0s autopkgtest [00:09:04]: starting date and time: 2024-03-20 00:09:04+0000 0s autopkgtest [00:09:04]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [00:09:04]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fpn3hk6f/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:minimap2 --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=minimap2/2.26+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-7.secgroup --name adt-noble-ppc64el-tombo-20240320-000904-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 228s autopkgtest [00:12:52]: testbed dpkg architecture: ppc64el 228s autopkgtest [00:12:52]: testbed apt version: 2.7.12 228s autopkgtest [00:12:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 230s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 230s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3799 kB] 230s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.7 kB] 230s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [492 kB] 230s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 230s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [654 kB] 231s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 231s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 231s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 231s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4104 kB] 231s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 231s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [47.7 kB] 231s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 234s Fetched 9286 kB in 3s (3594 kB/s) 235s Reading package lists... 237s Reading package lists... 238s Building dependency tree... 238s Reading state information... 238s Calculating upgrade... 238s The following packages will be upgraded: 238s ubuntu-minimal ubuntu-standard 238s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 238s Need to get 21.5 kB of archives. 238s After this operation, 0 B of additional disk space will be used. 238s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-minimal ppc64el 1.536build1 [10.7 kB] 238s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-standard ppc64el 1.536build1 [10.7 kB] 238s Fetched 21.5 kB in 0s (81.3 kB/s) 238s (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 ... 70095 files and directories currently installed.) 239s Preparing to unpack .../ubuntu-minimal_1.536build1_ppc64el.deb ... 239s Unpacking ubuntu-minimal (1.536build1) over (1.536) ... 239s Preparing to unpack .../ubuntu-standard_1.536build1_ppc64el.deb ... 239s Unpacking ubuntu-standard (1.536build1) over (1.536) ... 239s Setting up ubuntu-minimal (1.536build1) ... 239s Setting up ubuntu-standard (1.536build1) ... 239s Reading package lists... 239s Building dependency tree... 239s Reading state information... 239s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 239s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 240s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 240s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 240s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 241s Reading package lists... 241s Reading package lists... 241s Building dependency tree... 241s Reading state information... 241s Calculating upgrade... 242s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 242s Reading package lists... 242s Building dependency tree... 242s Reading state information... 242s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 245s autopkgtest [00:13:09]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 245s autopkgtest [00:13:09]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 252s Get:1 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (dsc) [2292 B] 252s Get:2 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (tar) [22.3 MB] 252s Get:3 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (diff) [7024 B] 252s gpgv: Signature made Sun Dec 17 19:23:46 2023 UTC 252s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 252s gpgv: issuer "tille@debian.org" 252s gpgv: Can't check signature: No public key 252s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6.dsc: no acceptable signature found 252s autopkgtest [00:13:16]: testing package tombo version 1.5.1-6 253s autopkgtest [00:13:17]: build not needed 310s autopkgtest [00:14:14]: test run-unit-test: preparing testbed 311s Reading package lists... 311s Building dependency tree... 311s Reading state information... 312s Starting pkgProblemResolver with broken count: 0 312s Starting 2 pkgProblemResolver with broken count: 0 312s Done 312s The following additional packages will be installed: 312s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 312s libhdf5-103-1 libhdf5-hl-100 libjs-jquery libjs-mathjax libjs-sphinxdoc 312s libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 python3-decorator 312s python3-h5py python3-h5py-serial python3-mappy python3-numpy python3-scipy 312s python3-tqdm sphinx-rtd-theme-common tombo tombo-doc 312s Suggested packages: 312s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 312s gfortran python3-dev python3-pytest python-scipy-doc 312s Recommended packages: 312s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 312s python3-rpy2 312s The following NEW packages will be installed: 312s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 312s libblas3 libgfortran5 libhdf5-103-1 libhdf5-hl-100 libjs-jquery 312s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 312s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 312s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 312s tombo-doc 312s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 312s Need to get 69.1 MB/69.1 MB of archives. 