0s autopkgtest [16:57:55]: starting date and time: 2024-11-14 16:57:55+0000 0s autopkgtest [16:57:55]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:57:55]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gmb7b0_m/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-32.secgroup --name adt-plucky-s390x-tombo-20241114-165754-juju-7f2275-prod-proposed-migration-environment-20-f92f8426-d4b7-434a-a35f-482ce9234058 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -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/ 97s autopkgtest [16:59:32]: testbed dpkg architecture: s390x 98s autopkgtest [16:59:33]: testbed apt version: 2.9.8 98s autopkgtest [16:59:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 98s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 99s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [951 kB] 99s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 99s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 99s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.6 kB] 99s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [117 kB] 99s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [674 kB] 99s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [5020 B] 99s Fetched 1947 kB in 1s (2592 kB/s) 99s Reading package lists... 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s Calculating upgrade... 101s The following packages will be upgraded: 101s libcap-ng0 pastebinit python3-systemd 102s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Need to get 77.8 kB of archives. 102s After this operation, 123 kB of additional disk space will be used. 102s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libcap-ng0 s390x 0.8.5-3build1 [15.9 kB] 102s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pastebinit all 1.7.1-1 [14.9 kB] 102s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-systemd s390x 235-1build5 [46.9 kB] 102s Fetched 77.8 kB in 0s (234 kB/s) 102s (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 ... 55511 files and directories currently installed.) 102s Preparing to unpack .../libcap-ng0_0.8.5-3build1_s390x.deb ... 102s Unpacking libcap-ng0:s390x (0.8.5-3build1) over (0.8.5-1) ... 102s Setting up libcap-ng0:s390x (0.8.5-3build1) ... 102s (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 ... 55511 files and directories currently installed.) 102s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 102s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 102s Preparing to unpack .../python3-systemd_235-1build5_s390x.deb ... 102s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 102s Setting up pastebinit (1.7.1-1) ... 102s Setting up python3-systemd (235-1build5) ... 102s Processing triggers for man-db (2.12.1-3) ... 103s Processing triggers for libc-bin (2.40-1ubuntu3) ... 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 103s 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 104s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 105s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s autopkgtest [16:59:43]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 108s autopkgtest [16:59:43]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 111s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (dsc) [2291 B] 111s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (tar) [22.3 MB] 111s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (diff) [7100 B] 111s gpgv: Signature made Wed Apr 10 17:15:32 2024 UTC 111s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 111s gpgv: Can't check signature: No public key 111s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6build1.dsc: no acceptable signature found 111s autopkgtest [16:59:46]: testing package tombo version 1.5.1-6build1 112s autopkgtest [16:59:47]: build not needed 113s autopkgtest [16:59:48]: test run-unit-test: preparing testbed 114s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Starting pkgProblemResolver with broken count: 0 115s Starting 2 pkgProblemResolver with broken count: 0 115s Done 115s The following additional packages will be installed: 115s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 115s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 115s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 115s python3-decorator python3-h5py python3-h5py-serial python3-mappy 115s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 115s tombo-doc 115s Suggested packages: 115s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 115s gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 115s Recommended packages: 115s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 115s python3-rpy2 115s The following NEW packages will be installed: 115s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 115s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 115s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 115s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 115s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 115s tombo-doc 115s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 115s Need to get 63.9 MB/63.9 MB of archives. 115s After this operation, 210 MB of additional disk space will be used. 115s Get:1 /tmp/autopkgtest.5fGDGD/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [712 B] 115s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-lato all 2.015-1 [2781 kB] 116s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 116s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 116s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 116s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 116s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB] 116s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 116s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-103-1t64 s390x 1.10.10+repack-4ubuntu3 [1426 kB] 116s Get:10 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-100t64 s390x 1.10.10+repack-4ubuntu3 [58.0 kB] 116s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 116s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 116s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-sphinxdoc all 7.4.7-4 [158 kB] 116s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 116s Get:15 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 116s Get:16 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B] 116s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 116s Get:18 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-numpy s390x 1:1.26.4+ds-11ubuntu1 [4602 kB] 116s Get:19 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py-serial s390x 3.11.0-5ubuntu1 [1151 kB] 116s Get:20 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py all 3.11.0-5ubuntu1 [7974 B] 116s Get:21 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mappy s390x 2.27+dfsg-1 [208 kB] 116s Get:22 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-tqdm all 4.67.0-1 [91.6 kB] 116s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 116s Get:24 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.13.1-5 [17.5 MB] 117s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x tombo s390x 1.5.1-6build1 [465 kB] 117s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 117s Get:27 http://ftpmaster.internal/ubuntu plucky/universe s390x tombo-doc all 1.5.1-6build1 [21.7 MB] 118s Fetched 63.9 MB in 3s (24.2 MB/s) 118s Selecting previously unselected package fonts-lato. 118s (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 ... 55516 files and directories currently installed.) 118s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 118s Unpacking fonts-lato (2.015-1) ... 118s Selecting previously unselected package fonts-font-awesome. 118s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 118s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 118s Selecting previously unselected package fonts-mathjax. 118s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 118s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 118s Selecting previously unselected package libaec0:s390x. 118s Preparing to unpack .../03-libaec0_1.1.3-1_s390x.deb ... 118s Unpacking libaec0:s390x (1.1.3-1) ... 118s Selecting previously unselected package libblas3:s390x. 118s Preparing to unpack .../04-libblas3_3.12.0-3build2_s390x.deb ... 118s Unpacking libblas3:s390x (3.12.0-3build2) ... 118s Selecting previously unselected package libgfortran5:s390x. 118s Preparing to unpack .../05-libgfortran5_14.2.0-8ubuntu1_s390x.deb ... 118s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ... 118s Selecting previously unselected package libsz2:s390x. 118s Preparing to unpack .../06-libsz2_1.1.3-1_s390x.deb ... 118s Unpacking libsz2:s390x (1.1.3-1) ... 118s Selecting previously unselected package libhdf5-103-1t64:s390x. 118s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_s390x.deb ... 118s Unpacking libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 118s Selecting previously unselected package libhdf5-hl-100t64:s390x. 118s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_s390x.deb ... 118s Unpacking libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ... 118s Selecting previously unselected package libjs-jquery. 118s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 118s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 118s Selecting previously unselected package libjs-underscore. 118s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 118s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 118s Selecting previously unselected package libjs-sphinxdoc. 118s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-4_all.deb ... 118s Unpacking libjs-sphinxdoc (7.4.7-4) ... 118s Selecting previously unselected package liblapack3:s390x. 118s Preparing to unpack .../12-liblapack3_3.12.0-3build2_s390x.deb ... 118s Unpacking liblapack3:s390x (3.12.0-3build2) ... 118s Selecting previously unselected package liblbfgsb0:s390x. 118s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 118s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 118s Selecting previously unselected package liblzf1:s390x. 118s Preparing to unpack .../14-liblzf1_3.6-4_s390x.deb ... 118s Unpacking liblzf1:s390x (3.6-4) ... 119s Selecting previously unselected package python3-decorator. 119s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 119s Unpacking python3-decorator (5.1.1-5) ... 119s Selecting previously unselected package python3-numpy. 119s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-11ubuntu1_s390x.deb ... 119s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 119s Selecting previously unselected package python3-h5py-serial. 119s Preparing to unpack .../17-python3-h5py-serial_3.11.0-5ubuntu1_s390x.deb ... 119s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 119s Selecting previously unselected package python3-h5py. 119s Preparing to unpack .../18-python3-h5py_3.11.0-5ubuntu1_all.deb ... 119s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 119s Selecting previously unselected package python3-mappy. 119s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1_s390x.deb ... 119s Unpacking python3-mappy (2.27+dfsg-1) ... 119s Selecting previously unselected package python3-tqdm. 119s Preparing to unpack .../20-python3-tqdm_4.67.0-1_all.deb ... 