0s autopkgtest [16:48:04]: starting date and time: 2024-11-14 16:48:04+0000 0s autopkgtest [16:48:04]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:48:04]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fkw8zmc4/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-21.secgroup --name adt-plucky-arm64-tombo-20241114-164803-juju-7f2275-prod-proposed-migration-environment-15-fe4f66bd-58a8-471e-bde0-798f662788fa --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 67s autopkgtest [16:49:11]: testbed dpkg architecture: arm64 68s autopkgtest [16:49:12]: testbed apt version: 2.9.8 68s autopkgtest [16:49:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 68s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 69s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 69s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.6 kB] 69s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [951 kB] 69s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 69s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [136 kB] 69s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 69s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [711 kB] 69s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [5488 B] 69s Fetched 2054 kB in 1s (2095 kB/s) 69s Reading package lists... 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 73s Calculating upgrade... 73s The following packages will be upgraded: 73s libcap-ng0 pastebinit python3-systemd 74s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s Need to get 76.6 kB of archives. 74s After this operation, 349 kB of additional disk space will be used. 74s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libcap-ng0 arm64 0.8.5-3build1 [15.0 kB] 74s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pastebinit all 1.7.1-1 [14.9 kB] 74s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-systemd arm64 235-1build5 [46.7 kB] 74s Fetched 76.6 kB in 0s (219 kB/s) 74s (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 ... 79925 files and directories currently installed.) 74s Preparing to unpack .../libcap-ng0_0.8.5-3build1_arm64.deb ... 74s Unpacking libcap-ng0:arm64 (0.8.5-3build1) over (0.8.5-1) ... 74s Setting up libcap-ng0:arm64 (0.8.5-3build1) ... 75s (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 ... 79925 files and directories currently installed.) 75s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 75s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 75s Preparing to unpack .../python3-systemd_235-1build5_arm64.deb ... 75s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 75s Setting up pastebinit (1.7.1-1) ... 75s Setting up python3-systemd (235-1build5) ... 75s Processing triggers for man-db (2.12.1-3) ... 76s Processing triggers for libc-bin (2.40-1ubuntu3) ... 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 77s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 77s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 77s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 77s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 77s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 79s Reading package lists... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 80s Calculating upgrade... 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s autopkgtest [16:49:28]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 84s autopkgtest [16:49:28]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 87s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (dsc) [2291 B] 88s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (tar) [22.3 MB] 88s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (diff) [7100 B] 88s gpgv: Signature made Wed Apr 10 17:15:32 2024 UTC 88s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 88s gpgv: Can't check signature: No public key 88s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6build1.dsc: no acceptable signature found 88s autopkgtest [16:49:32]: testing package tombo version 1.5.1-6build1 89s autopkgtest [16:49:33]: build not needed 90s autopkgtest [16:49:34]: test run-unit-test: preparing testbed 91s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s Starting pkgProblemResolver with broken count: 0 92s Starting 2 pkgProblemResolver with broken count: 0 92s Done 93s The following additional packages will be installed: 93s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 93s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 93s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 93s python3-decorator python3-h5py python3-h5py-serial python3-mappy 93s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 93s tombo-doc 93s Suggested packages: 93s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 93s gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 93s Recommended packages: 93s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 93s python3-rpy2 93s The following NEW packages will be installed: 93s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 93s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 93s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 93s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 93s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 93s tombo-doc 93s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 93s Need to get 61.0 MB/61.0 MB of archives. 93s After this operation, 201 MB of additional disk space will be used. 93s Get:1 /tmp/autopkgtest.9qt5pu/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 93s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB] 94s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 94s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 94s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 94s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 94s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 94s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 94s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 94s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 94s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 94s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 94s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 94s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 94s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 94s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 94s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 94s Get:18 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB] 94s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-5ubuntu1 [1064 kB] 94s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 94s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mappy arm64 2.27+dfsg-1 [167 kB] 94s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.0-1 [91.6 kB] 94s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 94s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 94s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 tombo arm64 1.5.1-6build1 [446 kB] 94s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 95s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 tombo-doc all 1.5.1-6build1 [21.7 MB] 96s Fetched 61.0 MB in 2s (27.1 MB/s) 96s Selecting previously unselected package fonts-lato. 96s (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 ... 79930 files and directories currently installed.) 96s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 96s Unpacking fonts-lato (2.015-1) ... 96s Selecting previously unselected package fonts-font-awesome. 96s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 96s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 96s Selecting previously unselected package fonts-mathjax. 96s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 96s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 96s Selecting previously unselected package libaec0:arm64. 96s Preparing to unpack .../03-libaec0_1.1.3-1_arm64.deb ... 96s Unpacking libaec0:arm64 (1.1.3-1) ... 96s Selecting previously unselected package libblas3:arm64. 96s Preparing to unpack .../04-libblas3_3.12.0-3build2_arm64.deb ... 96s Unpacking libblas3:arm64 (3.12.0-3build2) ... 96s Selecting previously unselected package libgfortran5:arm64. 96s Preparing to unpack .../05-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 96s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 96s Selecting previously unselected package libsz2:arm64. 96s Preparing to unpack .../06-libsz2_1.1.3-1_arm64.deb ... 96s Unpacking libsz2:arm64 (1.1.3-1) ... 96s Selecting previously unselected package libhdf5-103-1t64:arm64. 96s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 96s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 96s Selecting previously unselected package libhdf5-hl-100t64:arm64. 96s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 96s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 96s Selecting previously unselected package libjs-jquery. 96s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 96s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 96s Selecting previously unselected package libjs-underscore. 96s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 96s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 97s Selecting previously unselected package libjs-sphinxdoc. 97s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-4_all.deb ... 97s Unpacking libjs-sphinxdoc (7.4.7-4) ... 97s Selecting previously unselected package liblapack3:arm64. 97s Preparing to unpack .../12-liblapack3_3.12.0-3build2_arm64.deb ... 97s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 97s Selecting previously unselected package liblbfgsb0:arm64. 97s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 97s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 97s Selecting previously unselected package liblzf1:arm64. 97s Preparing to unpack .../14-liblzf1_3.6-4_arm64.deb ... 97s Unpacking liblzf1:arm64 (3.6-4) ... 97s Selecting previously unselected package python3-decorator. 97s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 97s Unpacking python3-decorator (5.1.1-5) ... 97s Selecting previously unselected package python3-numpy. 97s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-11ubuntu1_arm64.deb ... 97s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 97s Selecting previously unselected package python3-h5py-serial. 97s Preparing to unpack .../17-python3-h5py-serial_3.11.0-5ubuntu1_arm64.deb ... 97s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 97s Selecting previously unselected package python3-h5py. 97s Preparing to unpack .../18-python3-h5py_3.11.0-5ubuntu1_all.deb ... 97s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 97s Selecting previously unselected package python3-mappy. 97s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1_arm64.deb ... 97s Unpacking python3-mappy (2.27+dfsg-1) ... 97s Selecting previously unselected package python3-tqdm. 97s Preparing to unpack .../20-python3-tqdm_4.67.0-1_all.deb ... 97s Unpacking python3-tqdm (4.67.0-1) ... 97s Selecting previously unselected package sphinx-rtd-theme-common. 97s Preparing to unpack .../21-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 97s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 97s Selecting previously unselected package python3-scipy. 