Basecall_1D_000 148s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 148s FAST5 subgroup(s) (under /Analyses/[--basecall- 148s group]/) containing basecalls and created within 148s [--corrected-group] containing re-squiggle results. 148s Default: ['BaseCalled_template'] 148s 148s Multiprocessing Arguments: 148s --processes PROCESSES 148s Number of processes. Default: 2 148s --align-processes ALIGN_PROCESSES 148s Number of processes to use for parsing and aligning 148s original basecalls. Each process will independently 148s load the genome into memory, so use caution with 148s larger genomes (e.g. human). Default: 1 148s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 148s Number of threads to use for aligner system call. 148s Default: [--processes] / (2 * [--align-processes)] 148s --resquiggle-processes RESQUIGGLE_PROCESSES 148s Number of processes to use for resquiggle algorithm. 148s Default: [--processes] / 2 148s 148s Miscellaneous Arguments: 148s --quiet, -q Don't print status information. 148s --help, -h Print this help message and exit 148s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 148s [FAST5_BASEDIRS ...] 148s --tombo-model-filename 148s TOMBO_MODEL_FILENAME 148s [--estimate-mean] 148s [--kmer-specific-sd] 148s [--upstream-bases {0,1,2,3,4}] 148s [--downstream-bases {0,1,2,3,4}] 148s [--minimum-test-reads MINIMUM_TEST_READS] 148s [--coverage-threshold COVERAGE_THRESHOLD] 148s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 148s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 148s [--processes PROCESSES] 148s [--corrected-group CORRECTED_GROUP] 148s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 148s [--quiet] [--help] 148s 148s Required Arguments: 148s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 148s Directories containing fast5 files. 148s --tombo-model-filename TOMBO_MODEL_FILENAME 148s Filename to save Tombo model. 148s 148s Modeling Arguments: 148s --estimate-mean Use the mean instead of median for model level 148s estimation. Note: This can cause poor fits due to 148s outliers 148s --kmer-specific-sd Estimate standard deviation for each k-mers 148s individually. 148s --upstream-bases {0,1,2,3,4} 148s Upstream bases in k-mer. Default: 1 148s --downstream-bases {0,1,2,3,4} 148s Downstream bases in k-mer. Default: 2 148s 148s Filtering Arguments: 148s --minimum-test-reads MINIMUM_TEST_READS 148s Number of reads required at a position to perform 148s significance testing or contribute to model 148s estimation. Default: 10 148s --coverage-threshold COVERAGE_THRESHOLD 148s Maximum mean coverage per region when estimating k-mer 148s model (limits compute time for deep samples). Default: 148s 100 148s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 148s Number of each k-mer observations required in order to 148s produce a reference (genomic locations for standard 148s reference and per-read for alternative reference). 148s Default: 5 148s 148s Multiprocessing Arguments: 148s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 148s Size of regions over which to multiprocesses statistic 148s computation. For very deep samples a smaller value is 148s recommmended in order to control memory consumption. 148s Default: 10000 148s --processes PROCESSES 148s Number of processes. Default: 1 148s 148s FAST5 Data Arguments: 148s --corrected-group CORRECTED_GROUP 148s FAST5 group created by resquiggle command. Default: 148s RawGenomeCorrected_000 148s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 148s FAST5 subgroup(s) (under /Analyses/[--basecall- 148s group]/) containing basecalls and created within 148s [--corrected-group] containing re-squiggle results. 148s Default: ['BaseCalled_template'] 148s 148s Miscellaneous Arguments: 148s --quiet, -q Don't print status information. 148s --help, -h Print this help message and exit 148s usage: tombo build_model estimate_alt_reference --alternate-model-filename 148s ALTERNATE_MODEL_FILENAME 148s --alternate-model-name 148s ALTERNATE_MODEL_NAME 148s --alternate-model-base 148s {A,C,G,T} 148s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 148s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 148s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 148s [--control-density-filename CONTROL_DENSITY_FILENAME] 148s [--dna] [--rna] 148s [--tombo-model-filename TOMBO_MODEL_FILENAME] 148s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 148s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 148s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 148s [--save-density-basename SAVE_DENSITY_BASENAME] 148s [--processes PROCESSES] 148s [--corrected-group CORRECTED_GROUP] 148s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 148s [--quiet] [--help] 148s 148s Required Arguments: 148s --alternate-model-filename ALTERNATE_MODEL_FILENAME 148s Tombo model for alternative likelihood ratio 148s significance testing. 