119s Unpacking python3-tqdm (4.67.0-1) ... 119s Selecting previously unselected package sphinx-rtd-theme-common. 119s Preparing to unpack .../21-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 119s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 119s Selecting previously unselected package python3-scipy. 119s Preparing to unpack .../22-python3-scipy_1.13.1-5_s390x.deb ... 119s Unpacking python3-scipy (1.13.1-5) ... 119s Selecting previously unselected package tombo. 119s Preparing to unpack .../23-tombo_1.5.1-6build1_s390x.deb ... 119s Unpacking tombo (1.5.1-6build1) ... 119s Selecting previously unselected package libjs-mathjax. 119s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 119s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 120s Selecting previously unselected package tombo-doc. 120s Preparing to unpack .../25-tombo-doc_1.5.1-6build1_all.deb ... 120s Unpacking tombo-doc (1.5.1-6build1) ... 120s Selecting previously unselected package autopkgtest-satdep. 120s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 120s Unpacking autopkgtest-satdep (0) ... 120s Setting up fonts-lato (2.015-1) ... 120s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 120s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 120s Setting up python3-tqdm (4.67.0-1) ... 120s Setting up python3-mappy (2.27+dfsg-1) ... 120s Setting up libaec0:s390x (1.1.3-1) ... 120s Setting up python3-decorator (5.1.1-5) ... 120s Setting up libblas3:s390x (3.12.0-3build2) ... 120s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 120s Setting up liblzf1:s390x (3.6-4) ... 120s Setting up libgfortran5:s390x (14.2.0-8ubuntu1) ... 120s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 120s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 120s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 120s Setting up libsz2:s390x (1.1.3-1) ... 120s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 120s Setting up liblapack3:s390x (3.12.0-3build2) ... 120s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 120s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 122s Setting up libjs-sphinxdoc (7.4.7-4) ... 122s Setting up tombo-doc (1.5.1-6build1) ... 122s Setting up libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 122s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 122s Setting up libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ... 122s Setting up python3-scipy (1.13.1-5) ... 126s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 126s Setting up python3-h5py (3.11.0-5ubuntu1) ... 126s Setting up tombo (1.5.1-6build1) ... 126s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 126s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 126s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 126s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 126s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 126s re.match('\+', fastq_rec[2]) is None): 126s Setting up autopkgtest-satdep (0) ... 126s Processing triggers for man-db (2.12.1-3) ... 127s Processing triggers for libc-bin (2.40-1ubuntu3) ... 129s (Reading database ... 62738 files and directories currently installed.) 129s Removing autopkgtest-satdep (0) ... 129s autopkgtest [17:00:04]: test run-unit-test: [----------------------- 130s ********* Testing help commands ********** 130s usage: tombo [-h] [-v] 130s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 130s ... 130s 130s ********** Tombo ********* 130s 130s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 130s 130s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 130s 130s Tombo command groups (additional help available within each command group): 130s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 130s preprocess Pre-process nanopore reads for Tombo processing. 130s filter Apply filter to Tombo index file for specified criterion. 130s detect_modifications Perform statistical testing to detect non-standard nucleotides. 130s text_output Output Tombo results in text files. 130s build_model Create canonical and alternative base Tombo models. 130s plot Save plots to visualize raw nanopore signal or testing results. 130s 130s options: 130s -h, --help show this help message and exit 130s -v, --version show Tombo version and exit. 130s usage: tombo resquiggle [--dna] [--rna] 130s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 130s [--q-score Q_SCORE] 130s [--signal-matching-score SIGNAL_MATCHING_SCORE] 130s [--processes PROCESSES] 130s [--corrected-group CORRECTED_GROUP] 130s [--basecall-group BASECALL_GROUP] 130s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 130s [--overwrite] 130s [--failed-reads-filename FAILED_READS_FILENAME] 130s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 130s [--print-advanced-arguments] [--quiet] [--help] 130s fast5s_basedir reference 130s 130s Required Arguments: 130s fast5s_basedir Directory containing fast5 files. All files ending in 130s "fast5" found recursively within this base directory 130s will be processed. 130s reference Reference genome/transcriptome FASTA file or minimap2 130s index (with "map-ont" preset) for mapping. 130s 130s Model Parameters: 130s --dna Explicitly select canonical DNA model. Default: 130s Automatically determine from FAST5s 130s --rna Explicitly select canonical RNA model. Default: 130s Automatically determine from FAST5s 130s 130s Read Filtering Argument: 130s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 130s Filter reads based on observations per base percentile 130s thresholds. Format thresholds as "percentile:thresh 130s [pctl2:thresh2 ...]". For example to filter reads with 130s 99th pctl > 200 obs/base or max > 5k obs/base use 130s "99:200 100:5000". 130s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 130s Default: 0.000000 130s --signal-matching-score SIGNAL_MATCHING_SCORE 130s Observed to expected signal matching score (higher 130s score indicates poor matching). Sample type defaults: 130s RNA : 2 || DNA : 1.1 130s 130s Multiprocessing Arguments: 130s --processes PROCESSES 130s Number of processes. Default: 1 130s 130s FAST5 Data Arguments: 130s --corrected-group CORRECTED_GROUP 130s FAST5 group created by resquiggle command. Default: 130s RawGenomeCorrected_000 130s --basecall-group BASECALL_GROUP 130s FAST5 group obtain original basecalls (under Analyses 130s group). Default: Basecall_1D_000 130s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 130s FAST5 subgroup(s) (under /Analyses/[--basecall- 130s group]/) containing basecalls and created within 130s [--corrected-group] containing re-squiggle results. 130s Default: ['BaseCalled_template'] 130s --overwrite Overwrite previous corrected group in FAST5 files. 130s Note: only effects --corrected-group or --new- 130s corrected-group. 130s 130s Input/Output Arguments: 130s --failed-reads-filename FAILED_READS_FILENAME 130s Output failed read filenames with assoicated error. 130s Default: Do not store failed reads. 130s --num-most-common-errors NUM_MOST_COMMON_ERRORS 130s Dynamically show this many most common errors so far 130s through run. Default: 0; Just show progress 130s 130s Advanced Arguments: 130s --print-advanced-arguments 130s Print advanced re-squiggle arguments and exit. 130s 130s Miscellaneous Arguments: 130s --quiet, -q Don't print status information. 130s --help, -h Print this help message and exit 130s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 130s --fastq-filenames 130s FASTQ_FILENAMES 130s [FASTQ_FILENAMES ...] 130s [--basecall-group BASECALL_GROUP] 130s [--basecall-subgroup BASECALL_SUBGROUP] 130s [--overwrite] 130s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 130s [--processes PROCESSES] 130s [--quiet] [--help] 130s 130s Required Arguments: 130s --fast5-basedir FAST5_BASEDIR 130s Directory containing fast5 files. 130s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 130s FASTQ filenames containing basecalls to be added to 130s raw FAST5 files. 130s 130s FAST5 Data Arguments: 130s --basecall-group BASECALL_GROUP 130s FAST5 group obtain original basecalls (under Analyses 130s group). Default: Basecall_1D_000 130s --basecall-subgroup BASECALL_SUBGROUP 130s FAST5 subgroup (under /Analyses/[--basecall-group]/) 130s under which to store basecalls from FASTQs. Default: 130s BaseCalled_template 130s --overwrite Overwrite previous corrected group in FAST5 files. 130s Note: only effects --corrected-group or --new- 130s corrected-group. 130s 130s Sequencing Summary Argument: 130s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 130s Sequencing summary filenames produced by albacore. 130s These can make annotation of raw FAST5 files with 130s FASTQ sequence much faster. 130s 130s Multiprocessing Argument: 130s --processes PROCESSES 130s Number of processes. Default: 1 130s 130s Miscellaneous Arguments: 130s --quiet, -q Don't print status information. 130s --help, -h Print this help message and exit 130s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 130s [FAST5_BASEDIRS ...] 130s [--corrected-group CORRECTED_GROUP] 130s [--quiet] [--help] 130s 130s Required Argument: 130s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 130s Directories containing fast5 files. 130s 130s FAST5 Data Argument: 130s --corrected-group CORRECTED_GROUP 130s FAST5 group created by resquiggle command. Default: 130s RawGenomeCorrected_000 130s 130s Miscellaneous Arguments: 130s --quiet, -q Don't print status information. 130s --help, -h Print this help message and exit 130s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 130s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 130s [--corrected-group CORRECTED_GROUP] [--quiet] 130s [--help] 130s 130s Required Argument: 130s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 130s Directories containing fast5 files. 130s 130s Read Filtering Argument: 130s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 130s Filter reads based on observations per base percentile 130s thresholds. Format thresholds as "percentile:thresh 130s [pctl2:thresh2 ...]". For example to filter reads with 130s 99th pctl > 200 obs/base or max > 5k obs/base use 130s "99:200 100:5000". 130s 130s FAST5 Data Argument: 130s --corrected-group CORRECTED_GROUP 130s FAST5 group created by resquiggle command. Default: 130s RawGenomeCorrected_000 130s 130s Miscellaneous Arguments: 130s --quiet, -q Don't print status information. 130s --help, -h Print this help message and exit 130s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 130s [FAST5_BASEDIRS ...] 130s [--percent-to-filter PERCENT_TO_FILTER] 130s [--corrected-group CORRECTED_GROUP] 130s [--quiet] [--help] 130s 130s Required Arguments: 130s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 130s Directories containing fast5 files. 130s 130s Read Filtering Argument: 130s --percent-to-filter PERCENT_TO_FILTER 130s Percentage of all reads to filter. Reads are randomly 130s selected weighted according to the approximate 130s coverage at the mapped genomic location. This can be 130s useful in modeling and testing. Default: 10.000000 130s 130s FAST5 Data Arguments: 130s --corrected-group CORRECTED_GROUP 130s FAST5 group created by resquiggle command. Default: 130s RawGenomeCorrected_000 130s 130s Miscellaneous Arguments: 130s --quiet, -q Don't print status information. 