97s Preparing to unpack .../22-python3-scipy_1.13.1-5_arm64.deb ... 97s Unpacking python3-scipy (1.13.1-5) ... 98s Selecting previously unselected package tombo. 98s Preparing to unpack .../23-tombo_1.5.1-6build1_arm64.deb ... 98s Unpacking tombo (1.5.1-6build1) ... 98s Selecting previously unselected package libjs-mathjax. 98s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 98s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 98s Selecting previously unselected package tombo-doc. 98s Preparing to unpack .../25-tombo-doc_1.5.1-6build1_all.deb ... 98s Unpacking tombo-doc (1.5.1-6build1) ... 99s Selecting previously unselected package autopkgtest-satdep. 99s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 99s Unpacking autopkgtest-satdep (0) ... 99s Setting up fonts-lato (2.015-1) ... 99s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 99s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 99s Setting up python3-tqdm (4.67.0-1) ... 99s Setting up python3-mappy (2.27+dfsg-1) ... 99s Setting up libaec0:arm64 (1.1.3-1) ... 99s Setting up python3-decorator (5.1.1-5) ... 99s Setting up libblas3:arm64 (3.12.0-3build2) ... 99s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 99s Setting up liblzf1:arm64 (3.6-4) ... 99s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 99s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 99s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 99s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 99s Setting up libsz2:arm64 (1.1.3-1) ... 99s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 99s Setting up liblapack3:arm64 (3.12.0-3build2) ... 99s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 99s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 101s Setting up libjs-sphinxdoc (7.4.7-4) ... 101s Setting up tombo-doc (1.5.1-6build1) ... 101s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 101s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 101s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 101s Setting up python3-scipy (1.13.1-5) ... 105s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 105s Setting up python3-h5py (3.11.0-5ubuntu1) ... 105s Setting up tombo (1.5.1-6build1) ... 105s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 105s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 106s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 106s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 106s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 106s re.match('\+', fastq_rec[2]) is None): 106s Setting up autopkgtest-satdep (0) ... 106s Processing triggers for man-db (2.12.1-3) ... 106s Processing triggers for libc-bin (2.40-1ubuntu3) ... 110s (Reading database ... 87152 files and directories currently installed.) 110s Removing autopkgtest-satdep (0) ... 112s autopkgtest [16:49:56]: test run-unit-test: [----------------------- 112s ********* Testing help commands ********** 112s usage: tombo [-h] [-v] 112s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 112s ... 112s 112s ********** Tombo ********* 112s 112s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 112s 112s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 112s 112s Tombo command groups (additional help available within each command group): 112s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 112s preprocess Pre-process nanopore reads for Tombo processing. 112s filter Apply filter to Tombo index file for specified criterion. 112s detect_modifications Perform statistical testing to detect non-standard nucleotides. 112s text_output Output Tombo results in text files. 112s build_model Create canonical and alternative base Tombo models. 112s plot Save plots to visualize raw nanopore signal or testing results. 112s 112s options: 112s -h, --help show this help message and exit 112s -v, --version show Tombo version and exit. 112s usage: tombo resquiggle [--dna] [--rna] 112s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 112s [--q-score Q_SCORE] 112s [--signal-matching-score SIGNAL_MATCHING_SCORE] 112s [--processes PROCESSES] 112s [--corrected-group CORRECTED_GROUP] 112s [--basecall-group BASECALL_GROUP] 112s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 112s [--overwrite] 112s [--failed-reads-filename FAILED_READS_FILENAME] 112s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 112s [--print-advanced-arguments] [--quiet] [--help] 112s fast5s_basedir reference 112s 112s Required Arguments: 112s fast5s_basedir Directory containing fast5 files. All files ending in 112s "fast5" found recursively within this base directory 112s will be processed. 112s reference Reference genome/transcriptome FASTA file or minimap2 112s index (with "map-ont" preset) for mapping. 112s 112s Model Parameters: 112s --dna Explicitly select canonical DNA model. Default: 112s Automatically determine from FAST5s 112s --rna Explicitly select canonical RNA model. Default: 112s Automatically determine from FAST5s 112s 112s Read Filtering Argument: 112s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 112s Filter reads based on observations per base percentile 112s thresholds. Format thresholds as "percentile:thresh 112s [pctl2:thresh2 ...]". For example to filter reads with 112s 99th pctl > 200 obs/base or max > 5k obs/base use 112s "99:200 100:5000". 112s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 112s Default: 0.000000 112s --signal-matching-score SIGNAL_MATCHING_SCORE 112s Observed to expected signal matching score (higher 112s score indicates poor matching). Sample type defaults: 112s RNA : 2 || DNA : 1.1 112s 112s Multiprocessing Arguments: 112s --processes PROCESSES 112s Number of processes. Default: 1 112s 112s FAST5 Data Arguments: 112s --corrected-group CORRECTED_GROUP 112s FAST5 group created by resquiggle command. Default: 112s RawGenomeCorrected_000 112s --basecall-group BASECALL_GROUP 112s FAST5 group obtain original basecalls (under Analyses 112s group). Default: Basecall_1D_000 112s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 112s FAST5 subgroup(s) (under /Analyses/[--basecall- 112s group]/) containing basecalls and created within 112s [--corrected-group] containing re-squiggle results. 112s Default: ['BaseCalled_template'] 112s --overwrite Overwrite previous corrected group in FAST5 files. 112s Note: only effects --corrected-group or --new- 112s corrected-group. 112s 112s Input/Output Arguments: 112s --failed-reads-filename FAILED_READS_FILENAME 112s Output failed read filenames with assoicated error. 112s Default: Do not store failed reads. 112s --num-most-common-errors NUM_MOST_COMMON_ERRORS 112s Dynamically show this many most common errors so far 112s through run. Default: 0; Just show progress 112s 112s Advanced Arguments: 112s --print-advanced-arguments 112s Print advanced re-squiggle arguments and exit. 112s 112s Miscellaneous Arguments: 112s --quiet, -q Don't print status information. 112s --help, -h Print this help message and exit 113s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 113s --fastq-filenames 113s FASTQ_FILENAMES 113s [FASTQ_FILENAMES ...] 113s [--basecall-group BASECALL_GROUP] 113s [--basecall-subgroup BASECALL_SUBGROUP] 113s [--overwrite] 113s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 113s [--processes PROCESSES] 113s [--quiet] [--help] 113s 113s Required Arguments: 113s --fast5-basedir FAST5_BASEDIR 113s Directory containing fast5 files. 113s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 113s FASTQ filenames containing basecalls to be added to 113s raw FAST5 files. 113s 113s FAST5 Data Arguments: 113s --basecall-group BASECALL_GROUP 113s FAST5 group obtain original basecalls (under Analyses 113s group). Default: Basecall_1D_000 113s --basecall-subgroup BASECALL_SUBGROUP 113s FAST5 subgroup (under /Analyses/[--basecall-group]/) 113s under which to store basecalls from FASTQs. Default: 113s BaseCalled_template 113s --overwrite Overwrite previous corrected group in FAST5 files. 113s Note: only effects --corrected-group or --new- 113s corrected-group. 113s 113s Sequencing Summary Argument: 113s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 113s Sequencing summary filenames produced by albacore. 113s These can make annotation of raw FAST5 files with 113s FASTQ sequence much faster. 113s 113s Multiprocessing Argument: 113s --processes PROCESSES 113s Number of processes. Default: 1 113s 113s Miscellaneous Arguments: 113s --quiet, -q Don't print status information. 113s --help, -h Print this help message and exit 113s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 113s [FAST5_BASEDIRS ...] 113s [--corrected-group CORRECTED_GROUP] 113s [--quiet] [--help] 113s 113s Required Argument: 113s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 113s Directories containing fast5 files. 113s 113s FAST5 Data Argument: 113s --corrected-group CORRECTED_GROUP 113s FAST5 group created by resquiggle command. Default: 113s RawGenomeCorrected_000 113s 113s Miscellaneous Arguments: 113s --quiet, -q Don't print status information. 113s --help, -h Print this help message and exit 113s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 113s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 113s [--corrected-group CORRECTED_GROUP] [--quiet] 113s [--help] 113s 113s Required Argument: 113s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 113s Directories containing fast5 files. 113s 113s Read Filtering Argument: 113s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 113s Filter reads based on observations per base percentile 113s thresholds. Format thresholds as "percentile:thresh 113s [pctl2:thresh2 ...]". For example to filter reads with 113s 99th pctl > 200 obs/base or max > 5k obs/base use 113s "99:200 100:5000". 113s 113s FAST5 Data Argument: 113s --corrected-group CORRECTED_GROUP 113s FAST5 group created by resquiggle command. Default: 113s RawGenomeCorrected_000 113s 113s Miscellaneous Arguments: 113s --quiet, -q Don't print status information. 113s --help, -h Print this help message and exit 113s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 113s [FAST5_BASEDIRS ...] 113s [--percent-to-filter PERCENT_TO_FILTER] 113s [--corrected-group CORRECTED_GROUP] 113s [--quiet] [--help] 113s 113s Required Arguments: 113s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 113s Directories containing fast5 files. 113s 113s Read Filtering Argument: 113s --percent-to-filter PERCENT_TO_FILTER 113s Percentage of all reads to filter. Reads are randomly 113s selected weighted according to the approximate 113s coverage at the mapped genomic location. This can be 113s useful in modeling and testing. Default: 10.000000 113s 113s FAST5 Data Arguments: 113s --corrected-group CORRECTED_GROUP 113s FAST5 group created by resquiggle command. Default: 113s RawGenomeCorrected_000 113s 113s Miscellaneous Arguments: 113s --quiet, -q Don't print status information. 113s --help, -h Print this help message and exit 113s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 113s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 113s [--corrected-group CORRECTED_GROUP] 113s [--basecall-group BASECALL_GROUP] [--quiet] 113s [--help] 113s 113s Required Arguments: 113s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 113s Directories containing fast5 files. 