312s After this operation, 272 MB of additional disk space will be used. 312s Get:1 /tmp/autopkgtest.vUNNik/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [708 B] 312s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-lato all 2.015-1 [2781 kB] 313s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 313s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 313s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libaec0 ppc64el 1.1.2-1 [29.9 kB] 313s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 313s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 313s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsz2 ppc64el 1.1.2-1 [5472 B] 313s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-103-1 ppc64el 1.10.10+repack-3ubuntu1 [1375 kB] 313s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-hl-100 ppc64el 1.10.10+repack-3ubuntu1 [69.9 kB] 313s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 313s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 313s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-sphinxdoc all 7.2.6-4 [149 kB] 313s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 313s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1 [32.8 kB] 313s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 313s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 313s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 314s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-h5py-serial ppc64el 3.10.0-1ubuntu1 [1635 kB] 314s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-h5py all 3.10.0-1ubuntu1 [7970 B] 314s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-mappy ppc64el 2.26+dfsg-1 [193 kB] 314s Get:22 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-tqdm all 4.64.1-2 [95.2 kB] 314s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] 314s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-scipy ppc64el 1.11.4-6 [21.4 MB] 316s Get:25 http://ftpmaster.internal/ubuntu noble/universe ppc64el tombo ppc64el 1.5.1-6 [514 kB] 316s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 316s Get:27 http://ftpmaster.internal/ubuntu noble/universe ppc64el tombo-doc all 1.5.1-6 [21.7 MB] 318s Fetched 69.1 MB in 6s (11.6 MB/s) 318s Selecting previously unselected package fonts-lato. 318s (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 ... 70095 files and directories currently installed.) 318s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 318s Unpacking fonts-lato (2.015-1) ... 318s Selecting previously unselected package fonts-font-awesome. 318s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 318s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 319s Selecting previously unselected package fonts-mathjax. 319s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 319s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 319s Selecting previously unselected package libaec0:ppc64el. 319s Preparing to unpack .../03-libaec0_1.1.2-1_ppc64el.deb ... 319s Unpacking libaec0:ppc64el (1.1.2-1) ... 319s Selecting previously unselected package libblas3:ppc64el. 319s Preparing to unpack .../04-libblas3_3.12.0-3_ppc64el.deb ... 319s Unpacking libblas3:ppc64el (3.12.0-3) ... 319s Selecting previously unselected package libgfortran5:ppc64el. 319s Preparing to unpack .../05-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 319s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 319s Selecting previously unselected package libsz2:ppc64el. 319s Preparing to unpack .../06-libsz2_1.1.2-1_ppc64el.deb ... 319s Unpacking libsz2:ppc64el (1.1.2-1) ... 319s Selecting previously unselected package libhdf5-103-1:ppc64el. 319s Preparing to unpack .../07-libhdf5-103-1_1.10.10+repack-3ubuntu1_ppc64el.deb ... 319s Unpacking libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 319s Selecting previously unselected package libhdf5-hl-100:ppc64el. 319s Preparing to unpack .../08-libhdf5-hl-100_1.10.10+repack-3ubuntu1_ppc64el.deb ... 319s Unpacking libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 319s Selecting previously unselected package libjs-jquery. 319s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 319s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 319s Selecting previously unselected package libjs-underscore. 319s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 319s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 319s Selecting previously unselected package libjs-sphinxdoc. 319s Preparing to unpack .../11-libjs-sphinxdoc_7.2.6-4_all.deb ... 319s Unpacking libjs-sphinxdoc (7.2.6-4) ... 319s Selecting previously unselected package liblapack3:ppc64el. 319s Preparing to unpack .../12-liblapack3_3.12.0-3_ppc64el.deb ... 