130s --help, -h Print this help message and exit 130s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 130s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 130s [--corrected-group CORRECTED_GROUP] 130s [--basecall-group BASECALL_GROUP] [--quiet] 130s [--help] 130s 130s Required Arguments: 130s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 130s Directories containing fast5 files. 130s 130s Read Filtering Argument: 130s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 130s Default: 7.000000 130s 130s FAST5 Data Arguments: 130s --corrected-group CORRECTED_GROUP 130s FAST5 group created by resquiggle command. Default: 130s RawGenomeCorrected_000 130s --basecall-group BASECALL_GROUP 130s FAST5 group obtain original basecalls (under Analyses 130s group). Default: Basecall_1D_000 130s 130s Miscellaneous Arguments: 130s --quiet, -q Don't print status information. 130s --help, -h Print this help message and exit 130s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 130s [FAST5_BASEDIRS ...] 130s --signal-matching-score 130s SIGNAL_MATCHING_SCORE 130s [--corrected-group CORRECTED_GROUP] 130s [--quiet] [--help] 130s 130s Required Arguments: 130s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 130s Directories containing fast5 files. 130s --signal-matching-score SIGNAL_MATCHING_SCORE 130s Observed to expected signal matching score (higher 130s score indicates poor matching). Sample type defaults: 130s RNA : 2 || DNA : 1.1 130s 130s FAST5 Data Arguments: 130s --corrected-group CORRECTED_GROUP 130s FAST5 group created by resquiggle command. Default: 130s RawGenomeCorrected_000 130s 130s Miscellaneous Arguments: 130s --quiet, -q Don't print status information. 130s --help, -h Print this help message and exit 130s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 130s [FAST5_BASEDIRS ...] 130s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 130s [--include-partial-overlap] 130s [--corrected-group CORRECTED_GROUP] 130s [--quiet] [--help] 130s 130s Required Arguments: 130s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 130s Directories containing fast5 files. 130s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 130s Filter out reads not falling completely within include 130s regions. Omit start and end coordinates to include an 130s entire chromosome/sequence record. Format regions as 130s "chrm[:start-end] [chrm2[:start2-end2] ...]". 130s 130s Filter Argument: 130s --include-partial-overlap 130s Include reads that partially overlap the specified 130s region. Default: Only include reads completely 130s contained in a specified region 130s 130s FAST5 Data Argument: 130s --corrected-group CORRECTED_GROUP 130s FAST5 group created by resquiggle command. Default: 130s RawGenomeCorrected_000 130s 130s Miscellaneous Arguments: 130s --quiet, -q Don't print status information. 130s --help, -h Print this help message and exit 130s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 130s [FAST5_BASEDIRS ...] 130s --statistics-file-basename 130s STATISTICS_FILE_BASENAME [--dna] 130s [--rna] 130s [--fishers-method-context FISHERS_METHOD_CONTEXT] 130s [--minimum-test-reads MINIMUM_TEST_READS] 130s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 130s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 130s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 130s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 130s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 130s [--processes PROCESSES] 130s [--corrected-group CORRECTED_GROUP] 130s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 130s [--quiet] [--help] 130s 130s Required Argument: 130s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 130s Directories containing fast5 files. 130s --statistics-file-basename STATISTICS_FILE_BASENAME 130s File base name to save base by base statistics from 130s testing. Filenames will be [--statistics-file- 130s basename].[--alternate-bases]?.tombo.stats 130s 130s Comparison Model Arguments: 130s --dna Explicitly select canonical DNA model. Default: 130s Automatically determine from FAST5s 130s --rna Explicitly select canonical RNA model. Default: 130s Automatically determine from FAST5s 130s 130s Significance Test Arguments: 130s --fishers-method-context FISHERS_METHOD_CONTEXT 130s Number of context bases up and downstream over which 130s to compute Fisher's method combined p-values. Note: 130s Not applicable for alternative model likelihood ratio 130s tests. Default: 1. 130s --minimum-test-reads MINIMUM_TEST_READS 130s Number of reads required at a position to perform 130s significance testing or contribute to model 130s estimation. Default: 1 130s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 130s P-value threshold when computing fraction of 130s significant reads at each genomic position. If two 130s values are provided, statistics between these values 130s are not considered. Default thresholds: DNA:0.15-0.5 , 130s RNA:0.05-0.4 130s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 130s Dampen fraction modified estimates for low coverage 130s sites. Two parameters are unmodified and modified 130s pseudo read counts. This is equivalent to a beta prior 130s on the fraction estimate. Set to "0 0" to disable 130s dampened fraction estimation. Default: [2, 0] 130s 130s Output Argument: 130s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 130s Base for binary files containing per-read statistics 130s from statistical testing. Filenames will be [--per- 130s read-statistics-basename].[--alternate- 130s bases]?.tombo.per_read_stats 130s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 130s Number of the most significant sites to store for 130s faster access. If a longer list of most significant 130s sites is required the list must be re-computed from 130s all batches. Very large values can increase RAM usage. 130s Default: 100000 130s 130s Multiprocessing Arguments: 130s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 130s Size of regions over which to multiprocesses statistic 130s computation. For very deep samples a smaller value is 130s recommmended in order to control memory consumption. 130s Default: 10000 130s --processes PROCESSES 130s Number of processes. Default: 1 130s 130s FAST5 Data Arguments: 130s --corrected-group CORRECTED_GROUP 130s FAST5 group created by resquiggle command. Default: 130s RawGenomeCorrected_000 130s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 130s FAST5 subgroup(s) (under /Analyses/[--basecall- 130s group]/) containing basecalls and created within 130s [--corrected-group] containing re-squiggle results. 130s Default: ['BaseCalled_template'] 130s 130s Miscellaneous Arguments: 130s --quiet, -q Don't print status information. 130s --help, -h Print this help message and exit 130s usage: tombo detect_modifications alternative_model 130s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 130s [--statistics-file-basename STATISTICS_FILE_BASENAME] 130s [--alternate-bases {5mC,6mA,CpG,dam,dcm} [{5mC,6mA,CpG,dam,dcm} ...]] 130s [--print-available-models] 130s [--dna] [--rna] 130s [--minimum-test-reads MINIMUM_TEST_READS] 130s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 130s [--standard-log-likelihood-ratio] 130s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 130s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 130s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 130s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 130s [--processes PROCESSES] 130s [--corrected-group CORRECTED_GROUP] 130s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 130s [--quiet] [--help] 130s 130s Required Argument: 130s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 130s Directories containing fast5 files. 130s --statistics-file-basename STATISTICS_FILE_BASENAME 130s File base name to save base by base statistics from 130s testing. Filenames will be [--statistics-file- 130s basename].[--alternate-bases]?.tombo.stats 130s --alternate-bases {5mC,6mA,CpG,dam,dcm} [{5mC,6mA,CpG,dam,dcm} ...] 130s Default non-standard base model for testing (not 130s required if user created --alternate-model-filenames 130s is provided). 130s 130s Comparison Arguments: 130s --print-available-models 130s Print available alternative models and exit. 130s --dna Explicitly select canonical DNA model. Default: 130s Automatically determine from FAST5s 130s --rna Explicitly select canonical RNA model. Default: 130s Automatically determine from FAST5s 130s 130s Significance Test Arguments: 130s --minimum-test-reads MINIMUM_TEST_READS 130s Number of reads required at a position to perform 130s significance testing or contribute to model 130s estimation. Default: 1 130s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 130s Log likelihood ratio threshold when computing fraction 130s of significant reads at each genomic position. If two 130s values are provided, statistics between these values 130s are not considered. Default thresholds: DNA:-1.5-2.5 , 130s RNA:-2.5-2.5 130s --standard-log-likelihood-ratio 130s Use a standard log likelihood ratio (LLR) statistic. 130s Default is to use an outlier-robust LLR-like 130s statistic. Detail in full online documentation. 130s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 130s Dampen fraction modified estimates for low coverage 130s sites. Two parameters are unmodified and modified 130s pseudo read counts. This is equivalent to a beta prior 130s on the fraction estimate. Set to "0 0" to disable 130s dampened fraction estimation. Default: [2, 0] 130s 130s Output Argument: 130s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 130s Base for binary files containing per-read statistics 130s from statistical testing. Filenames will be [--per- 130s read-statistics-basename].[--alternate- 130s bases]?.tombo.per_read_stats 130s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 130s Number of the most significant sites to store for 130s faster access. If a longer list of most significant 130s sites is required the list must be re-computed from 130s all batches. Very large values can increase RAM usage. 130s Default: 100000 130s 130s Multiprocessing Arguments: 130s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 130s Size of regions over which to multiprocesses statistic 130s computation. For very deep samples a smaller value is 130s recommmended in order to control memory consumption. 130s Default: 10000 130s --processes PROCESSES 130s Number of processes. Default: 1 130s 130s FAST5 Data Arguments: 130s --corrected-group CORRECTED_GROUP 130s FAST5 group created by resquiggle command. Default: 130s RawGenomeCorrected_000 130s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 130s FAST5 subgroup(s) (under /Analyses/[--basecall- 130s group]/) containing basecalls and created within 130s [--corrected-group] containing re-squiggle results. 130s Default: ['BaseCalled_template'] 130s 130s Miscellaneous Arguments: 130s --quiet, -q Don't print status information. 130s --help, -h Print this help message and exit 130s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 130s FAST5_BASEDIRS 130s [FAST5_BASEDIRS ...] 