113s 113s Read Filtering Argument: 113s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 113s Default: 7.000000 113s 113s FAST5 Data Arguments: 113s --corrected-group CORRECTED_GROUP 113s FAST5 group created by resquiggle command. Default: 113s RawGenomeCorrected_000 113s --basecall-group BASECALL_GROUP 113s FAST5 group obtain original basecalls (under Analyses 113s group). Default: Basecall_1D_000 113s 113s Miscellaneous Arguments: 113s --quiet, -q Don't print status information. 113s --help, -h Print this help message and exit 113s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 113s [FAST5_BASEDIRS ...] 113s --signal-matching-score 113s SIGNAL_MATCHING_SCORE 113s [--corrected-group CORRECTED_GROUP] 113s [--quiet] [--help] 113s 113s Required Arguments: 113s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 113s Directories containing fast5 files. 113s --signal-matching-score SIGNAL_MATCHING_SCORE 113s Observed to expected signal matching score (higher 113s score indicates poor matching). Sample type defaults: 113s RNA : 2 || DNA : 1.1 113s 113s FAST5 Data Arguments: 113s --corrected-group CORRECTED_GROUP 113s FAST5 group created by resquiggle command. Default: 113s RawGenomeCorrected_000 113s 113s Miscellaneous Arguments: 113s --quiet, -q Don't print status information. 113s --help, -h Print this help message and exit 113s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 113s [FAST5_BASEDIRS ...] 113s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 113s [--include-partial-overlap] 113s [--corrected-group CORRECTED_GROUP] 113s [--quiet] [--help] 113s 113s Required Arguments: 113s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 113s Directories containing fast5 files. 113s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 113s Filter out reads not falling completely within include 113s regions. Omit start and end coordinates to include an 113s entire chromosome/sequence record. Format regions as 113s "chrm[:start-end] [chrm2[:start2-end2] ...]". 113s 113s Filter Argument: 113s --include-partial-overlap 113s Include reads that partially overlap the specified 113s region. Default: Only include reads completely 113s contained in a specified region 113s 113s FAST5 Data Argument: 113s --corrected-group CORRECTED_GROUP 113s FAST5 group created by resquiggle command. Default: 113s RawGenomeCorrected_000 113s 113s Miscellaneous Arguments: 113s --quiet, -q Don't print status information. 113s --help, -h Print this help message and exit 113s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 113s [FAST5_BASEDIRS ...] 113s --statistics-file-basename 113s STATISTICS_FILE_BASENAME [--dna] 113s [--rna] 113s [--fishers-method-context FISHERS_METHOD_CONTEXT] 113s [--minimum-test-reads MINIMUM_TEST_READS] 113s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 113s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 113s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 113s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 113s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 113s [--processes PROCESSES] 113s [--corrected-group CORRECTED_GROUP] 113s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 113s [--quiet] [--help] 113s 113s Required Argument: 113s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 113s Directories containing fast5 files. 113s --statistics-file-basename STATISTICS_FILE_BASENAME 113s File base name to save base by base statistics from 113s testing. Filenames will be [--statistics-file- 113s basename].[--alternate-bases]?.tombo.stats 113s 113s Comparison Model Arguments: 113s --dna Explicitly select canonical DNA model. Default: 113s Automatically determine from FAST5s 113s --rna Explicitly select canonical RNA model. Default: 113s Automatically determine from FAST5s 113s 113s Significance Test Arguments: 113s --fishers-method-context FISHERS_METHOD_CONTEXT 113s Number of context bases up and downstream over which 113s to compute Fisher's method combined p-values. Note: 113s Not applicable for alternative model likelihood ratio 113s tests. Default: 1. 113s --minimum-test-reads MINIMUM_TEST_READS 113s Number of reads required at a position to perform 113s significance testing or contribute to model 113s estimation. Default: 1 113s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 113s P-value threshold when computing fraction of 113s significant reads at each genomic position. If two 113s values are provided, statistics between these values 113s are not considered. Default thresholds: DNA:0.15-0.5 , 113s RNA:0.05-0.4 113s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 113s Dampen fraction modified estimates for low coverage 113s sites. Two parameters are unmodified and modified 113s pseudo read counts. This is equivalent to a beta prior 113s on the fraction estimate. Set to "0 0" to disable 113s dampened fraction estimation. Default: [2, 0] 113s 113s Output Argument: 113s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 113s Base for binary files containing per-read statistics 113s from statistical testing. Filenames will be [--per- 113s read-statistics-basename].[--alternate- 113s bases]?.tombo.per_read_stats 113s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 113s Number of the most significant sites to store for 113s faster access. If a longer list of most significant 113s sites is required the list must be re-computed from 113s all batches. Very large values can increase RAM usage. 113s Default: 100000 113s 113s Multiprocessing Arguments: 113s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 113s Size of regions over which to multiprocesses statistic 113s computation. For very deep samples a smaller value is 113s recommmended in order to control memory consumption. 113s Default: 10000 113s --processes PROCESSES 113s Number of processes. Default: 1 113s 113s FAST5 Data Arguments: 113s --corrected-group CORRECTED_GROUP 113s FAST5 group created by resquiggle command. Default: 113s RawGenomeCorrected_000 113s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 113s FAST5 subgroup(s) (under /Analyses/[--basecall- 113s group]/) containing basecalls and created within 113s [--corrected-group] containing re-squiggle results. 113s Default: ['BaseCalled_template'] 113s 113s Miscellaneous Arguments: 113s --quiet, -q Don't print status information. 113s --help, -h Print this help message and exit 114s usage: tombo detect_modifications alternative_model 114s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 114s [--statistics-file-basename STATISTICS_FILE_BASENAME] 114s [--alternate-bases {dcm,5mC,dam,CpG,6mA} [{dcm,5mC,dam,CpG,6mA} ...]] 114s [--print-available-models] 114s [--dna] [--rna] 114s [--minimum-test-reads MINIMUM_TEST_READS] 114s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 114s [--standard-log-likelihood-ratio] 114s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 114s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 114s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 114s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 114s [--processes PROCESSES] 114s [--corrected-group CORRECTED_GROUP] 114s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 114s [--quiet] [--help] 114s 114s Required Argument: 114s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 114s Directories containing fast5 files. 114s --statistics-file-basename STATISTICS_FILE_BASENAME 114s File base name to save base by base statistics from 114s testing. Filenames will be [--statistics-file- 114s basename].[--alternate-bases]?.tombo.stats 114s --alternate-bases {dcm,5mC,dam,CpG,6mA} [{dcm,5mC,dam,CpG,6mA} ...] 114s Default non-standard base model for testing (not 114s required if user created --alternate-model-filenames 114s is provided). 114s 114s Comparison Arguments: 114s --print-available-models 114s Print available alternative models and exit. 114s --dna Explicitly select canonical DNA model. Default: 114s Automatically determine from FAST5s 114s --rna Explicitly select canonical RNA model. Default: 114s Automatically determine from FAST5s 114s 114s Significance Test Arguments: 114s --minimum-test-reads MINIMUM_TEST_READS 114s Number of reads required at a position to perform 114s significance testing or contribute to model 114s estimation. Default: 1 114s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 114s Log likelihood ratio threshold when computing fraction 114s of significant reads at each genomic position. If two 114s values are provided, statistics between these values 114s are not considered. Default thresholds: DNA:-1.5-2.5 , 114s RNA:-2.5-2.5 114s --standard-log-likelihood-ratio 114s Use a standard log likelihood ratio (LLR) statistic. 114s Default is to use an outlier-robust LLR-like 114s statistic. Detail in full online documentation. 114s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 114s Dampen fraction modified estimates for low coverage 114s sites. Two parameters are unmodified and modified 114s pseudo read counts. This is equivalent to a beta prior 114s on the fraction estimate. Set to "0 0" to disable 114s dampened fraction estimation. Default: [2, 0] 114s 114s Output Argument: 114s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 114s Base for binary files containing per-read statistics 114s from statistical testing. Filenames will be [--per- 114s read-statistics-basename].[--alternate- 114s bases]?.tombo.per_read_stats 114s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 114s Number of the most significant sites to store for 114s faster access. If a longer list of most significant 114s sites is required the list must be re-computed from 114s all batches. Very large values can increase RAM usage. 114s Default: 100000 114s 114s Multiprocessing Arguments: 114s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 114s Size of regions over which to multiprocesses statistic 114s computation. For very deep samples a smaller value is 114s recommmended in order to control memory consumption. 114s Default: 10000 114s --processes PROCESSES 114s Number of processes. Default: 1 114s 114s FAST5 Data Arguments: 114s --corrected-group CORRECTED_GROUP 114s FAST5 group created by resquiggle command. Default: 114s RawGenomeCorrected_000 114s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 114s FAST5 subgroup(s) (under /Analyses/[--basecall- 114s group]/) containing basecalls and created within 114s [--corrected-group] containing re-squiggle results. 114s Default: ['BaseCalled_template'] 114s 114s Miscellaneous Arguments: 114s --quiet, -q Don't print status information. 114s --help, -h Print this help message and exit 114s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 114s FAST5_BASEDIRS 114s [FAST5_BASEDIRS ...] 114s --statistics-file-basename 114s STATISTICS_FILE_BASENAME 114s --control-fast5-basedirs 114s CONTROL_FAST5_BASEDIRS 114s [CONTROL_FAST5_BASEDIRS ...] 