319s Unpacking liblapack3:ppc64el (3.12.0-3) ... 319s Selecting previously unselected package liblbfgsb0:ppc64el. 319s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1_ppc64el.deb ... 319s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 319s Selecting previously unselected package liblzf1:ppc64el. 319s Preparing to unpack .../14-liblzf1_3.6-4_ppc64el.deb ... 319s Unpacking liblzf1:ppc64el (3.6-4) ... 319s Selecting previously unselected package python3-decorator. 319s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 319s Unpacking python3-decorator (5.1.1-5) ... 319s Selecting previously unselected package python3-numpy. 319s Preparing to unpack .../16-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 319s Unpacking python3-numpy (1:1.24.2-2) ... 319s Selecting previously unselected package python3-h5py-serial. 319s Preparing to unpack .../17-python3-h5py-serial_3.10.0-1ubuntu1_ppc64el.deb ... 319s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 320s Selecting previously unselected package python3-h5py. 320s Preparing to unpack .../18-python3-h5py_3.10.0-1ubuntu1_all.deb ... 320s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 320s Selecting previously unselected package python3-mappy. 320s Preparing to unpack .../19-python3-mappy_2.26+dfsg-1_ppc64el.deb ... 320s Unpacking python3-mappy (2.26+dfsg-1) ... 320s Selecting previously unselected package python3-tqdm. 320s Preparing to unpack .../20-python3-tqdm_4.64.1-2_all.deb ... 320s Unpacking python3-tqdm (4.64.1-2) ... 320s Selecting previously unselected package sphinx-rtd-theme-common. 320s Preparing to unpack .../21-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... 320s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 320s Selecting previously unselected package python3-scipy. 320s Preparing to unpack .../22-python3-scipy_1.11.4-6_ppc64el.deb ... 320s Unpacking python3-scipy (1.11.4-6) ... 321s Selecting previously unselected package tombo. 321s Preparing to unpack .../23-tombo_1.5.1-6_ppc64el.deb ... 321s Unpacking tombo (1.5.1-6) ... 321s Selecting previously unselected package libjs-mathjax. 321s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 321s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 322s Selecting previously unselected package tombo-doc. 322s Preparing to unpack .../25-tombo-doc_1.5.1-6_all.deb ... 322s Unpacking tombo-doc (1.5.1-6) ... 322s Selecting previously unselected package autopkgtest-satdep. 322s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 322s Unpacking autopkgtest-satdep (0) ... 322s Setting up fonts-lato (2.015-1) ... 322s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 322s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 322s Setting up python3-tqdm (4.64.1-2) ... 322s Setting up python3-mappy (2.26+dfsg-1) ... 322s Setting up libaec0:ppc64el (1.1.2-1) ... 322s Setting up python3-decorator (5.1.1-5) ... 323s Setting up libblas3:ppc64el (3.12.0-3) ... 323s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 323s Setting up liblzf1:ppc64el (3.6-4) ... 323s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 323s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 323s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 323s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 323s Setting up libsz2:ppc64el (1.1.2-1) ... 323s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 323s Setting up liblapack3:ppc64el (3.12.0-3) ... 323s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 323s Setting up python3-numpy (1:1.24.2-2) ... 325s Setting up libjs-sphinxdoc (7.2.6-4) ... 325s Setting up tombo-doc (1.5.1-6) ... 325s Setting up libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 325s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 325s Setting up libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 325s Setting up python3-scipy (1.11.4-6) ... 328s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 328s Setting up python3-h5py (3.10.0-1ubuntu1) ... 329s Setting up tombo (1.5.1-6) ... 329s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 329s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 329s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 329s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 329s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 329s re.match('\+', fastq_rec[2]) is None): 329s Setting up autopkgtest-satdep (0) ... 329s Processing triggers for man-db (2.12.0-3) ... 329s Processing triggers for libc-bin (2.39-0ubuntu2) ... 333s (Reading database ... 77494 files and directories currently installed.) 333s Removing autopkgtest-satdep (0) ... 333s autopkgtest [00:14:37]: test run-unit-test: [----------------------- 333s ********* Testing help commands ********** 334s usage: tombo [-h] [-v] 334s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 334s ... 334s 334s ********** Tombo ********* 334s 334s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 334s 334s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 334s 334s Tombo command groups (additional help available within each command group): 334s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 334s preprocess Pre-process nanopore reads for Tombo processing. 