130s --statistics-file-basename 130s STATISTICS_FILE_BASENAME 130s --control-fast5-basedirs 130s CONTROL_FAST5_BASEDIRS 130s [CONTROL_FAST5_BASEDIRS ...] 130s [--sample-only-estimates] 130s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 130s [--dna] [--rna] 130s [--fishers-method-context FISHERS_METHOD_CONTEXT] 130s [--minimum-test-reads MINIMUM_TEST_READS] 130s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 130s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 130s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 130s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 130s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 130s [--processes PROCESSES] 130s [--corrected-group CORRECTED_GROUP] 130s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 130s [--quiet] [--help] 130s 130s Required Argument: 130s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 130s Directories containing fast5 files. 130s --statistics-file-basename STATISTICS_FILE_BASENAME 130s File base name to save base by base statistics from 130s testing. Filenames will be [--statistics-file- 130s basename].[--alternate-bases]?.tombo.stats 130s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 130s Set of directories containing fast5 files for control 130s reads, containing only canonical nucleotides. 130s 130s Model Prior Arguments: 130s --sample-only-estimates 130s Only use canonical sample to estimate expected signal 130s level and spread. Default: Use canonical model to 130s improve estimtates (esp. for low coverage regions) 130s using baysian posterior estimates. 130s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 130s Prior weights (one each for mean and spread) applied 130s to canonical base model for estimating posterior model 130s parameters for sample comparison. Default: [5, 40] 130s --dna Explicitly select canonical DNA model. Default: 130s Automatically determine from FAST5s 130s --rna Explicitly select canonical RNA model. Default: 130s Automatically determine from FAST5s 130s 130s Significance Test Arguments: 130s --fishers-method-context FISHERS_METHOD_CONTEXT 130s Number of context bases up and downstream over which 130s to compute Fisher's method combined p-values. Note: 130s Not applicable for alternative model likelihood ratio 130s tests. Default: 1. 130s --minimum-test-reads MINIMUM_TEST_READS 130s Number of reads required at a position to perform 130s significance testing or contribute to model 130s estimation. Default: 1 130s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 130s P-value threshold when computing fraction of 130s significant reads at each genomic position. If two 130s values are provided, statistics between these values 130s are not considered. Default thresholds: DNA:0.15-0.5 , 130s RNA:0.05-0.4 130s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 130s Dampen fraction modified estimates for low coverage 130s sites. Two parameters are unmodified and modified 130s pseudo read counts. This is equivalent to a beta prior 130s on the fraction estimate. Set to "0 0" to disable 130s dampened fraction estimation. Default: [2, 0] 130s 130s Output Argument: 130s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 130s Base for binary files containing per-read statistics 130s from statistical testing. Filenames will be [--per- 130s read-statistics-basename].[--alternate- 130s bases]?.tombo.per_read_stats 130s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 130s Number of the most significant sites to store for 130s faster access. If a longer list of most significant 130s sites is required the list must be re-computed from 130s all batches. Very large values can increase RAM usage. 130s Default: 100000 130s 130s Multiprocessing Arguments: 130s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 130s Size of regions over which to multiprocesses statistic 130s computation. For very deep samples a smaller value is 130s recommmended in order to control memory consumption. 130s Default: 10000 130s --processes PROCESSES 130s Number of processes. Default: 1 130s 130s FAST5 Data Arguments: 130s --corrected-group CORRECTED_GROUP 130s FAST5 group created by resquiggle command. Default: 130s RawGenomeCorrected_000 130s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 130s FAST5 subgroup(s) (under /Analyses/[--basecall- 130s group]/) containing basecalls and created within 130s [--corrected-group] containing re-squiggle results. 130s Default: ['BaseCalled_template'] 130s 130s Miscellaneous Arguments: 130s --quiet, -q Don't print status information. 130s --help, -h Print this help message and exit 130s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 130s FAST5_BASEDIRS 130s [FAST5_BASEDIRS ...] 130s --statistics-file-basename 130s STATISTICS_FILE_BASENAME 130s --alternate-fast5-basedirs 130s ALTERNATE_FAST5_BASEDIRS 130s [ALTERNATE_FAST5_BASEDIRS ...] 130s [--fishers-method-context FISHERS_METHOD_CONTEXT] 130s [--minimum-test-reads MINIMUM_TEST_READS] 130s [--statistic-type {ks,u,t}] 130s [--store-p-value] 130s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 130s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 130s [--processes PROCESSES] 130s [--corrected-group CORRECTED_GROUP] 130s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 130s [--quiet] [--help] 130s 130s Required Argument: 130s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 130s Directories containing fast5 files. 130s --statistics-file-basename STATISTICS_FILE_BASENAME 130s File base name to save base by base statistics from 130s testing. Filenames will be [--statistics-file- 130s basename].[--alternate-bases]?.tombo.stats 130s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 130s Set of directories containing fast5 files for 130s alternate set of reads. 130s 130s Significance Test Arguments: 130s --fishers-method-context FISHERS_METHOD_CONTEXT 130s Number of context bases up and downstream over which 130s to compute Fisher's method combined p-values. Note: 130s Not applicable for alternative model likelihood ratio 130s tests. Default: 1. 130s --minimum-test-reads MINIMUM_TEST_READS 130s Number of reads required at a position to perform 130s significance testing or contribute to model 130s estimation. Default: 50 130s --statistic-type {ks,u,t} 130s Type of statistical test to apply. Default: "ks" 130s --store-p-value Store p-value instead of effect-size statistic. 130s Statistics are D-statistic (KS-test), deviation from 130s even common language effect size (u-test), and Cohen's 130s D (t-test). 130s 130s Output Argument: 130s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 130s Number of the most significant sites to store for 130s faster access. If a longer list of most significant 130s sites is required the list must be re-computed from 130s all batches. Very large values can increase RAM usage. 130s Default: 100000 130s 130s Multiprocessing Arguments: 130s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 130s Size of regions over which to multiprocesses statistic 130s computation. For very deep samples a smaller value is 130s recommmended in order to control memory consumption. 130s Default: 10000 130s --processes PROCESSES 130s Number of processes. Default: 1 130s 130s FAST5 Data Arguments: 130s --corrected-group CORRECTED_GROUP 130s FAST5 group created by resquiggle command. Default: 130s RawGenomeCorrected_000 130s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 130s FAST5 subgroup(s) (under /Analyses/[--basecall- 130s group]/) containing basecalls and created within 130s [--corrected-group] containing re-squiggle results. 130s Default: ['BaseCalled_template'] 130s 130s Miscellaneous Arguments: 130s --quiet, -q Don't print status information. 130s --help, -h Print this help message and exit 131s usage: tombo detect_modifications aggregate_per_read_stats 131s --per-read-statistics-filename 131s PER_READ_STATISTICS_FILENAME 131s --statistics-filename 131s STATISTICS_FILENAME 131s --single-read-threshold 131s SINGLE_READ_THRESHOLD 131s [SINGLE_READ_THRESHOLD ...] 131s [--minimum-test-reads MINIMUM_TEST_READS] 131s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 131s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 131s [--processes PROCESSES] 131s [--corrected-group CORRECTED_GROUP] 131s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 131s [--quiet] [--help] 131s 131s Required Argument: 131s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 131s Binary file containing per-read statistics from 131s statistical testing. 131s --statistics-filename STATISTICS_FILENAME 131s File to save/load genomic base anchored statistics. 131s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 131s P-value or log likelihood ratio threshold when 131s computing fraction of significant reads at each 131s genomic position. If two values are provided, 131s statistics between these values are not considered. 131s 131s Significance Test Arguments: 131s --minimum-test-reads MINIMUM_TEST_READS 131s Number of reads required at a position to perform 131s significance testing or contribute to model 131s estimation. Default: 1 131s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 131s Dampen fraction modified estimates for low coverage 131s sites. Two parameters are unmodified and modified 131s pseudo read counts. This is equivalent to a beta prior 131s on the fraction estimate. Set to "0 0" to disable 131s dampened fraction estimation. Default: [2, 0] 131s 131s Output Argument: 131s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 131s Number of the most significant sites to store for 131s faster access. If a longer list of most significant 131s sites is required the list must be re-computed from 131s all batches. Very large values can increase RAM usage. 131s Default: 100000 131s 131s Multiprocessing Arguments: 131s --processes PROCESSES 131s Number of processes. Default: 1 131s 131s FAST5 Data Arguments: 131s --corrected-group CORRECTED_GROUP 131s FAST5 group created by resquiggle command. Default: 131s RawGenomeCorrected_000 131s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 131s FAST5 subgroup(s) (under /Analyses/[--basecall- 131s group]/) containing basecalls and created within 131s [--corrected-group] containing re-squiggle results. 131s Default: ['BaseCalled_template'] 131s 131s Miscellaneous Arguments: 131s --quiet, -q Don't print status information. 131s --help, -h Print this help message and exit 131s usage: tombo text_output browser_files 131s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 131s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 131s [--statistics-filename STATISTICS_FILENAME] 131s [--genome-fasta GENOME_FASTA] 131s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 131s [--browser-file-basename BROWSER_FILE_BASENAME] 131s [--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} ...]] 131s [--corrected-group CORRECTED_GROUP] 131s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 131s [--quiet] [--help] 131s 131s Data Arguments: 131s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 131s Directories containing fast5 files. 131s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 131s Set of directories containing fast5 files for control 131s reads, containing only canonical nucleotides. 