114s [--sample-only-estimates] 114s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 114s [--dna] [--rna] 114s [--fishers-method-context FISHERS_METHOD_CONTEXT] 114s [--minimum-test-reads MINIMUM_TEST_READS] 114s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 114s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 114s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 114s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 114s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 114s [--processes PROCESSES] 114s [--corrected-group CORRECTED_GROUP] 114s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 114s [--quiet] [--help] 114s 114s Required Argument: 114s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 114s Directories containing fast5 files. 114s --statistics-file-basename STATISTICS_FILE_BASENAME 114s File base name to save base by base statistics from 114s testing. Filenames will be [--statistics-file- 114s basename].[--alternate-bases]?.tombo.stats 114s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 114s Set of directories containing fast5 files for control 114s reads, containing only canonical nucleotides. 114s 114s Model Prior Arguments: 114s --sample-only-estimates 114s Only use canonical sample to estimate expected signal 114s level and spread. Default: Use canonical model to 114s improve estimtates (esp. for low coverage regions) 114s using baysian posterior estimates. 114s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 114s Prior weights (one each for mean and spread) applied 114s to canonical base model for estimating posterior model 114s parameters for sample comparison. Default: [5, 40] 114s --dna Explicitly select canonical DNA model. Default: 114s Automatically determine from FAST5s 114s --rna Explicitly select canonical RNA model. Default: 114s Automatically determine from FAST5s 114s 114s Significance Test Arguments: 114s --fishers-method-context FISHERS_METHOD_CONTEXT 114s Number of context bases up and downstream over which 114s to compute Fisher's method combined p-values. Note: 114s Not applicable for alternative model likelihood ratio 114s tests. Default: 1. 114s --minimum-test-reads MINIMUM_TEST_READS 114s Number of reads required at a position to perform 114s significance testing or contribute to model 114s estimation. Default: 1 114s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 114s P-value threshold when computing fraction of 114s significant reads at each genomic position. If two 114s values are provided, statistics between these values 114s are not considered. Default thresholds: DNA:0.15-0.5 , 114s RNA:0.05-0.4 114s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 114s Dampen fraction modified estimates for low coverage 114s sites. Two parameters are unmodified and modified 114s pseudo read counts. This is equivalent to a beta prior 114s on the fraction estimate. Set to "0 0" to disable 114s dampened fraction estimation. Default: [2, 0] 114s 114s Output Argument: 114s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 114s Base for binary files containing per-read statistics 114s from statistical testing. Filenames will be [--per- 114s read-statistics-basename].[--alternate- 114s bases]?.tombo.per_read_stats 114s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 114s Number of the most significant sites to store for 114s faster access. If a longer list of most significant 114s sites is required the list must be re-computed from 114s all batches. Very large values can increase RAM usage. 114s Default: 100000 114s 114s Multiprocessing Arguments: 114s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 114s Size of regions over which to multiprocesses statistic 114s computation. For very deep samples a smaller value is 114s recommmended in order to control memory consumption. 114s Default: 10000 114s --processes PROCESSES 114s Number of processes. Default: 1 114s 114s FAST5 Data Arguments: 114s --corrected-group CORRECTED_GROUP 114s FAST5 group created by resquiggle command. Default: 114s RawGenomeCorrected_000 114s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 114s FAST5 subgroup(s) (under /Analyses/[--basecall- 114s group]/) containing basecalls and created within 114s [--corrected-group] containing re-squiggle results. 114s Default: ['BaseCalled_template'] 114s 114s Miscellaneous Arguments: 114s --quiet, -q Don't print status information. 114s --help, -h Print this help message and exit 114s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 114s FAST5_BASEDIRS 114s [FAST5_BASEDIRS ...] 114s --statistics-file-basename 114s STATISTICS_FILE_BASENAME 114s --alternate-fast5-basedirs 114s ALTERNATE_FAST5_BASEDIRS 114s [ALTERNATE_FAST5_BASEDIRS ...] 114s [--fishers-method-context FISHERS_METHOD_CONTEXT] 114s [--minimum-test-reads MINIMUM_TEST_READS] 114s [--statistic-type {ks,u,t}] 114s [--store-p-value] 114s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 114s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 114s [--processes PROCESSES] 114s [--corrected-group CORRECTED_GROUP] 114s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 114s [--quiet] [--help] 114s 114s Required Argument: 114s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 114s Directories containing fast5 files. 114s --statistics-file-basename STATISTICS_FILE_BASENAME 114s File base name to save base by base statistics from 114s testing. Filenames will be [--statistics-file- 114s basename].[--alternate-bases]?.tombo.stats 114s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 114s Set of directories containing fast5 files for 114s alternate set of reads. 114s 114s Significance Test Arguments: 114s --fishers-method-context FISHERS_METHOD_CONTEXT 114s Number of context bases up and downstream over which 114s to compute Fisher's method combined p-values. Note: 114s Not applicable for alternative model likelihood ratio 114s tests. Default: 1. 114s --minimum-test-reads MINIMUM_TEST_READS 114s Number of reads required at a position to perform 114s significance testing or contribute to model 114s estimation. Default: 50 114s --statistic-type {ks,u,t} 114s Type of statistical test to apply. Default: "ks" 114s --store-p-value Store p-value instead of effect-size statistic. 114s Statistics are D-statistic (KS-test), deviation from 114s even common language effect size (u-test), and Cohen's 114s D (t-test). 114s 114s Output Argument: 114s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 114s Number of the most significant sites to store for 114s faster access. If a longer list of most significant 114s sites is required the list must be re-computed from 114s all batches. Very large values can increase RAM usage. 114s Default: 100000 114s 114s Multiprocessing Arguments: 114s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 114s Size of regions over which to multiprocesses statistic 114s computation. For very deep samples a smaller value is 114s recommmended in order to control memory consumption. 114s Default: 10000 114s --processes PROCESSES 114s Number of processes. Default: 1 114s 114s FAST5 Data Arguments: 114s --corrected-group CORRECTED_GROUP 114s FAST5 group created by resquiggle command. Default: 114s RawGenomeCorrected_000 114s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 114s FAST5 subgroup(s) (under /Analyses/[--basecall- 114s group]/) containing basecalls and created within 114s [--corrected-group] containing re-squiggle results. 114s Default: ['BaseCalled_template'] 114s 114s Miscellaneous Arguments: 114s --quiet, -q Don't print status information. 114s --help, -h Print this help message and exit 114s usage: tombo detect_modifications aggregate_per_read_stats 114s --per-read-statistics-filename 114s PER_READ_STATISTICS_FILENAME 114s --statistics-filename 114s STATISTICS_FILENAME 114s --single-read-threshold 114s SINGLE_READ_THRESHOLD 114s [SINGLE_READ_THRESHOLD ...] 114s [--minimum-test-reads MINIMUM_TEST_READS] 114s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 114s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 114s [--processes PROCESSES] 114s [--corrected-group CORRECTED_GROUP] 114s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 114s [--quiet] [--help] 114s 114s Required Argument: 114s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 114s Binary file containing per-read statistics from 114s statistical testing. 114s --statistics-filename STATISTICS_FILENAME 114s File to save/load genomic base anchored statistics. 114s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 114s P-value or log likelihood ratio threshold when 114s computing fraction of significant reads at each 114s genomic position. If two values are provided, 114s statistics between these values are not considered. 114s 114s Significance Test Arguments: 114s --minimum-test-reads MINIMUM_TEST_READS 114s Number of reads required at a position to perform 114s significance testing or contribute to model 114s estimation. Default: 1 114s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 114s Dampen fraction modified estimates for low coverage 114s sites. Two parameters are unmodified and modified 114s pseudo read counts. This is equivalent to a beta prior 114s on the fraction estimate. Set to "0 0" to disable 114s dampened fraction estimation. Default: [2, 0] 114s 114s Output Argument: 114s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 114s Number of the most significant sites to store for 114s faster access. If a longer list of most significant 114s sites is required the list must be re-computed from 114s all batches. Very large values can increase RAM usage. 114s Default: 100000 114s 114s Multiprocessing Arguments: 114s --processes PROCESSES 114s Number of processes. Default: 1 114s 114s FAST5 Data Arguments: 114s --corrected-group CORRECTED_GROUP 114s FAST5 group created by resquiggle command. Default: 114s RawGenomeCorrected_000 114s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 114s FAST5 subgroup(s) (under /Analyses/[--basecall- 114s group]/) containing basecalls and created within 114s [--corrected-group] containing re-squiggle results. 114s Default: ['BaseCalled_template'] 114s 114s Miscellaneous Arguments: 114s --quiet, -q Don't print status information. 114s --help, -h Print this help message and exit 114s usage: tombo text_output browser_files 114s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 114s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 114s [--statistics-filename STATISTICS_FILENAME] 114s [--genome-fasta GENOME_FASTA] 114s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 114s [--browser-file-basename BROWSER_FILE_BASENAME] 114s [--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} ...]] 114s [--corrected-group CORRECTED_GROUP] 114s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 114s [--quiet] [--help] 114s 114s Data Arguments: 114s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 114s Directories containing fast5 files. 114s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 114s Set of directories containing fast5 files for control 114s reads, containing only canonical nucleotides. 114s --statistics-filename STATISTICS_FILENAME 114s File to save/load genomic base anchored statistics. 