334s filter Apply filter to Tombo index file for specified criterion. 334s detect_modifications Perform statistical testing to detect non-standard nucleotides. 334s text_output Output Tombo results in text files. 334s build_model Create canonical and alternative base Tombo models. 334s plot Save plots to visualize raw nanopore signal or testing results. 334s 334s options: 334s -h, --help show this help message and exit 334s -v, --version show Tombo version and exit. 334s usage: tombo resquiggle [--dna] [--rna] 334s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 334s [--q-score Q_SCORE] 334s [--signal-matching-score SIGNAL_MATCHING_SCORE] 334s [--processes PROCESSES] 334s [--corrected-group CORRECTED_GROUP] 334s [--basecall-group BASECALL_GROUP] 334s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 334s [--overwrite] 334s [--failed-reads-filename FAILED_READS_FILENAME] 334s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 334s [--print-advanced-arguments] [--quiet] [--help] 334s fast5s_basedir reference 334s 334s Required Arguments: 334s fast5s_basedir Directory containing fast5 files. All files ending in 334s "fast5" found recursively within this base directory 334s will be processed. 334s reference Reference genome/transcriptome FASTA file or minimap2 334s index (with "map-ont" preset) for mapping. 334s 334s Model Parameters: 334s --dna Explicitly select canonical DNA model. Default: 334s Automatically determine from FAST5s 334s --rna Explicitly select canonical RNA model. Default: 334s Automatically determine from FAST5s 334s 334s Read Filtering Argument: 334s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 334s Filter reads based on observations per base percentile 334s thresholds. Format thresholds as "percentile:thresh 334s [pctl2:thresh2 ...]". For example to filter reads with 334s 99th pctl > 200 obs/base or max > 5k obs/base use 334s "99:200 100:5000". 334s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 334s Default: 0.000000 334s --signal-matching-score SIGNAL_MATCHING_SCORE 334s Observed to expected signal matching score (higher 334s score indicates poor matching). Sample type defaults: 334s RNA : 2 || DNA : 1.1 334s 334s Multiprocessing Arguments: 334s --processes PROCESSES 334s Number of processes. Default: 1 334s 334s FAST5 Data Arguments: 334s --corrected-group CORRECTED_GROUP 334s FAST5 group created by resquiggle command. Default: 334s RawGenomeCorrected_000 334s --basecall-group BASECALL_GROUP 334s FAST5 group obtain original basecalls (under Analyses 334s group). Default: Basecall_1D_000 334s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 334s FAST5 subgroup(s) (under /Analyses/[--basecall- 334s group]/) containing basecalls and created within 334s [--corrected-group] containing re-squiggle results. 334s Default: ['BaseCalled_template'] 334s --overwrite Overwrite previous corrected group in FAST5 files. 334s Note: only effects --corrected-group or --new- 334s corrected-group. 334s 334s Input/Output Arguments: 334s --failed-reads-filename FAILED_READS_FILENAME 334s Output failed read filenames with assoicated error. 334s Default: Do not store failed reads. 334s --num-most-common-errors NUM_MOST_COMMON_ERRORS 334s Dynamically show this many most common errors so far 334s through run. Default: 0; Just show progress 334s 334s Advanced Arguments: 334s --print-advanced-arguments 334s Print advanced re-squiggle arguments and exit. 334s 334s Miscellaneous Arguments: 334s --quiet, -q Don't print status information. 334s --help, -h Print this help message and exit 334s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 334s --fastq-filenames 334s FASTQ_FILENAMES 334s [FASTQ_FILENAMES ...] 334s [--basecall-group BASECALL_GROUP] 334s [--basecall-subgroup BASECALL_SUBGROUP] 334s [--overwrite] 334s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 334s [--processes PROCESSES] 334s [--quiet] [--help] 334s 334s Required Arguments: 334s --fast5-basedir FAST5_BASEDIR 334s Directory containing fast5 files. 334s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 334s FASTQ filenames containing basecalls to be added to 334s raw FAST5 files. 334s 334s FAST5 Data Arguments: 334s --basecall-group BASECALL_GROUP 334s FAST5 group obtain original basecalls (under Analyses 334s group). Default: Basecall_1D_000 334s --basecall-subgroup BASECALL_SUBGROUP 334s FAST5 subgroup (under /Analyses/[--basecall-group]/) 334s under which to store basecalls from FASTQs. Default: 334s BaseCalled_template 334s --overwrite Overwrite previous corrected group in FAST5 files. 334s Note: only effects --corrected-group or --new- 334s corrected-group. 334s 334s Sequencing Summary Argument: 334s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 334s Sequencing summary filenames produced by albacore. 334s These can make annotation of raw FAST5 files with 334s FASTQ sequence much faster. 334s 334s Multiprocessing Argument: 334s --processes PROCESSES 334s Number of processes. Default: 1 334s 334s Miscellaneous Arguments: 334s --quiet, -q Don't print status information. 