131s --statistics-filename STATISTICS_FILENAME 131s File to save/load genomic base anchored statistics. 131s 131s Statistic Motif Filter Arguments: 131s --genome-fasta GENOME_FASTA 131s FASTA file used to re-squiggle. For faster sequence 131s access. 131s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 131s Ground truth, motif centered, modified base 131s descriptions for output filtering. Format descriptions 131s as: "motif:mod_pos:name". The mod_pos indicates the 131s modified base within the motif (1-based index). 131s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 131s output for identification of E. coli dam and dcm 131s methylation. 131s 131s Output Arguments: 131s --browser-file-basename BROWSER_FILE_BASENAME 131s Basename for output browser files. Two files (plus and 131s minus strand) will be produced for each --file-types 131s supplied. Filenames formatted as "[browser-file- 131s basename].[file- 131s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 131s Default: tombo_results 131s --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} ...] 131s Data types of genome browser files to produce. 131s Produced coverage files are in bedGraph format, while 131s all other file types will be in wiggle format 131s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 131s Default: "coverage" 131s 131s FAST5 Data Arguments: 131s --corrected-group CORRECTED_GROUP 131s FAST5 group created by resquiggle command. Default: 131s RawGenomeCorrected_000 131s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 131s FAST5 subgroup(s) (under /Analyses/[--basecall- 131s group]/) containing basecalls and created within 131s [--corrected-group] containing re-squiggle results. 131s Default: ['BaseCalled_template'] 131s 131s Miscellaneous Arguments: 131s --quiet, -q Don't print status information. 131s --help, -h Print this help message and exit 131s usage: tombo text_output signif_sequence_context --statistics-filename 131s STATISTICS_FILENAME 131s [--genome-fasta GENOME_FASTA] 131s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 131s [--num-regions NUM_REGIONS] 131s [--num-bases NUM_BASES] 131s [--sequences-filename SEQUENCES_FILENAME] 131s [--corrected-group CORRECTED_GROUP] 131s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 131s [--quiet] [--help] 131s 131s Required Argument: 131s --statistics-filename STATISTICS_FILENAME 131s File to save/load genomic base anchored statistics. 131s 131s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 131s --genome-fasta GENOME_FASTA 131s FASTA file used to re-squiggle. For faster sequence 131s access. 131s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 131s Directories containing fast5 files. 131s 131s Region Selection Arguments: 131s --num-regions NUM_REGIONS 131s Number of regions to plot. Default: 100 131s --num-bases NUM_BASES 131s Number of bases to plot/output. Default: 15 131s 131s Output Arguments: 131s --sequences-filename SEQUENCES_FILENAME 131s File for sequences from selected regions. Sequences 131s will be stored in FASTA format. Default: 131s tombo_results.significant_regions.fasta. 131s 131s FAST5 Data Arguments: 131s --corrected-group CORRECTED_GROUP 131s FAST5 group created by resquiggle command. Default: 131s RawGenomeCorrected_000 131s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 131s FAST5 subgroup(s) (under /Analyses/[--basecall- 131s group]/) containing basecalls and created within 131s [--corrected-group] containing re-squiggle results. 131s Default: ['BaseCalled_template'] 131s 131s Miscellaneous Arguments: 131s --quiet, -q Don't print status information. 131s --help, -h Print this help message and exit 131s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 131s [FAST5_BASEDIRS ...] 131s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 131s [--plot-standard-model] 131s [--plot-alternate-model {6mA,dcm,dam,5mC,CpG}] 131s [--overplot-threshold OVERPLOT_THRESHOLD] 131s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 131s [--num-regions NUM_REGIONS] 131s [--num-bases NUM_BASES] 131s [--pdf-filename PDF_FILENAME] 131s [--corrected-group CORRECTED_GROUP] 131s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 131s [--quiet] [--help] 131s 131s Required Argument: 131s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 131s Directories containing fast5 files. 131s 131s Comparison Arguments: 131s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 131s Set of directories containing fast5 files for control 131s reads, containing only canonical nucleotides. 131s --plot-standard-model 131s Add default standard model distribution to the plot. 131s --plot-alternate-model {6mA,dcm,dam,5mC,CpG} 131s Add alternative model distribution to the plot. 131s 131s Overplotting Arguments: 131s --overplot-threshold OVERPLOT_THRESHOLD 131s Coverage level to trigger alternative plot type 131s instead of raw signal. Default: 50 131s --overplot-type {Downsample,Boxplot,Quantile,Density} 131s Plot type for regions with higher coverage. Default: 131s Downsample 131s 131s Plotting Region Arguments: 131s --num-regions NUM_REGIONS 131s Number of regions to plot. Default: 10 131s --num-bases NUM_BASES 131s Number of bases to plot/output. Default: 21 131s 131s Output Argument: 131s --pdf-filename PDF_FILENAME 131s PDF filename to store plot(s). Default: 131s tombo_results.max_coverage.pdf 131s 131s FAST5 Data Arguments: 131s --corrected-group CORRECTED_GROUP 131s FAST5 group created by resquiggle command. Default: 131s RawGenomeCorrected_000 131s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 131s FAST5 subgroup(s) (under /Analyses/[--basecall- 131s group]/) containing basecalls and created within 131s [--corrected-group] containing re-squiggle results. 131s Default: ['BaseCalled_template'] 131s 131s Miscellaneous Arguments: 131s --quiet, -q Don't print status information. 131s --help, -h Print this help message and exit 131s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 131s [FAST5_BASEDIRS ...] --genome-locations 131s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 131s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 131s [--plot-standard-model] 131s [--plot-alternate-model {CpG,dcm,dam,5mC,6mA}] 131s [--overplot-threshold OVERPLOT_THRESHOLD] 131s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 131s [--num-bases NUM_BASES] 131s [--pdf-filename PDF_FILENAME] 131s [--corrected-group CORRECTED_GROUP] 131s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 131s [--quiet] [--help] 131s 131s Required Arguments: 131s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 131s Directories containing fast5 files. 131s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 131s Genomic locations at which to plot signal. Format 131s locations as "chrm:position[:strand] 131s [chrm2:position2[:strand2] ...]" (strand not 131s applicable for all applications) 131s 131s Comparison Arguments: 131s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 131s Set of directories containing fast5 files for control 131s reads, containing only canonical nucleotides. 131s --plot-standard-model 131s Add default standard model distribution to the plot. 131s --plot-alternate-model {CpG,dcm,dam,5mC,6mA} 131s Add alternative model distribution to the plot. 131s 131s Overplotting Arguments: 131s --overplot-threshold OVERPLOT_THRESHOLD 131s Coverage level to trigger alternative plot type 131s instead of raw signal. Default: 50 131s --overplot-type {Downsample,Boxplot,Quantile,Density} 131s Plot type for regions with higher coverage. Default: 131s Downsample 131s 131s Plotting Region Argument: 131s --num-bases NUM_BASES 131s Number of bases to plot/output. Default: 21 131s 131s Output Argument: 131s --pdf-filename PDF_FILENAME 131s PDF filename to store plot(s). Default: 131s tombo_results.genome_locations.pdf 131s 131s FAST5 Data Arguments: 131s --corrected-group CORRECTED_GROUP 131s FAST5 group created by resquiggle command. Default: 131s RawGenomeCorrected_000 131s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 131s FAST5 subgroup(s) (under /Analyses/[--basecall- 131s group]/) containing basecalls and created within 131s [--corrected-group] containing re-squiggle results. 131s Default: ['BaseCalled_template'] 131s 131s Miscellaneous Arguments: 131s --quiet, -q Don't print status information. 131s --help, -h Print this help message and exit 131s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 131s [FAST5_BASEDIRS ...] --motif MOTIF 131s --genome-fasta GENOME_FASTA 131s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 131s [--plot-standard-model] 131s [--plot-alternate-model {6mA,dam,5mC,CpG,dcm}] 131s [--overplot-threshold OVERPLOT_THRESHOLD] 131s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 131s [--num-regions NUM_REGIONS] 131s [--num-bases NUM_BASES] [--deepest-coverage] 131s [--pdf-filename PDF_FILENAME] 131s [--corrected-group CORRECTED_GROUP] 131s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 131s [--quiet] [--help] 131s 131s Required Arguments: 131s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 131s Directories containing fast5 files. 131s --motif MOTIF Motif of interest at which to plot signal and 131s statsitics. Supports IUPAC single letter codes (use T 131s for RNA). 131s --genome-fasta GENOME_FASTA 131s FASTA file used to re-squiggle. For faster sequence 131s access. 131s 131s Comparison Arguments: 131s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 131s Set of directories containing fast5 files for control 131s reads, containing only canonical nucleotides. 131s --plot-standard-model 131s Add default standard model distribution to the plot. 131s --plot-alternate-model {6mA,dam,5mC,CpG,dcm} 131s Add alternative model distribution to the plot. 131s 131s Overplotting Arguments: 131s --overplot-threshold OVERPLOT_THRESHOLD 131s Coverage level to trigger alternative plot type 131s instead of raw signal. Default: 50 131s --overplot-type {Downsample,Boxplot,Quantile,Density} 131s Plot type for regions with higher coverage. Default: 131s Downsample 131s 131s Plotting Region Arguments: 131s --num-regions NUM_REGIONS 131s Number of regions to plot. Default: 10 131s --num-bases NUM_BASES 131s Number of bases to plot/output. Default: 21 131s --deepest-coverage Plot the deepest coverage regions. 131s 131s Output Argument: 131s --pdf-filename PDF_FILENAME 131s PDF filename to store plot(s). Default: 131s tombo_results.motif_centered.pdf 131s 131s FAST5 Data Arguments: 131s --corrected-group CORRECTED_GROUP 131s FAST5 group created by resquiggle command. Default: 131s RawGenomeCorrected_000 131s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 131s FAST5 subgroup(s) (under /Analyses/[--basecall- 131s group]/) containing basecalls and created within 131s [--corrected-group] containing re-squiggle results. 131s Default: ['BaseCalled_template'] 131s 131s Miscellaneous Arguments: 131s --quiet, -q Don't print status information. 131s --help, -h Print this help message and exit 131s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 131s [FAST5_BASEDIRS ...] --control-fast5-basedirs 131s CONTROL_FAST5_BASEDIRS 131s [CONTROL_FAST5_BASEDIRS ...] 