114s 114s Statistic Motif Filter Arguments: 114s --genome-fasta GENOME_FASTA 114s FASTA file used to re-squiggle. For faster sequence 114s access. 114s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 114s Ground truth, motif centered, modified base 114s descriptions for output filtering. Format descriptions 114s as: "motif:mod_pos:name". The mod_pos indicates the 114s modified base within the motif (1-based index). 114s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 114s output for identification of E. coli dam and dcm 114s methylation. 114s 114s Output Arguments: 114s --browser-file-basename BROWSER_FILE_BASENAME 114s Basename for output browser files. Two files (plus and 114s minus strand) will be produced for each --file-types 114s supplied. Filenames formatted as "[browser-file- 114s basename].[file- 114s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 114s Default: tombo_results 114s --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} ...] 114s Data types of genome browser files to produce. 114s Produced coverage files are in bedGraph format, while 114s all other file types will be in wiggle format 114s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 114s Default: "coverage" 114s 114s FAST5 Data Arguments: 114s --corrected-group CORRECTED_GROUP 114s FAST5 group created by resquiggle command. Default: 114s RawGenomeCorrected_000 114s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 114s FAST5 subgroup(s) (under /Analyses/[--basecall- 114s group]/) containing basecalls and created within 114s [--corrected-group] containing re-squiggle results. 114s Default: ['BaseCalled_template'] 114s 114s Miscellaneous Arguments: 114s --quiet, -q Don't print status information. 114s --help, -h Print this help message and exit 114s usage: tombo text_output signif_sequence_context --statistics-filename 114s STATISTICS_FILENAME 114s [--genome-fasta GENOME_FASTA] 114s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 114s [--num-regions NUM_REGIONS] 114s [--num-bases NUM_BASES] 114s [--sequences-filename SEQUENCES_FILENAME] 114s [--corrected-group CORRECTED_GROUP] 114s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 114s [--quiet] [--help] 114s 114s Required Argument: 114s --statistics-filename STATISTICS_FILENAME 114s File to save/load genomic base anchored statistics. 114s 114s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 114s --genome-fasta GENOME_FASTA 114s FASTA file used to re-squiggle. For faster sequence 114s access. 114s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 114s Directories containing fast5 files. 114s 114s Region Selection Arguments: 114s --num-regions NUM_REGIONS 114s Number of regions to plot. Default: 100 114s --num-bases NUM_BASES 114s Number of bases to plot/output. Default: 15 114s 114s Output Arguments: 114s --sequences-filename SEQUENCES_FILENAME 114s File for sequences from selected regions. Sequences 114s will be stored in FASTA format. Default: 114s tombo_results.significant_regions.fasta. 114s 114s FAST5 Data Arguments: 114s --corrected-group CORRECTED_GROUP 114s FAST5 group created by resquiggle command. Default: 114s RawGenomeCorrected_000 114s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 114s FAST5 subgroup(s) (under /Analyses/[--basecall- 114s group]/) containing basecalls and created within 114s [--corrected-group] containing re-squiggle results. 114s Default: ['BaseCalled_template'] 114s 114s Miscellaneous Arguments: 114s --quiet, -q Don't print status information. 114s --help, -h Print this help message and exit 114s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 114s [FAST5_BASEDIRS ...] 114s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 114s [--plot-standard-model] 114s [--plot-alternate-model {dam,5mC,dcm,6mA,CpG}] 114s [--overplot-threshold OVERPLOT_THRESHOLD] 114s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 114s [--num-regions NUM_REGIONS] 114s [--num-bases NUM_BASES] 114s [--pdf-filename PDF_FILENAME] 114s [--corrected-group CORRECTED_GROUP] 114s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 114s [--quiet] [--help] 114s 114s Required Argument: 114s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 114s Directories containing fast5 files. 114s 114s Comparison Arguments: 114s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 114s Set of directories containing fast5 files for control 114s reads, containing only canonical nucleotides. 114s --plot-standard-model 114s Add default standard model distribution to the plot. 114s --plot-alternate-model {dam,5mC,dcm,6mA,CpG} 114s Add alternative model distribution to the plot. 114s 114s Overplotting Arguments: 114s --overplot-threshold OVERPLOT_THRESHOLD 114s Coverage level to trigger alternative plot type 114s instead of raw signal. Default: 50 114s --overplot-type {Downsample,Boxplot,Quantile,Density} 114s Plot type for regions with higher coverage. Default: 114s Downsample 114s 114s Plotting Region Arguments: 114s --num-regions NUM_REGIONS 114s Number of regions to plot. Default: 10 114s --num-bases NUM_BASES 114s Number of bases to plot/output. Default: 21 114s 114s Output Argument: 114s --pdf-filename PDF_FILENAME 114s PDF filename to store plot(s). Default: 114s tombo_results.max_coverage.pdf 114s 114s FAST5 Data Arguments: 114s --corrected-group CORRECTED_GROUP 114s FAST5 group created by resquiggle command. Default: 114s RawGenomeCorrected_000 114s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 114s FAST5 subgroup(s) (under /Analyses/[--basecall- 114s group]/) containing basecalls and created within 114s [--corrected-group] containing re-squiggle results. 114s Default: ['BaseCalled_template'] 114s 114s Miscellaneous Arguments: 114s --quiet, -q Don't print status information. 114s --help, -h Print this help message and exit 114s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 114s [FAST5_BASEDIRS ...] --genome-locations 114s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 114s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 114s [--plot-standard-model] 114s [--plot-alternate-model {5mC,dam,6mA,CpG,dcm}] 114s [--overplot-threshold OVERPLOT_THRESHOLD] 114s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 114s [--num-bases NUM_BASES] 114s [--pdf-filename PDF_FILENAME] 114s [--corrected-group CORRECTED_GROUP] 114s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 114s [--quiet] [--help] 114s 114s Required Arguments: 114s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 114s Directories containing fast5 files. 114s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 114s Genomic locations at which to plot signal. Format 114s locations as "chrm:position[:strand] 114s [chrm2:position2[:strand2] ...]" (strand not 114s applicable for all applications) 114s 114s Comparison Arguments: 114s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 114s Set of directories containing fast5 files for control 114s reads, containing only canonical nucleotides. 114s --plot-standard-model 114s Add default standard model distribution to the plot. 114s --plot-alternate-model {5mC,dam,6mA,CpG,dcm} 114s Add alternative model distribution to the plot. 114s 114s Overplotting Arguments: 114s --overplot-threshold OVERPLOT_THRESHOLD 114s Coverage level to trigger alternative plot type 114s instead of raw signal. Default: 50 114s --overplot-type {Downsample,Boxplot,Quantile,Density} 114s Plot type for regions with higher coverage. Default: 114s Downsample 114s 114s Plotting Region Argument: 114s --num-bases NUM_BASES 114s Number of bases to plot/output. Default: 21 114s 114s Output Argument: 114s --pdf-filename PDF_FILENAME 114s PDF filename to store plot(s). Default: 114s tombo_results.genome_locations.pdf 114s 114s FAST5 Data Arguments: 114s --corrected-group CORRECTED_GROUP 114s FAST5 group created by resquiggle command. Default: 114s RawGenomeCorrected_000 114s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 114s FAST5 subgroup(s) (under /Analyses/[--basecall- 114s group]/) containing basecalls and created within 114s [--corrected-group] containing re-squiggle results. 114s Default: ['BaseCalled_template'] 114s 114s Miscellaneous Arguments: 114s --quiet, -q Don't print status information. 114s --help, -h Print this help message and exit 114s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 114s [FAST5_BASEDIRS ...] --motif MOTIF 114s --genome-fasta GENOME_FASTA 114s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 114s [--plot-standard-model] 114s [--plot-alternate-model {5mC,CpG,6mA,dcm,dam}] 114s [--overplot-threshold OVERPLOT_THRESHOLD] 114s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 114s [--num-regions NUM_REGIONS] 114s [--num-bases NUM_BASES] [--deepest-coverage] 114s [--pdf-filename PDF_FILENAME] 114s [--corrected-group CORRECTED_GROUP] 114s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 114s [--quiet] [--help] 114s 114s Required Arguments: 114s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 114s Directories containing fast5 files. 114s --motif MOTIF Motif of interest at which to plot signal and 114s statsitics. Supports IUPAC single letter codes (use T 114s for RNA). 114s --genome-fasta GENOME_FASTA 114s FASTA file used to re-squiggle. For faster sequence 114s access. 114s 114s Comparison Arguments: 114s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 114s Set of directories containing fast5 files for control 114s reads, containing only canonical nucleotides. 114s --plot-standard-model 114s Add default standard model distribution to the plot. 114s --plot-alternate-model {5mC,CpG,6mA,dcm,dam} 114s Add alternative model distribution to the plot. 114s 114s Overplotting Arguments: 114s --overplot-threshold OVERPLOT_THRESHOLD 114s Coverage level to trigger alternative plot type 114s instead of raw signal. Default: 50 114s --overplot-type {Downsample,Boxplot,Quantile,Density} 114s Plot type for regions with higher coverage. Default: 114s Downsample 114s 114s Plotting Region Arguments: 114s --num-regions NUM_REGIONS 114s Number of regions to plot. Default: 10 114s --num-bases NUM_BASES 114s Number of bases to plot/output. Default: 21 114s --deepest-coverage Plot the deepest coverage regions. 114s 114s Output Argument: 114s --pdf-filename PDF_FILENAME 114s PDF filename to store plot(s). Default: 114s tombo_results.motif_centered.pdf 114s 114s FAST5 Data Arguments: 114s --corrected-group CORRECTED_GROUP 114s FAST5 group created by resquiggle command. Default: 114s RawGenomeCorrected_000 114s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 114s FAST5 subgroup(s) (under /Analyses/[--basecall- 114s group]/) containing basecalls and created within 114s [--corrected-group] containing re-squiggle results. 114s Default: ['BaseCalled_template'] 114s 114s Miscellaneous Arguments: 114s --quiet, -q Don't print status information. 114s --help, -h Print this help message and exit 115s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 115s [FAST5_BASEDIRS ...] --control-fast5-basedirs 115s CONTROL_FAST5_BASEDIRS 115s [CONTROL_FAST5_BASEDIRS ...] 