148s --alternate-model-name ALTERNATE_MODEL_NAME 148s A short name to associate with this alternate model 148s (e.g. 5mC, 6mA, etc.). This text will be included in 148s output filenames when this model is used for testing. 148s --alternate-model-base {A,C,G,T} 148s Non-standard base is an alternative to this base. 148s 148s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 148s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 148s Directories containing fast5 files. 148s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 148s Set of directories containing fast5 files for control 148s reads, containing only canonical nucleotides. 148s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 148s File containing k-mer level kernel density estimates 148s for the alternative sample saved using --save-density- 148s basename. 148s --control-density-filename CONTROL_DENSITY_FILENAME 148s File containing k-mer level kernel density estimates 148s for the control sample saved using --save-density- 148s basename. 148s 148s Standard Model Arguments: 148s --dna Explicitly select canonical DNA model. Default: 148s Automatically determine from FAST5s 148s --rna Explicitly select canonical RNA model. Default: 148s Automatically determine from FAST5s 148s --tombo-model-filename TOMBO_MODEL_FILENAME 148s Tombo model filename. If no file is provided, the 148s default DNA or RNA Tombo model will be used. 148s 148s Model Fitting Arguments: 148s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 148s When esitmating the alternative base incorporation 148s rate, this percent of k-mers are assumed to have 148s significantly shifted signal so the alternative 148s distribution minimally overlaps the standard base 148s distribution. Default: 5.000000 148s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 148s Bandwidth applied when performing Gaussian kernal 148s density esitmation on standard and alternative base 148s signal distributions. Default: 0.050000 148s 148s Filtering Argument: 148s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 148s Number of each k-mer observations required in order to 148s produce a reference (genomic locations for standard 148s reference and per-read for alternative reference). 148s Default: 1000 148s 148s Output Argument: 148s --save-density-basename SAVE_DENSITY_BASENAME 148s Basename to save alternative model estimation density 148s estimation information. See scripts/debug_est_alt.R 148s for info use example. Default: Don't save. 148s 148s Multiprocessing Arguments: 148s --processes PROCESSES 148s Number of processes. Default: 1 148s 148s FAST5 Data Arguments: 148s --corrected-group CORRECTED_GROUP 148s FAST5 group created by resquiggle command. Default: 148s RawGenomeCorrected_000 148s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 148s FAST5 subgroup(s) (under /Analyses/[--basecall- 148s group]/) containing basecalls and created within 148s [--corrected-group] containing re-squiggle results. 148s Default: ['BaseCalled_template'] 148s 148s Miscellaneous Arguments: 148s --quiet, -q Don't print status information. 148s --help, -h Print this help message and exit 148s This test only tests the help system 148s There is an extensive test in 148s 148s tombo/tests/shell_tests.sh 148s 148s but this requires to download larger data 148s sets which is not done for the moment. 149s autopkgtest [09:51:30]: test run-unit-test: -----------------------] 149s run-unit-test PASS 149s autopkgtest [09:51:30]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 150s autopkgtest [09:51:31]: @@@@@@@@@@@@@@@@@@@@ summary 150s run-unit-test PASS 162s nova [W] Skipping flock in bos03-arm64 162s Creating nova instance adt-plucky-arm64-tombo-20241030-094901-juju-7f2275-prod-proposed-migration-environment-2-12964161-7681-43fc-b7c8-7cc6c1647e0d from image adt/ubuntu-plucky-arm64-server-20241029.img (UUID b10dda10-7c97-4e89-a4a8-9b73e189f96e)...