131s [--overplot-threshold OVERPLOT_THRESHOLD] 131s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 131s [--num-regions NUM_REGIONS] 131s [--num-bases NUM_BASES] 131s [--pdf-filename PDF_FILENAME] 131s [--sequences-filename SEQUENCES_FILENAME] 131s [--corrected-group CORRECTED_GROUP] 131s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 131s [--quiet] [--help] 131s 131s Required Arguments: 131s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 131s Directories containing fast5 files. 131s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 131s Set of directories containing fast5 files for control 131s reads, containing only canonical nucleotides. 131s 131s Overplotting Arguments: 131s --overplot-threshold OVERPLOT_THRESHOLD 131s Coverage level to trigger alternative plot type 131s instead of raw signal. Default: 50 131s --overplot-type {Downsample,Boxplot,Quantile,Density} 131s Plot type for regions with higher coverage. Default: 131s Downsample 131s 131s Plotting Region Arguments: 131s --num-regions NUM_REGIONS 131s Number of regions to plot. Default: 10 131s --num-bases NUM_BASES 131s Number of bases to plot/output. Default: 21 131s 131s Output Arguments: 131s --pdf-filename PDF_FILENAME 131s PDF filename to store plot(s). Default: 131s tombo_results.max_difference.pdf 131s --sequences-filename SEQUENCES_FILENAME 131s File for sequences from selected regions. Sequences 131s will be stored in FASTA format. Default: None. 131s 131s FAST5 Data Arguments: 131s --corrected-group CORRECTED_GROUP 131s FAST5 group created by resquiggle command. Default: 131s RawGenomeCorrected_000 131s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 131s FAST5 subgroup(s) (under /Analyses/[--basecall- 131s group]/) containing basecalls and created within 131s [--corrected-group] containing re-squiggle results. 131s Default: ['BaseCalled_template'] 131s 131s Miscellaneous Arguments: 131s --quiet, -q Don't print status information. 131s --help, -h Print this help message and exit 131s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 131s [FAST5_BASEDIRS ...] --statistics-filename 131s STATISTICS_FILENAME 131s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 131s [--plot-standard-model] 131s [--plot-alternate-model {dam,dcm,6mA,5mC,CpG}] 131s [--overplot-threshold OVERPLOT_THRESHOLD] 131s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 131s [--num-regions NUM_REGIONS] 131s [--num-bases NUM_BASES] 131s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 131s [--pdf-filename PDF_FILENAME] 131s [--sequences-filename SEQUENCES_FILENAME] 131s [--corrected-group CORRECTED_GROUP] 131s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 131s [--quiet] [--help] 131s 131s Required Arguments: 131s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 131s Directories containing fast5 files. 131s --statistics-filename STATISTICS_FILENAME 131s File to save/load genomic base anchored statistics. 131s 131s Comparison Arguments: 131s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 131s Set of directories containing fast5 files for control 131s reads, containing only canonical nucleotides. 131s --plot-standard-model 131s Add default standard model distribution to the plot. 131s --plot-alternate-model {dam,dcm,6mA,5mC,CpG} 131s Add alternative model distribution to the plot. 131s 131s Overplotting Arguments: 131s --overplot-threshold OVERPLOT_THRESHOLD 131s Coverage level to trigger alternative plot type 131s instead of raw signal. Default: 50 131s --overplot-type {Downsample,Boxplot,Quantile,Density} 131s Plot type for regions with higher coverage. Default: 131s Downsample 131s 131s Plotting Region Arguments: 131s --num-regions NUM_REGIONS 131s Number of regions to plot. Default: 10 131s --num-bases NUM_BASES 131s Number of bases to plot/output. Default: 21 131s 131s Statistical Argument: 131s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 131s Dampen fraction modified estimates for low coverage 131s sites. Two parameters are unmodified and modified 131s pseudo read counts. This is equivalent to a beta prior 131s on the fraction estimate. Set to "0 0" to disable 131s dampened fraction estimation. Default: [2, 0] 131s 131s Output Arguments: 131s --pdf-filename PDF_FILENAME 131s PDF filename to store plot(s). Default: 131s tombo_results.significant_difference.pdf 131s --sequences-filename SEQUENCES_FILENAME 131s File for sequences from selected regions. Sequences 131s will be stored in FASTA format. Default: None. 131s 131s FAST5 Data Arguments: 131s --corrected-group CORRECTED_GROUP 131s FAST5 group created by resquiggle command. Default: 131s RawGenomeCorrected_000 131s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 131s FAST5 subgroup(s) (under /Analyses/[--basecall- 131s group]/) containing basecalls and created within 131s [--corrected-group] containing re-squiggle results. 131s Default: ['BaseCalled_template'] 131s 131s Miscellaneous Arguments: 131s --quiet, -q Don't print status information. 131s --help, -h Print this help message and exit 131s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 131s [FAST5_BASEDIRS ...] --motif MOTIF 131s --statistics-filename STATISTICS_FILENAME 131s --genome-fasta GENOME_FASTA 131s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 131s [--plot-standard-model] 131s [--plot-alternate-model {dam,dcm,6mA,CpG,5mC}] 131s [--overplot-threshold OVERPLOT_THRESHOLD] 131s [--num-regions NUM_REGIONS] 131s [--num-context NUM_CONTEXT] 131s [--num-statistics NUM_STATISTICS] 131s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 131s [--pdf-filename PDF_FILENAME] 131s [--corrected-group CORRECTED_GROUP] 131s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 131s [--quiet] [--help] 131s 131s Required Arguments: 131s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 131s Directories containing fast5 files. 131s --motif MOTIF Motif of interest at which to plot signal and 131s statsitics. Supports IUPAC single letter codes (use T 131s for RNA). 131s --statistics-filename STATISTICS_FILENAME 131s File to save/load genomic base anchored statistics. 131s --genome-fasta GENOME_FASTA 131s FASTA file used to re-squiggle. For faster sequence 131s access. 131s 131s Comparison Arguments: 131s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 131s Set of directories containing fast5 files for control 131s reads, containing only canonical nucleotides. 131s --plot-standard-model 131s Add default standard model distribution to the plot. 131s --plot-alternate-model {dam,dcm,6mA,CpG,5mC} 131s Add alternative model distribution to the plot. 131s 131s Overplotting Argument: 131s --overplot-threshold OVERPLOT_THRESHOLD 131s Coverage level to trigger alternative plot type 131s instead of raw signal. Default: 50 131s 131s Plotting Region Arguments: 131s --num-regions NUM_REGIONS 131s Number of regions to plot. Default: 3 131s --num-context NUM_CONTEXT 131s Number of context bases around motif. Default: 5 131s --num-statistics NUM_STATISTICS 131s Number of motif centered regions to include in 131s statistic distributions. Default: 200 131s 131s Statistical Argument: 131s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 131s Dampen fraction modified estimates for low coverage 131s sites. Two parameters are unmodified and modified 131s pseudo read counts. This is equivalent to a beta prior 131s on the fraction estimate. Set to "0 0" to disable 131s dampened fraction estimation. Default: [2, 0] 131s 131s Output Argument: 131s --pdf-filename PDF_FILENAME 131s PDF filename to store plot(s). Default: 131s tombo_results.motif_statistics.pdf 131s 131s FAST5 Data Arguments: 131s --corrected-group CORRECTED_GROUP 131s FAST5 group created by resquiggle command. Default: 131s RawGenomeCorrected_000 131s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 131s FAST5 subgroup(s) (under /Analyses/[--basecall- 131s group]/) containing basecalls and created within 131s [--corrected-group] containing re-squiggle results. 131s Default: ['BaseCalled_template'] 131s 131s Miscellaneous Arguments: 131s --quiet, -q Don't print status information. 131s --help, -h Print this help message and exit 131s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 131s [GENOME_LOCATIONS ...] 131s --per-read-statistics-filename 131s PER_READ_STATISTICS_FILENAME 131s [--genome-fasta GENOME_FASTA] 131s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 131s [--num-reads NUM_READS] [--num-bases NUM_BASES] 131s [--box-center] [--pdf-filename PDF_FILENAME] 131s [--corrected-group CORRECTED_GROUP] 131s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 131s [--quiet] [--help] 131s 131s Required Arguments: 131s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 131s Genomic locations at which to plot signal. Format 131s locations as "chrm:position[:strand] 131s [chrm2:position2[:strand2] ...]" (strand not 131s applicable for all applications) 131s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 131s Binary file containing per-read statistics from 131s statistical testing. 131s 131s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 131s --genome-fasta GENOME_FASTA 131s FASTA file used to re-squiggle. For faster sequence 131s access. 131s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 131s Directories containing fast5 files. 131s 131s Plotting Region Arguments: 131s --num-reads NUM_READS 131s Number of reads to plot. Default: 100 131s --num-bases NUM_BASES 131s Number of bases to plot/output. Default: 51 131s --box-center Plot a box around the central base. 131s 131s Output Argument: 131s --pdf-filename PDF_FILENAME 131s PDF filename to store plot(s). Default: 131s tombo_results.per_read_stats.pdf 131s 131s FAST5 Data Arguments: 131s --corrected-group CORRECTED_GROUP 131s FAST5 group created by resquiggle command. Default: 131s RawGenomeCorrected_000 131s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 131s FAST5 subgroup(s) (under /Analyses/[--basecall- 131s group]/) containing basecalls and created within 131s [--corrected-group] containing re-squiggle results. 131s Default: ['BaseCalled_template'] 131s 131s Miscellaneous Arguments: 131s --quiet, -q Don't print status information. 131s --help, -h Print this help message and exit 131s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 131s [STATISTICS_FILENAMES ...] 131s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 131s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 131s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 131s [--genome-fasta GENOME_FASTA] 131s [--pdf-filename PDF_FILENAME] 131s [--statistics-per-block STATISTICS_PER_BLOCK] 131s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 131s [--quiet] [--help] 131s 131s Required Argument: 131s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 131s Files to load genomic base anchored statistics. 131s 131s Ground Truth Arguments (provide bed files or motifs): 131s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 131s Modification description and bed format files 131s containing single base locations of ground truth 131s modified sites. Bed files should contain 6 fields 131s including strand. Format descriptions as 131s "mod_name:locs.bed". Example: "CpG 131s bisulfite":bisulfite_locs.bed 131s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 131s Bed format files containing single base locations of 131s ground truth unmodified sites. Bed files should 131s contain 6 fields including strand. 