115s [--overplot-threshold OVERPLOT_THRESHOLD] 115s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 115s [--num-regions NUM_REGIONS] 115s [--num-bases NUM_BASES] 115s [--pdf-filename PDF_FILENAME] 115s [--sequences-filename SEQUENCES_FILENAME] 115s [--corrected-group CORRECTED_GROUP] 115s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 115s [--quiet] [--help] 115s 115s Required Arguments: 115s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 115s Directories containing fast5 files. 115s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 115s Set of directories containing fast5 files for control 115s reads, containing only canonical nucleotides. 115s 115s Overplotting Arguments: 115s --overplot-threshold OVERPLOT_THRESHOLD 115s Coverage level to trigger alternative plot type 115s instead of raw signal. Default: 50 115s --overplot-type {Downsample,Boxplot,Quantile,Density} 115s Plot type for regions with higher coverage. Default: 115s Downsample 115s 115s Plotting Region Arguments: 115s --num-regions NUM_REGIONS 115s Number of regions to plot. Default: 10 115s --num-bases NUM_BASES 115s Number of bases to plot/output. Default: 21 115s 115s Output Arguments: 115s --pdf-filename PDF_FILENAME 115s PDF filename to store plot(s). Default: 115s tombo_results.max_difference.pdf 115s --sequences-filename SEQUENCES_FILENAME 115s File for sequences from selected regions. Sequences 115s will be stored in FASTA format. Default: None. 115s 115s FAST5 Data Arguments: 115s --corrected-group CORRECTED_GROUP 115s FAST5 group created by resquiggle command. Default: 115s RawGenomeCorrected_000 115s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 115s FAST5 subgroup(s) (under /Analyses/[--basecall- 115s group]/) containing basecalls and created within 115s [--corrected-group] containing re-squiggle results. 115s Default: ['BaseCalled_template'] 115s 115s Miscellaneous Arguments: 115s --quiet, -q Don't print status information. 115s --help, -h Print this help message and exit 115s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 115s [FAST5_BASEDIRS ...] --statistics-filename 115s STATISTICS_FILENAME 115s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 115s [--plot-standard-model] 115s [--plot-alternate-model {5mC,dam,6mA,dcm,CpG}] 115s [--overplot-threshold OVERPLOT_THRESHOLD] 115s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 115s [--num-regions NUM_REGIONS] 115s [--num-bases NUM_BASES] 115s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 115s [--pdf-filename PDF_FILENAME] 115s [--sequences-filename SEQUENCES_FILENAME] 115s [--corrected-group CORRECTED_GROUP] 115s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 115s [--quiet] [--help] 115s 115s Required Arguments: 115s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 115s Directories containing fast5 files. 115s --statistics-filename STATISTICS_FILENAME 115s File to save/load genomic base anchored statistics. 115s 115s Comparison Arguments: 115s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 115s Set of directories containing fast5 files for control 115s reads, containing only canonical nucleotides. 115s --plot-standard-model 115s Add default standard model distribution to the plot. 115s --plot-alternate-model {5mC,dam,6mA,dcm,CpG} 115s Add alternative model distribution to the plot. 115s 115s Overplotting Arguments: 115s --overplot-threshold OVERPLOT_THRESHOLD 115s Coverage level to trigger alternative plot type 115s instead of raw signal. Default: 50 115s --overplot-type {Downsample,Boxplot,Quantile,Density} 115s Plot type for regions with higher coverage. Default: 115s Downsample 115s 115s Plotting Region Arguments: 115s --num-regions NUM_REGIONS 115s Number of regions to plot. Default: 10 115s --num-bases NUM_BASES 115s Number of bases to plot/output. Default: 21 115s 115s Statistical Argument: 115s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 115s Dampen fraction modified estimates for low coverage 115s sites. Two parameters are unmodified and modified 115s pseudo read counts. This is equivalent to a beta prior 115s on the fraction estimate. Set to "0 0" to disable 115s dampened fraction estimation. Default: [2, 0] 115s 115s Output Arguments: 115s --pdf-filename PDF_FILENAME 115s PDF filename to store plot(s). Default: 115s tombo_results.significant_difference.pdf 115s --sequences-filename SEQUENCES_FILENAME 115s File for sequences from selected regions. Sequences 115s will be stored in FASTA format. Default: None. 115s 115s FAST5 Data Arguments: 115s --corrected-group CORRECTED_GROUP 115s FAST5 group created by resquiggle command. Default: 115s RawGenomeCorrected_000 115s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 115s FAST5 subgroup(s) (under /Analyses/[--basecall- 115s group]/) containing basecalls and created within 115s [--corrected-group] containing re-squiggle results. 115s Default: ['BaseCalled_template'] 115s 115s Miscellaneous Arguments: 115s --quiet, -q Don't print status information. 115s --help, -h Print this help message and exit 115s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 115s [FAST5_BASEDIRS ...] --motif MOTIF 115s --statistics-filename STATISTICS_FILENAME 115s --genome-fasta GENOME_FASTA 115s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 115s [--plot-standard-model] 115s [--plot-alternate-model {5mC,CpG,6mA,dam,dcm}] 115s [--overplot-threshold OVERPLOT_THRESHOLD] 115s [--num-regions NUM_REGIONS] 115s [--num-context NUM_CONTEXT] 115s [--num-statistics NUM_STATISTICS] 115s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 115s [--pdf-filename PDF_FILENAME] 115s [--corrected-group CORRECTED_GROUP] 115s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 115s [--quiet] [--help] 115s 115s Required Arguments: 115s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 115s Directories containing fast5 files. 115s --motif MOTIF Motif of interest at which to plot signal and 115s statsitics. Supports IUPAC single letter codes (use T 115s for RNA). 115s --statistics-filename STATISTICS_FILENAME 115s File to save/load genomic base anchored statistics. 115s --genome-fasta GENOME_FASTA 115s FASTA file used to re-squiggle. For faster sequence 115s access. 115s 115s Comparison Arguments: 115s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 115s Set of directories containing fast5 files for control 115s reads, containing only canonical nucleotides. 115s --plot-standard-model 115s Add default standard model distribution to the plot. 115s --plot-alternate-model {5mC,CpG,6mA,dam,dcm} 115s Add alternative model distribution to the plot. 115s 115s Overplotting Argument: 115s --overplot-threshold OVERPLOT_THRESHOLD 115s Coverage level to trigger alternative plot type 115s instead of raw signal. Default: 50 115s 115s Plotting Region Arguments: 115s --num-regions NUM_REGIONS 115s Number of regions to plot. Default: 3 115s --num-context NUM_CONTEXT 115s Number of context bases around motif. Default: 5 115s --num-statistics NUM_STATISTICS 115s Number of motif centered regions to include in 115s statistic distributions. Default: 200 115s 115s Statistical Argument: 115s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 115s Dampen fraction modified estimates for low coverage 115s sites. Two parameters are unmodified and modified 115s pseudo read counts. This is equivalent to a beta prior 115s on the fraction estimate. Set to "0 0" to disable 115s dampened fraction estimation. Default: [2, 0] 115s 115s Output Argument: 115s --pdf-filename PDF_FILENAME 115s PDF filename to store plot(s). Default: 115s tombo_results.motif_statistics.pdf 115s 115s FAST5 Data Arguments: 115s --corrected-group CORRECTED_GROUP 115s FAST5 group created by resquiggle command. Default: 115s RawGenomeCorrected_000 115s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 115s FAST5 subgroup(s) (under /Analyses/[--basecall- 115s group]/) containing basecalls and created within 115s [--corrected-group] containing re-squiggle results. 115s Default: ['BaseCalled_template'] 115s 115s Miscellaneous Arguments: 115s --quiet, -q Don't print status information. 115s --help, -h Print this help message and exit 115s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 115s [GENOME_LOCATIONS ...] 115s --per-read-statistics-filename 115s PER_READ_STATISTICS_FILENAME 115s [--genome-fasta GENOME_FASTA] 115s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 115s [--num-reads NUM_READS] [--num-bases NUM_BASES] 115s [--box-center] [--pdf-filename PDF_FILENAME] 115s [--corrected-group CORRECTED_GROUP] 115s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 115s [--quiet] [--help] 115s 115s Required Arguments: 115s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 115s Genomic locations at which to plot signal. Format 115s locations as "chrm:position[:strand] 115s [chrm2:position2[:strand2] ...]" (strand not 115s applicable for all applications) 115s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 115s Binary file containing per-read statistics from 115s statistical testing. 115s 115s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 115s --genome-fasta GENOME_FASTA 115s FASTA file used to re-squiggle. For faster sequence 115s access. 115s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 115s Directories containing fast5 files. 115s 115s Plotting Region Arguments: 115s --num-reads NUM_READS 115s Number of reads to plot. Default: 100 115s --num-bases NUM_BASES 115s Number of bases to plot/output. Default: 51 115s --box-center Plot a box around the central base. 115s 115s Output Argument: 115s --pdf-filename PDF_FILENAME 115s PDF filename to store plot(s). Default: 115s tombo_results.per_read_stats.pdf 115s 115s FAST5 Data Arguments: 115s --corrected-group CORRECTED_GROUP 115s FAST5 group created by resquiggle command. Default: 115s RawGenomeCorrected_000 115s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 115s FAST5 subgroup(s) (under /Analyses/[--basecall- 115s group]/) containing basecalls and created within 115s [--corrected-group] containing re-squiggle results. 115s Default: ['BaseCalled_template'] 115s 115s Miscellaneous Arguments: 115s --quiet, -q Don't print status information. 115s --help, -h Print this help message and exit 115s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 115s [STATISTICS_FILENAMES ...] 115s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 115s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 115s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 115s [--genome-fasta GENOME_FASTA] 115s [--pdf-filename PDF_FILENAME] 115s [--statistics-per-block STATISTICS_PER_BLOCK] 115s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 115s [--quiet] [--help] 115s 115s Required Argument: 115s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 115s Files to load genomic base anchored statistics. 115s 115s Ground Truth Arguments (provide bed files or motifs): 115s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 115s Modification description and bed format files 115s containing single base locations of ground truth 115s modified sites. Bed files should contain 6 fields 115s including strand. Format descriptions as 115s "mod_name:locs.bed". Example: "CpG 115s bisulfite":bisulfite_locs.bed 115s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 115s Bed format files containing single base locations of 115s ground truth unmodified sites. Bed files should 115s contain 6 fields including strand. 