334s --help, -h Print this help message and exit 334s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 334s [FAST5_BASEDIRS ...] 334s [--corrected-group CORRECTED_GROUP] 334s [--quiet] [--help] 334s 334s Required Argument: 334s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 334s Directories containing fast5 files. 334s 334s FAST5 Data Argument: 334s --corrected-group CORRECTED_GROUP 334s FAST5 group created by resquiggle command. Default: 334s RawGenomeCorrected_000 334s 334s Miscellaneous Arguments: 334s --quiet, -q Don't print status information. 334s --help, -h Print this help message and exit 334s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 334s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 334s [--corrected-group CORRECTED_GROUP] [--quiet] 334s [--help] 334s 334s Required Argument: 334s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 334s Directories containing fast5 files. 334s 334s Read Filtering Argument: 334s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 334s Filter reads based on observations per base percentile 334s thresholds. Format thresholds as "percentile:thresh 334s [pctl2:thresh2 ...]". For example to filter reads with 334s 99th pctl > 200 obs/base or max > 5k obs/base use 334s "99:200 100:5000". 334s 334s FAST5 Data Argument: 334s --corrected-group CORRECTED_GROUP 334s FAST5 group created by resquiggle command. Default: 334s RawGenomeCorrected_000 334s 334s Miscellaneous Arguments: 334s --quiet, -q Don't print status information. 334s --help, -h Print this help message and exit 334s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 334s [FAST5_BASEDIRS ...] 334s [--percent-to-filter PERCENT_TO_FILTER] 334s [--corrected-group CORRECTED_GROUP] 334s [--quiet] [--help] 334s 334s Required Arguments: 334s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 334s Directories containing fast5 files. 334s 334s Read Filtering Argument: 334s --percent-to-filter PERCENT_TO_FILTER 334s Percentage of all reads to filter. Reads are randomly 334s selected weighted according to the approximate 334s coverage at the mapped genomic location. This can be 334s useful in modeling and testing. Default: 10.000000 334s 334s FAST5 Data Arguments: 334s --corrected-group CORRECTED_GROUP 334s FAST5 group created by resquiggle command. Default: 334s RawGenomeCorrected_000 334s 334s Miscellaneous Arguments: 334s --quiet, -q Don't print status information. 334s --help, -h Print this help message and exit 334s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 334s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 334s [--corrected-group CORRECTED_GROUP] 334s [--basecall-group BASECALL_GROUP] [--quiet] 334s [--help] 334s 334s Required Arguments: 334s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 334s Directories containing fast5 files. 334s 334s Read Filtering Argument: 334s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 334s Default: 7.000000 334s 334s FAST5 Data Arguments: 334s --corrected-group CORRECTED_GROUP 334s FAST5 group created by resquiggle command. Default: 334s RawGenomeCorrected_000 334s --basecall-group BASECALL_GROUP 334s FAST5 group obtain original basecalls (under Analyses 334s group). Default: Basecall_1D_000 334s 334s Miscellaneous Arguments: 334s --quiet, -q Don't print status information. 334s --help, -h Print this help message and exit 334s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 334s [FAST5_BASEDIRS ...] 334s --signal-matching-score 334s SIGNAL_MATCHING_SCORE 334s [--corrected-group CORRECTED_GROUP] 334s [--quiet] [--help] 334s 334s Required Arguments: 334s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 334s Directories containing fast5 files. 334s --signal-matching-score SIGNAL_MATCHING_SCORE 334s Observed to expected signal matching score (higher 334s score indicates poor matching). Sample type defaults: 334s RNA : 2 || DNA : 1.1 334s 334s FAST5 Data Arguments: 334s --corrected-group CORRECTED_GROUP 334s FAST5 group created by resquiggle command. Default: 334s RawGenomeCorrected_000 334s 334s Miscellaneous Arguments: 334s --quiet, -q Don't print status information. 334s --help, -h Print this help message and exit 334s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 334s [FAST5_BASEDIRS ...] 334s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 334s [--include-partial-overlap] 334s [--corrected-group CORRECTED_GROUP] 334s [--quiet] [--help] 334s 334s Required Arguments: 334s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 334s Directories containing fast5 files. 334s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 334s Filter out reads not falling completely within include 334s regions. Omit start and end coordinates to include an 334s entire chromosome/sequence record. Format regions as 334s "chrm[:start-end] [chrm2[:start2-end2] ...]". 334s 334s Filter Argument: 334s --include-partial-overlap 334s Include reads that partially overlap the specified 334s region. Default: Only include reads completely 334s contained in a specified region 334s 334s FAST5 Data Argument: 334s --corrected-group CORRECTED_GROUP 334s FAST5 group created by resquiggle command. Default: 334s RawGenomeCorrected_000 334s 334s Miscellaneous Arguments: 334s --quiet, -q Don't print status information. 