131s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 131s Ground truth, motif centered, modified base 131s descriptions for computing ROC and PR curves. Each 131s statistics file is associated with a set of motif 131s descriptions. Format descriptions as: 131s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 131s mod_pos indicates the alternate-base within the motif 131s (1-based index). Example: CCWGG:2:"dcm 131s 5mC"::GATC:2:"dam 6mA" would assess the performance of 131s a single Tombo statistics file for identification of 131s E. coli dam and dcm methylation. 131s --genome-fasta GENOME_FASTA 131s FASTA file used to re-squiggle. For faster sequence 131s access. 131s 131s Output Arguments: 131s --pdf-filename PDF_FILENAME 131s PDF filename to store plot(s). Default: 131s tombo_results.roc.pdf 131s 131s Down-sampling Arguments: 131s --statistics-per-block STATISTICS_PER_BLOCK 131s Number of randomly selected per-read, per-base 131s statistics to extract from each genomic block for 131s plotting. Default: Include all stats 131s --total-statistics-limit TOTAL_STATISTICS_LIMIT 131s Total per-read statistics to be extracted for 131s plotting. Avoids memory overflow for large runs. 131s Default: 5000000 131s 131s Miscellaneous Arguments: 131s --quiet, -q Don't print status information. 131s --help, -h Print this help message and exit 131s usage: tombo plot per_read_roc --per-read-statistics-filenames 131s PER_READ_STATISTICS_FILENAMES 131s [PER_READ_STATISTICS_FILENAMES ...] 131s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 131s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 131s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 131s [--genome-fasta GENOME_FASTA] 131s [--statistics-per-block STATISTICS_PER_BLOCK] 131s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 131s [--pdf-filename PDF_FILENAME] [--quiet] 131s [--help] 131s 131s Required Argument: 131s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 131s Binary files containing per-read statistics from 131s statistical testing. 131s 131s Ground Truth Arguments (provide bed files or motifs): 131s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 131s Modification description and bed format files 131s containing single base locations of ground truth 131s modified sites. Bed files should contain 6 fields 131s including strand. Format descriptions as 131s "mod_name:locs.bed". Example: "CpG 131s bisulfite":bisulfite_locs.bed 131s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 131s Bed format files containing single base locations of 131s ground truth unmodified sites. Bed files should 131s contain 6 fields including strand. 131s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 131s Ground truth, motif centered, modified base 131s descriptions for computing ROC and PR curves. Each 131s statistics file is associated with a set of motif 131s descriptions. Format descriptions as: 131s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 131s mod_pos indicates the alternate-base within the motif 131s (1-based index). Example: CCWGG:2:"dcm 131s 5mC"::GATC:2:"dam 6mA" would assess the performance of 131s a single Tombo statistics file for identification of 131s E. coli dam and dcm methylation. 131s --genome-fasta GENOME_FASTA 131s FASTA file used to re-squiggle. For faster sequence 131s access. 131s 131s Down-sampling Arguments: 131s --statistics-per-block STATISTICS_PER_BLOCK 131s Number of randomly selected per-read, per-base 131s statistics to extract from each genomic block for 131s plotting. Default: 100000 131s --total-statistics-limit TOTAL_STATISTICS_LIMIT 131s Total per-read statistics to be extracted for 131s plotting. Avoids memory overflow for large runs. 131s Default: 5000000 131s 131s Output Arguments: 131s --pdf-filename PDF_FILENAME 131s PDF filename to store plot(s). Default: 131s tombo_results.per_reads_roc.pdf 131s 131s Miscellaneous Arguments: 131s --quiet, -q Don't print status information. 131s --help, -h Print this help message and exit 131s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 131s [--upstream-bases {0,1,2,3,4}] 131s [--downstream-bases {0,1,2,3,4}] [--read-mean] 131s [--num-kmer-threshold NUM_KMER_THRESHOLD] 131s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 131s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 131s [--corrected-group CORRECTED_GROUP] 131s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 131s [--quiet] [--help] 131s 131s Required Argument: 131s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 131s Directories containing fast5 files. 131s 131s Data Processing Arguments: 131s --upstream-bases {0,1,2,3,4} 131s Upstream bases in k-mer. Default: 1 131s --downstream-bases {0,1,2,3,4} 131s Downstream bases in k-mer. Default: 2 131s --read-mean Plot k-mer means across whole reads as opposed to 131s individual k-mer event levels. 131s --num-kmer-threshold NUM_KMER_THRESHOLD 131s Observations of each k-mer required to include a read 131s in read level averages. Default: 1 131s 131s Plotting Region Arguments: 131s --num-reads NUM_READS 131s Number of reads to plot. Default: 100 131s 131s Output Arguments: 131s --pdf-filename PDF_FILENAME 131s PDF filename to store plot(s). Default: 131s tombo_results.kmer_distribution.pdf 131s --r-data-filename R_DATA_FILENAME 131s Filename to save R data structure. Default: Don't save 131s --dont-plot Don't plot result. Useful to produce only R data file. 131s 131s FAST5 Data Arguments: 131s --corrected-group CORRECTED_GROUP 131s FAST5 group created by resquiggle command. Default: 131s RawGenomeCorrected_000 131s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 131s FAST5 subgroup(s) (under /Analyses/[--basecall- 131s group]/) containing basecalls and created within 131s [--corrected-group] containing re-squiggle results. 131s Default: ['BaseCalled_template'] 131s 131s Miscellaneous Arguments: 131s --quiet, -q Don't print status information. 131s --help, -h Print this help message and exit 132s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 132s [FAST5_BASEDIRS ...] 132s --control-fast5-basedirs 132s CONTROL_FAST5_BASEDIRS 132s [CONTROL_FAST5_BASEDIRS ...] 132s --statistics-filename 132s STATISTICS_FILENAME 132s [--genome-fasta GENOME_FASTA] 132s [--processes PROCESSES] 132s [--num-regions NUM_REGIONS] 132s [--num-bases NUM_BASES] 132s [--slide-span SLIDE_SPAN] 132s [--pdf-filename PDF_FILENAME] 132s [--r-data-filename R_DATA_FILENAME] 132s [--corrected-group CORRECTED_GROUP] 132s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 132s [--quiet] [--help] 132s 132s Required Arguments: 132s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 132s Directories containing fast5 files. 132s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 132s Set of directories containing fast5 files for control 132s reads, containing only canonical nucleotides. 132s --statistics-filename STATISTICS_FILENAME 132s File to save/load genomic base anchored statistics. 132s 132s FASTA Sequence Argument: 132s --genome-fasta GENOME_FASTA 132s FASTA file used to re-squiggle. For faster sequence 132s access. 132s 132s Multiprocessing Argument: 132s --processes PROCESSES 132s Number of processes. Default: 1 132s 132s Plotting Region Arguments: 132s --num-regions NUM_REGIONS 132s Number of regions to plot. Default: 10 132s --num-bases NUM_BASES 132s Number of bases to plot/output. Default: 21 132s --slide-span SLIDE_SPAN 132s Number of bases offset over which to search when 132s computing distances for signal cluster plotting. 132s Default: 0 (exact position) 132s 132s Output Arguments: 132s --pdf-filename PDF_FILENAME 132s PDF filename to store plot(s). Default: 132s tombo_results.signal_clusters.pdf 132s --r-data-filename R_DATA_FILENAME 132s Filename to save R data structure. Default: Don't save 132s 132s FAST5 Data Arguments: 132s --corrected-group CORRECTED_GROUP 132s FAST5 group created by resquiggle command. Default: 132s RawGenomeCorrected_000 132s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 132s FAST5 subgroup(s) (under /Analyses/[--basecall- 132s group]/) containing basecalls and created within 132s [--corrected-group] containing re-squiggle results. 132s Default: ['BaseCalled_template'] 132s 132s Miscellaneous Arguments: 132s --quiet, -q Don't print status information. 132s --help, -h Print this help message and exit 132s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 132s 132s Required Arguments: 132s fast5s_basedir Directory containing fast5 files. All files ending in 132s "fast5" found recursively within this base directory will be 132s processed. 132s 132s Miscellaneous Arguments: 132s --quiet, -q Don't print status information. 132s --help, -h Print this help message and exit 132s usage: tombo build_model event_resquiggle 132s [--minimap2-executable MINIMAP2_EXECUTABLE] 132s [--minimap2-index MINIMAP2_INDEX] 132s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 132s [--graphmap-executable GRAPHMAP_EXECUTABLE] 132s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 132s [--normalization-type {median,pA,pA_raw,none}] 132s [--pore-model-filename PORE_MODEL_FILENAME] 132s [--outlier-threshold OUTLIER_THRESHOLD] 132s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 132s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 132s [--timeout TIMEOUT] 132s [--cpts-limit CPTS_LIMIT] 132s [--skip-index] [--overwrite] 132s [--failed-reads-filename FAILED_READS_FILENAME] 132s [--include-event-stdev] 132s [--corrected-group CORRECTED_GROUP] 132s [--basecall-group BASECALL_GROUP] 132s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 132s [--processes PROCESSES] 132s [--align-processes ALIGN_PROCESSES] 132s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 132s [--resquiggle-processes RESQUIGGLE_PROCESSES] 132s [--quiet] [--help] 132s fast5s_basedir reference_fasta 132s 132s Required Arguments: 132s fast5s_basedir Directory containing fast5 files. All files ending in 132s "fast5" found recursively within this base directory 132s will be processed. 132s reference_fasta Reference genome/transcriptome FASTA file for mapping. 132s 132s Mapper Arguments (One mapper is required): 132s --minimap2-executable MINIMAP2_EXECUTABLE 132s Path to minimap2 executable. 132s --minimap2-index MINIMAP2_INDEX 132s Path to minimap2 index (with map-ont preset) file 132s corresponding to the [genome_fasta] provided. 132s --bwa-mem-executable BWA_MEM_EXECUTABLE 132s Path to bwa-mem executable. 132s --graphmap-executable GRAPHMAP_EXECUTABLE 132s Path to graphmap executable. 132s --alignment-batch-size ALIGNMENT_BATCH_SIZE 132s Number of reads included in each alignment call. Note: 132s A new system mapping call is made for each batch 132s (including loading of the genome), so it is advised to 132s use larger values for larger genomes. Default: 1000 132s 132s Signal Processing Arguments: 132s --normalization-type {median,pA,pA_raw,none} 132s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 132s as in the ONT events (using offset, range and 132s digitization), "pA": k-mer-based correction for pA 132s drift as in nanopolish (requires [--pore-model- 132s filename]), "median": median and MAD from raw signal. 