115s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 115s Ground truth, motif centered, modified base 115s descriptions for computing ROC and PR curves. Each 115s statistics file is associated with a set of motif 115s descriptions. Format descriptions as: 115s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 115s mod_pos indicates the alternate-base within the motif 115s (1-based index). Example: CCWGG:2:"dcm 115s 5mC"::GATC:2:"dam 6mA" would assess the performance of 115s a single Tombo statistics file for identification of 115s E. coli dam and dcm methylation. 115s --genome-fasta GENOME_FASTA 115s FASTA file used to re-squiggle. For faster sequence 115s access. 115s 115s Output Arguments: 115s --pdf-filename PDF_FILENAME 115s PDF filename to store plot(s). Default: 115s tombo_results.roc.pdf 115s 115s Down-sampling Arguments: 115s --statistics-per-block STATISTICS_PER_BLOCK 115s Number of randomly selected per-read, per-base 115s statistics to extract from each genomic block for 115s plotting. Default: Include all stats 115s --total-statistics-limit TOTAL_STATISTICS_LIMIT 115s Total per-read statistics to be extracted for 115s plotting. Avoids memory overflow for large runs. 115s Default: 5000000 115s 115s Miscellaneous Arguments: 115s --quiet, -q Don't print status information. 115s --help, -h Print this help message and exit 115s usage: tombo plot per_read_roc --per-read-statistics-filenames 115s PER_READ_STATISTICS_FILENAMES 115s [PER_READ_STATISTICS_FILENAMES ...] 115s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 115s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 115s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 115s [--genome-fasta GENOME_FASTA] 115s [--statistics-per-block STATISTICS_PER_BLOCK] 115s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 115s [--pdf-filename PDF_FILENAME] [--quiet] 115s [--help] 115s 115s Required Argument: 115s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 115s Binary files containing per-read statistics from 115s statistical testing. 115s 115s Ground Truth Arguments (provide bed files or motifs): 115s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 115s Modification description and bed format files 115s containing single base locations of ground truth 115s modified sites. Bed files should contain 6 fields 115s including strand. Format descriptions as 115s "mod_name:locs.bed". Example: "CpG 115s bisulfite":bisulfite_locs.bed 115s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 115s Bed format files containing single base locations of 115s ground truth unmodified sites. Bed files should 115s contain 6 fields including strand. 115s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 115s Ground truth, motif centered, modified base 115s descriptions for computing ROC and PR curves. Each 115s statistics file is associated with a set of motif 115s descriptions. Format descriptions as: 115s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 115s mod_pos indicates the alternate-base within the motif 115s (1-based index). Example: CCWGG:2:"dcm 115s 5mC"::GATC:2:"dam 6mA" would assess the performance of 115s a single Tombo statistics file for identification of 115s E. coli dam and dcm methylation. 115s --genome-fasta GENOME_FASTA 115s FASTA file used to re-squiggle. For faster sequence 115s access. 115s 115s Down-sampling Arguments: 115s --statistics-per-block STATISTICS_PER_BLOCK 115s Number of randomly selected per-read, per-base 115s statistics to extract from each genomic block for 115s plotting. Default: 100000 115s --total-statistics-limit TOTAL_STATISTICS_LIMIT 115s Total per-read statistics to be extracted for 115s plotting. Avoids memory overflow for large runs. 115s Default: 5000000 115s 115s Output Arguments: 115s --pdf-filename PDF_FILENAME 115s PDF filename to store plot(s). Default: 115s tombo_results.per_reads_roc.pdf 115s 115s Miscellaneous Arguments: 115s --quiet, -q Don't print status information. 115s --help, -h Print this help message and exit 115s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 115s [--upstream-bases {0,1,2,3,4}] 115s [--downstream-bases {0,1,2,3,4}] [--read-mean] 115s [--num-kmer-threshold NUM_KMER_THRESHOLD] 115s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 115s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 115s [--corrected-group CORRECTED_GROUP] 115s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 115s [--quiet] [--help] 115s 115s Required Argument: 115s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 115s Directories containing fast5 files. 115s 115s Data Processing Arguments: 115s --upstream-bases {0,1,2,3,4} 115s Upstream bases in k-mer. Default: 1 115s --downstream-bases {0,1,2,3,4} 115s Downstream bases in k-mer. Default: 2 115s --read-mean Plot k-mer means across whole reads as opposed to 115s individual k-mer event levels. 115s --num-kmer-threshold NUM_KMER_THRESHOLD 115s Observations of each k-mer required to include a read 115s in read level averages. Default: 1 115s 115s Plotting Region Arguments: 115s --num-reads NUM_READS 115s Number of reads to plot. Default: 100 115s 115s Output Arguments: 115s --pdf-filename PDF_FILENAME 115s PDF filename to store plot(s). Default: 115s tombo_results.kmer_distribution.pdf 115s --r-data-filename R_DATA_FILENAME 115s Filename to save R data structure. Default: Don't save 115s --dont-plot Don't plot result. Useful to produce only R data file. 115s 115s FAST5 Data Arguments: 115s --corrected-group CORRECTED_GROUP 115s FAST5 group created by resquiggle command. Default: 115s RawGenomeCorrected_000 115s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 115s FAST5 subgroup(s) (under /Analyses/[--basecall- 115s group]/) containing basecalls and created within 115s [--corrected-group] containing re-squiggle results. 115s Default: ['BaseCalled_template'] 115s 115s Miscellaneous Arguments: 115s --quiet, -q Don't print status information. 115s --help, -h Print this help message and exit 115s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 115s [FAST5_BASEDIRS ...] 115s --control-fast5-basedirs 115s CONTROL_FAST5_BASEDIRS 115s [CONTROL_FAST5_BASEDIRS ...] 115s --statistics-filename 115s STATISTICS_FILENAME 115s [--genome-fasta GENOME_FASTA] 115s [--processes PROCESSES] 115s [--num-regions NUM_REGIONS] 115s [--num-bases NUM_BASES] 115s [--slide-span SLIDE_SPAN] 115s [--pdf-filename PDF_FILENAME] 115s [--r-data-filename R_DATA_FILENAME] 115s [--corrected-group CORRECTED_GROUP] 115s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 115s [--quiet] [--help] 115s 115s Required Arguments: 115s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 115s Directories containing fast5 files. 115s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 115s Set of directories containing fast5 files for control 115s reads, containing only canonical nucleotides. 115s --statistics-filename STATISTICS_FILENAME 115s File to save/load genomic base anchored statistics. 115s 115s FASTA Sequence Argument: 115s --genome-fasta GENOME_FASTA 115s FASTA file used to re-squiggle. For faster sequence 115s access. 115s 115s Multiprocessing Argument: 115s --processes PROCESSES 115s Number of processes. Default: 1 115s 115s Plotting Region Arguments: 115s --num-regions NUM_REGIONS 115s Number of regions to plot. Default: 10 115s --num-bases NUM_BASES 115s Number of bases to plot/output. Default: 21 115s --slide-span SLIDE_SPAN 115s Number of bases offset over which to search when 115s computing distances for signal cluster plotting. 115s Default: 0 (exact position) 115s 115s Output Arguments: 115s --pdf-filename PDF_FILENAME 115s PDF filename to store plot(s). Default: 115s tombo_results.signal_clusters.pdf 115s --r-data-filename R_DATA_FILENAME 115s Filename to save R data structure. Default: Don't save 115s 115s FAST5 Data Arguments: 115s --corrected-group CORRECTED_GROUP 115s FAST5 group created by resquiggle command. Default: 115s RawGenomeCorrected_000 115s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 115s FAST5 subgroup(s) (under /Analyses/[--basecall- 115s group]/) containing basecalls and created within 115s [--corrected-group] containing re-squiggle results. 115s Default: ['BaseCalled_template'] 115s 115s Miscellaneous Arguments: 115s --quiet, -q Don't print status information. 115s --help, -h Print this help message and exit 116s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 116s 116s Required Arguments: 116s fast5s_basedir Directory containing fast5 files. All files ending in 116s "fast5" found recursively within this base directory will be 116s processed. 116s 116s Miscellaneous Arguments: 116s --quiet, -q Don't print status information. 116s --help, -h Print this help message and exit 116s usage: tombo build_model event_resquiggle 116s [--minimap2-executable MINIMAP2_EXECUTABLE] 116s [--minimap2-index MINIMAP2_INDEX] 116s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 116s [--graphmap-executable GRAPHMAP_EXECUTABLE] 116s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 116s [--normalization-type {median,pA,pA_raw,none}] 116s [--pore-model-filename PORE_MODEL_FILENAME] 116s [--outlier-threshold OUTLIER_THRESHOLD] 116s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 116s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 116s [--timeout TIMEOUT] 116s [--cpts-limit CPTS_LIMIT] 116s [--skip-index] [--overwrite] 116s [--failed-reads-filename FAILED_READS_FILENAME] 116s [--include-event-stdev] 116s [--corrected-group CORRECTED_GROUP] 116s [--basecall-group BASECALL_GROUP] 116s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 116s [--processes PROCESSES] 116s [--align-processes ALIGN_PROCESSES] 116s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 116s [--resquiggle-processes RESQUIGGLE_PROCESSES] 116s [--quiet] [--help] 116s fast5s_basedir reference_fasta 116s 116s Required Arguments: 116s fast5s_basedir Directory containing fast5 files. All files ending in 116s "fast5" found recursively within this base directory 116s will be processed. 116s reference_fasta Reference genome/transcriptome FASTA file for mapping. 116s 116s Mapper Arguments (One mapper is required): 116s --minimap2-executable MINIMAP2_EXECUTABLE 116s Path to minimap2 executable. 116s --minimap2-index MINIMAP2_INDEX 116s Path to minimap2 index (with map-ont preset) file 116s corresponding to the [genome_fasta] provided. 116s --bwa-mem-executable BWA_MEM_EXECUTABLE 116s Path to bwa-mem executable. 116s --graphmap-executable GRAPHMAP_EXECUTABLE 116s Path to graphmap executable. 116s --alignment-batch-size ALIGNMENT_BATCH_SIZE 116s Number of reads included in each alignment call. Note: 116s A new system mapping call is made for each batch 116s (including loading of the genome), so it is advised to 116s use larger values for larger genomes. Default: 1000 116s 116s Signal Processing Arguments: 116s --normalization-type {median,pA,pA_raw,none} 116s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 116s as in the ONT events (using offset, range and 116s digitization), "pA": k-mer-based correction for pA 116s drift as in nanopolish (requires [--pore-model- 116s filename]), "median": median and MAD from raw signal. 116s Default: median 116s --pore-model-filename PORE_MODEL_FILENAME 116s File containing kmer model parameters (level_mean and 116s level_stdv) used in order to compute kmer-based 116s corrected pA values. E.g. https://github.com/jts/nanop 116s olish/blob/master/etc/r9- 116s models/template_median68pA.5mers.model 116s --outlier-threshold OUTLIER_THRESHOLD 116s Windosrize the signal at this number of scale values. 116s Negative value disables outlier clipping. Default: 116s 5.000000 116s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 116s Specify the 2 parameters for segmentation 1) running 116s neighboring windows width 2) minimum raw observations 116s per genomic base. Sample type defaults: RNA : 12 6 || 116s DNA : 5 3 116s 116s Read Filtering Arguments: 116s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 116s Filter reads based on observations per base percentile 116s thresholds. Format thresholds as "percentile:thresh 116s [pctl2:thresh2 ...]". For example to filter reads with 116s 99th pctl > 200 obs/base or max > 5k obs/base use 116s "99:200 100:5000". 116s --timeout TIMEOUT Timeout in seconds for processing a single read. 116s Default: No timeout. 116s --cpts-limit CPTS_LIMIT 116s Maximum number of changepoints to find within a single 116s indel group. Default: No limit. 116s 116s Input/Output Arguments: 116s --skip-index Skip creation of tombo index. This drastically slows 116s downstream tombo commands. Default stores tombo index 116s named ".[--fast5-basedir].[--corrected- 116s group].tombo.index" to be loaded automatically for 116s downstream commands. 116s --overwrite Overwrite previous corrected group in FAST5 files. 116s Note: only effects --corrected-group or --new- 116s corrected-group. 116s --failed-reads-filename FAILED_READS_FILENAME 116s Output failed read filenames with assoicated error. 116s Default: Do not store failed reads. 116s --include-event-stdev 116s Include corrected event standard deviation in output 116s FAST5 data. 116s 116s FAST5 Data Arguments: 116s --corrected-group CORRECTED_GROUP 116s FAST5 group created by resquiggle command. Default: 116s RawGenomeCorrected_000 116s --basecall-group BASECALL_GROUP 116s FAST5 group obtain original basecalls (under Analyses 116s group). Default: Basecall_1D_000 116s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 116s FAST5 subgroup(s) (under /Analyses/[--basecall- 116s group]/) containing basecalls and created within 116s [--corrected-group] containing re-squiggle results. 116s Default: ['BaseCalled_template'] 116s 116s Multiprocessing Arguments: 116s --processes PROCESSES 116s Number of processes. Default: 2 116s --align-processes ALIGN_PROCESSES 116s Number of processes to use for parsing and aligning 116s original basecalls. Each process will independently 116s load the genome into memory, so use caution with 116s larger genomes (e.g. human). Default: 1 116s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 116s Number of threads to use for aligner system call. 116s Default: [--processes] / (2 * [--align-processes)] 116s --resquiggle-processes RESQUIGGLE_PROCESSES 116s Number of processes to use for resquiggle algorithm. 116s Default: [--processes] / 2 116s 116s Miscellaneous Arguments: 116s --quiet, -q Don't print status information. 116s --help, -h Print this help message and exit 116s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 116s [FAST5_BASEDIRS ...] 116s --tombo-model-filename 116s TOMBO_MODEL_FILENAME 116s [--estimate-mean] 116s [--kmer-specific-sd] 116s [--upstream-bases {0,1,2,3,4}] 116s [--downstream-bases {0,1,2,3,4}] 116s [--minimum-test-reads MINIMUM_TEST_READS] 116s [--coverage-threshold COVERAGE_THRESHOLD] 116s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 116s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 116s [--processes PROCESSES] 116s [--corrected-group CORRECTED_GROUP] 116s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 116s [--quiet] [--help] 116s 116s Required Arguments: 116s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 116s Directories containing fast5 files. 116s --tombo-model-filename TOMBO_MODEL_FILENAME 116s Filename to save Tombo model. 116s 116s Modeling Arguments: 116s --estimate-mean Use the mean instead of median for model level 116s estimation. Note: This can cause poor fits due to 116s outliers 116s --kmer-specific-sd Estimate standard deviation for each k-mers 116s individually. 116s --upstream-bases {0,1,2,3,4} 116s Upstream bases in k-mer. Default: 1 116s --downstream-bases {0,1,2,3,4} 116s Downstream bases in k-mer. Default: 2 116s 116s Filtering Arguments: 116s --minimum-test-reads MINIMUM_TEST_READS 116s Number of reads required at a position to perform 116s significance testing or contribute to model 116s estimation. Default: 10 116s --coverage-threshold COVERAGE_THRESHOLD 116s Maximum mean coverage per region when estimating k-mer 116s model (limits compute time for deep samples). Default: 116s 100 116s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 116s Number of each k-mer observations required in order to 116s produce a reference (genomic locations for standard 116s reference and per-read for alternative reference). 116s Default: 5 116s 116s Multiprocessing Arguments: 116s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 116s Size of regions over which to multiprocesses statistic 116s computation. For very deep samples a smaller value is 116s recommmended in order to control memory consumption. 116s Default: 10000 116s --processes PROCESSES 116s Number of processes. Default: 1 116s 116s FAST5 Data Arguments: 116s --corrected-group CORRECTED_GROUP 116s FAST5 group created by resquiggle command. Default: 116s RawGenomeCorrected_000 116s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 116s FAST5 subgroup(s) (under /Analyses/[--basecall- 116s group]/) containing basecalls and created within 116s [--corrected-group] containing re-squiggle results. 116s Default: ['BaseCalled_template'] 116s 116s Miscellaneous Arguments: 116s --quiet, -q Don't print status information. 116s --help, -h Print this help message and exit 116s usage: tombo build_model estimate_alt_reference --alternate-model-filename 116s ALTERNATE_MODEL_FILENAME 116s --alternate-model-name 116s ALTERNATE_MODEL_NAME 116s --alternate-model-base 116s {A,C,G,T} 116s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 116s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 116s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 116s [--control-density-filename CONTROL_DENSITY_FILENAME] 116s [--dna] [--rna] 116s [--tombo-model-filename TOMBO_MODEL_FILENAME] 116s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 116s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 116s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 116s [--save-density-basename SAVE_DENSITY_BASENAME] 116s [--processes PROCESSES] 116s [--corrected-group CORRECTED_GROUP] 116s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 116s [--quiet] [--help] 116s 116s Required Arguments: 116s --alternate-model-filename ALTERNATE_MODEL_FILENAME 116s Tombo model for alternative likelihood ratio 116s significance testing. 116s --alternate-model-name ALTERNATE_MODEL_NAME 116s A short name to associate with this alternate model 116s (e.g. 5mC, 6mA, etc.). This text will be included in 116s output filenames when this model is used for testing. 116s --alternate-model-base {A,C,G,T} 116s Non-standard base is an alternative to this base. 116s 116s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 116s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 116s Directories containing fast5 files. 116s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 116s Set of directories containing fast5 files for control 116s reads, containing only canonical nucleotides. 116s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 116s File containing k-mer level kernel density estimates 116s for the alternative sample saved using --save-density- 116s basename. 116s --control-density-filename CONTROL_DENSITY_FILENAME 116s File containing k-mer level kernel density estimates 116s for the control sample saved using --save-density- 116s basename. 116s 116s Standard Model Arguments: 116s --dna Explicitly select canonical DNA model. Default: 116s Automatically determine from FAST5s 116s --rna Explicitly select canonical RNA model. Default: 116s Automatically determine from FAST5s 116s --tombo-model-filename TOMBO_MODEL_FILENAME 116s Tombo model filename. If no file is provided, the 116s default DNA or RNA Tombo model will be used. 116s 116s Model Fitting Arguments: 116s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 116s When esitmating the alternative base incorporation 116s rate, this percent of k-mers are assumed to have 116s significantly shifted signal so the alternative 116s distribution minimally overlaps the standard base 116s distribution. Default: 5.000000 116s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 116s Bandwidth applied when performing Gaussian kernal 116s density esitmation on standard and alternative base 116s signal distributions. Default: 0.050000 116s 116s Filtering Argument: 116s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 116s Number of each k-mer observations required in order to 116s produce a reference (genomic locations for standard 116s reference and per-read for alternative reference). 116s Default: 1000 116s 116s Output Argument: 116s --save-density-basename SAVE_DENSITY_BASENAME 116s Basename to save alternative model estimation density 116s estimation information. See scripts/debug_est_alt.R 116s for info use example. Default: Don't save. 116s 116s Multiprocessing Arguments: 116s --processes PROCESSES 116s Number of processes. Default: 1 116s 116s FAST5 Data Arguments: 116s --corrected-group CORRECTED_GROUP 116s FAST5 group created by resquiggle command. Default: 116s RawGenomeCorrected_000 116s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 116s FAST5 subgroup(s) (under /Analyses/[--basecall- 116s group]/) containing basecalls and created within 116s [--corrected-group] containing re-squiggle results. 116s Default: ['BaseCalled_template'] 116s 116s Miscellaneous Arguments: 116s --quiet, -q Don't print status information. 116s --help, -h Print this help message and exit 116s This test only tests the help system 116s There is an extensive test in 116s 116s tombo/tests/shell_tests.sh 116s 116s but this requires to download larger data 116s sets which is not done for the moment. 116s autopkgtest [16:50:00]: test run-unit-test: -----------------------] 117s autopkgtest [16:50:01]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 117s run-unit-test PASS 117s autopkgtest [16:50:01]: @@@@@@@@@@@@@@@@@@@@ summary 117s run-unit-test PASS 134s nova [W] Skipping flock in bos03-arm64 134s Creating nova instance adt-plucky-arm64-tombo-20241114-164803-juju-7f2275-prod-proposed-migration-environment-15-fe4f66bd-58a8-471e-bde0-798f662788fa from image adt/ubuntu-plucky-arm64-server-20241114.img (UUID 4472f5f7-859f-4441-9e8e-9550fb35f210)...