132s Default: median 132s --pore-model-filename PORE_MODEL_FILENAME 132s File containing kmer model parameters (level_mean and 132s level_stdv) used in order to compute kmer-based 132s corrected pA values. E.g. https://github.com/jts/nanop 132s olish/blob/master/etc/r9- 132s models/template_median68pA.5mers.model 132s --outlier-threshold OUTLIER_THRESHOLD 132s Windosrize the signal at this number of scale values. 132s Negative value disables outlier clipping. Default: 132s 5.000000 132s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 132s Specify the 2 parameters for segmentation 1) running 132s neighboring windows width 2) minimum raw observations 132s per genomic base. Sample type defaults: RNA : 12 6 || 132s DNA : 5 3 132s 132s Read Filtering Arguments: 132s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 132s Filter reads based on observations per base percentile 132s thresholds. Format thresholds as "percentile:thresh 132s [pctl2:thresh2 ...]". For example to filter reads with 132s 99th pctl > 200 obs/base or max > 5k obs/base use 132s "99:200 100:5000". 132s --timeout TIMEOUT Timeout in seconds for processing a single read. 132s Default: No timeout. 132s --cpts-limit CPTS_LIMIT 132s Maximum number of changepoints to find within a single 132s indel group. Default: No limit. 132s 132s Input/Output Arguments: 132s --skip-index Skip creation of tombo index. This drastically slows 132s downstream tombo commands. Default stores tombo index 132s named ".[--fast5-basedir].[--corrected- 132s group].tombo.index" to be loaded automatically for 132s downstream commands. 132s --overwrite Overwrite previous corrected group in FAST5 files. 132s Note: only effects --corrected-group or --new- 132s corrected-group. 132s --failed-reads-filename FAILED_READS_FILENAME 132s Output failed read filenames with assoicated error. 132s Default: Do not store failed reads. 132s --include-event-stdev 132s Include corrected event standard deviation in output 132s FAST5 data. 132s 132s FAST5 Data Arguments: 132s --corrected-group CORRECTED_GROUP 132s FAST5 group created by resquiggle command. Default: 132s RawGenomeCorrected_000 132s --basecall-group BASECALL_GROUP 132s FAST5 group obtain original basecalls (under Analyses 132s group). Default: Basecall_1D_000 132s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 132s FAST5 subgroup(s) (under /Analyses/[--basecall- 132s group]/) containing basecalls and created within 132s [--corrected-group] containing re-squiggle results. 132s Default: ['BaseCalled_template'] 132s 132s Multiprocessing Arguments: 132s --processes PROCESSES 132s Number of processes. Default: 2 132s --align-processes ALIGN_PROCESSES 132s Number of processes to use for parsing and aligning 132s original basecalls. Each process will independently 132s load the genome into memory, so use caution with 132s larger genomes (e.g. human). Default: 1 132s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 132s Number of threads to use for aligner system call. 132s Default: [--processes] / (2 * [--align-processes)] 132s --resquiggle-processes RESQUIGGLE_PROCESSES 132s Number of processes to use for resquiggle algorithm. 132s Default: [--processes] / 2 132s 132s Miscellaneous Arguments: 132s --quiet, -q Don't print status information. 132s --help, -h Print this help message and exit 132s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 132s [FAST5_BASEDIRS ...] 132s --tombo-model-filename 132s TOMBO_MODEL_FILENAME 132s [--estimate-mean] 132s [--kmer-specific-sd] 132s [--upstream-bases {0,1,2,3,4}] 132s [--downstream-bases {0,1,2,3,4}] 132s [--minimum-test-reads MINIMUM_TEST_READS] 132s [--coverage-threshold COVERAGE_THRESHOLD] 132s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 132s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 132s [--processes PROCESSES] 132s [--corrected-group CORRECTED_GROUP] 132s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 132s [--quiet] [--help] 132s 132s Required Arguments: 132s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 132s Directories containing fast5 files. 132s --tombo-model-filename TOMBO_MODEL_FILENAME 132s Filename to save Tombo model. 132s 132s Modeling Arguments: 132s --estimate-mean Use the mean instead of median for model level 132s estimation. Note: This can cause poor fits due to 132s outliers 132s --kmer-specific-sd Estimate standard deviation for each k-mers 132s individually. 132s --upstream-bases {0,1,2,3,4} 132s Upstream bases in k-mer. Default: 1 132s --downstream-bases {0,1,2,3,4} 132s Downstream bases in k-mer. Default: 2 132s 132s Filtering Arguments: 132s --minimum-test-reads MINIMUM_TEST_READS 132s Number of reads required at a position to perform 132s significance testing or contribute to model 132s estimation. Default: 10 132s --coverage-threshold COVERAGE_THRESHOLD 132s Maximum mean coverage per region when estimating k-mer 132s model (limits compute time for deep samples). Default: 132s 100 132s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 132s Number of each k-mer observations required in order to 132s produce a reference (genomic locations for standard 132s reference and per-read for alternative reference). 132s Default: 5 132s 132s Multiprocessing Arguments: 132s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 132s Size of regions over which to multiprocesses statistic 132s computation. For very deep samples a smaller value is 132s recommmended in order to control memory consumption. 132s Default: 10000 132s --processes PROCESSES 132s Number of processes. Default: 1 132s 132s FAST5 Data Arguments: 132s --corrected-group CORRECTED_GROUP 132s FAST5 group created by resquiggle command. Default: 132s RawGenomeCorrected_000 132s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 132s FAST5 subgroup(s) (under /Analyses/[--basecall- 132s group]/) containing basecalls and created within 132s [--corrected-group] containing re-squiggle results. 132s Default: ['BaseCalled_template'] 132s 132s Miscellaneous Arguments: 132s --quiet, -q Don't print status information. 132s --help, -h Print this help message and exit 132s usage: tombo build_model estimate_alt_reference --alternate-model-filename 132s ALTERNATE_MODEL_FILENAME 132s --alternate-model-name 132s ALTERNATE_MODEL_NAME 132s --alternate-model-base 132s {A,C,G,T} 132s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 132s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 132s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 132s [--control-density-filename CONTROL_DENSITY_FILENAME] 132s [--dna] [--rna] 132s [--tombo-model-filename TOMBO_MODEL_FILENAME] 132s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 132s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 132s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 132s [--save-density-basename SAVE_DENSITY_BASENAME] 132s [--processes PROCESSES] 132s [--corrected-group CORRECTED_GROUP] 132s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 132s [--quiet] [--help] 132s 132s Required Arguments: 132s --alternate-model-filename ALTERNATE_MODEL_FILENAME 132s Tombo model for alternative likelihood ratio 132s significance testing. 132s --alternate-model-name ALTERNATE_MODEL_NAME 132s A short name to associate with this alternate model 132s (e.g. 5mC, 6mA, etc.). This text will be included in 132s output filenames when this model is used for testing. 132s --alternate-model-base {A,C,G,T} 132s Non-standard base is an alternative to this base. 132s 132s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 132s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 132s Directories containing fast5 files. 132s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 132s Set of directories containing fast5 files for control 132s reads, containing only canonical nucleotides. 132s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 132s File containing k-mer level kernel density estimates 132s for the alternative sample saved using --save-density- 132s basename. 132s --control-density-filename CONTROL_DENSITY_FILENAME 132s File containing k-mer level kernel density estimates 132s for the control sample saved using --save-density- 132s basename. 132s 132s Standard Model Arguments: 132s --dna Explicitly select canonical DNA model. Default: 132s Automatically determine from FAST5s 132s --rna Explicitly select canonical RNA model. Default: 132s Automatically determine from FAST5s 132s --tombo-model-filename TOMBO_MODEL_FILENAME 132s Tombo model filename. If no file is provided, the 132s default DNA or RNA Tombo model will be used. 132s 132s Model Fitting Arguments: 132s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 132s When esitmating the alternative base incorporation 132s rate, this percent of k-mers are assumed to have 132s significantly shifted signal so the alternative 132s distribution minimally overlaps the standard base 132s distribution. Default: 5.000000 132s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 132s Bandwidth applied when performing Gaussian kernal 132s density esitmation on standard and alternative base 132s signal distributions. Default: 0.050000 132s 132s Filtering Argument: 132s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 132s Number of each k-mer observations required in order to 132s produce a reference (genomic locations for standard 132s reference and per-read for alternative reference). 132s Default: 1000 132s 132s Output Argument: 132s --save-density-basename SAVE_DENSITY_BASENAME 132s Basename to save alternative model estimation density 132s estimation information. See scripts/debug_est_alt.R 132s for info use example. Default: Don't save. 132s 132s Multiprocessing Arguments: 132s --processes PROCESSES 132s Number of processes. Default: 1 132s 132s FAST5 Data Arguments: 132s --corrected-group CORRECTED_GROUP 132s FAST5 group created by resquiggle command. Default: 132s RawGenomeCorrected_000 132s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 132s FAST5 subgroup(s) (under /Analyses/[--basecall- 132s group]/) containing basecalls and created within 132s [--corrected-group] containing re-squiggle results. 132s Default: ['BaseCalled_template'] 132s 132s Miscellaneous Arguments: 132s --quiet, -q Don't print status information. 132s --help, -h Print this help message and exit 132s This test only tests the help system 132s There is an extensive test in 132s 132s tombo/tests/shell_tests.sh 132s 132s but this requires to download larger data 132s sets which is not done for the moment. 132s autopkgtest [17:00:07]: test run-unit-test: -----------------------] 133s run-unit-test PASS 133s autopkgtest [17:00:08]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 133s autopkgtest [17:00:08]: @@@@@@@@@@@@@@@@@@@@ summary 133s run-unit-test PASS 146s nova [W] Using flock in prodstack6-s390x 146s Creating nova instance adt-plucky-s390x-tombo-20241114-165754-juju-7f2275-prod-proposed-migration-environment-20-f92f8426-d4b7-434a-a35f-482ce9234058 from image adt/ubuntu-plucky-s390x-server-20241114.img (UUID 41a907ef-1f3c-4685-a0eb-228b0d61c6b5)...