334s --help, -h Print this help message and exit 334s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 334s [FAST5_BASEDIRS ...] 334s --statistics-file-basename 334s STATISTICS_FILE_BASENAME [--dna] 334s [--rna] 334s [--fishers-method-context FISHERS_METHOD_CONTEXT] 334s [--minimum-test-reads MINIMUM_TEST_READS] 334s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 334s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 334s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 334s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 334s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 334s [--processes PROCESSES] 334s [--corrected-group CORRECTED_GROUP] 334s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 334s [--quiet] [--help] 334s 334s Required Argument: 334s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 334s Directories containing fast5 files. 334s --statistics-file-basename STATISTICS_FILE_BASENAME 334s File base name to save base by base statistics from 334s testing. Filenames will be [--statistics-file- 334s basename].[--alternate-bases]?.tombo.stats 334s 334s Comparison Model Arguments: 334s --dna Explicitly select canonical DNA model. Default: 334s Automatically determine from FAST5s 334s --rna Explicitly select canonical RNA model. Default: 334s Automatically determine from FAST5s 334s 334s Significance Test Arguments: 334s --fishers-method-context FISHERS_METHOD_CONTEXT 334s Number of context bases up and downstream over which 334s to compute Fisher's method combined p-values. Note: 334s Not applicable for alternative model likelihood ratio 334s tests. Default: 1. 334s --minimum-test-reads MINIMUM_TEST_READS 334s Number of reads required at a position to perform 334s significance testing or contribute to model 334s estimation. Default: 1 334s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 334s P-value threshold when computing fraction of 334s significant reads at each genomic position. If two 334s values are provided, statistics between these values 334s are not considered. Default thresholds: DNA:0.15-0.5 , 334s RNA:0.05-0.4 334s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 334s Dampen fraction modified estimates for low coverage 334s sites. Two parameters are unmodified and modified 334s pseudo read counts. This is equivalent to a beta prior 334s on the fraction estimate. Set to "0 0" to disable 334s dampened fraction estimation. Default: [2, 0] 334s 334s Output Argument: 334s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 334s Base for binary files containing per-read statistics 334s from statistical testing. Filenames will be [--per- 334s read-statistics-basename].[--alternate- 334s bases]?.tombo.per_read_stats 334s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 334s Number of the most significant sites to store for 334s faster access. If a longer list of most significant 334s sites is required the list must be re-computed from 334s all batches. Very large values can increase RAM usage. 334s Default: 100000 334s 334s Multiprocessing Arguments: 334s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 334s Size of regions over which to multiprocesses statistic 334s computation. For very deep samples a smaller value is 334s recommmended in order to control memory consumption. 334s Default: 10000 334s --processes PROCESSES 334s Number of processes. Default: 1 334s 334s FAST5 Data Arguments: 334s --corrected-group CORRECTED_GROUP 334s FAST5 group created by resquiggle command. Default: 334s RawGenomeCorrected_000 334s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 334s FAST5 subgroup(s) (under /Analyses/[--basecall- 334s group]/) containing basecalls and created within 334s [--corrected-group] containing re-squiggle results. 334s Default: ['BaseCalled_template'] 334s 334s Miscellaneous Arguments: 334s --quiet, -q Don't print status information. 334s --help, -h Print this help message and exit 335s usage: tombo detect_modifications alternative_model 335s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 335s [--statistics-file-basename STATISTICS_FILE_BASENAME] 335s [--alternate-bases {dam,6mA,CpG,5mC,dcm} [{dam,6mA,CpG,5mC,dcm} ...]] 335s [--print-available-models] 335s [--dna] [--rna] 335s [--minimum-test-reads MINIMUM_TEST_READS] 335s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 335s [--standard-log-likelihood-ratio] 335s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 335s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 335s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 335s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 335s [--processes PROCESSES] 335s [--corrected-group CORRECTED_GROUP] 335s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 335s [--quiet] [--help] 335s 335s Required Argument: 335s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 335s Directories containing fast5 files. 335s --statistics-file-basename STATISTICS_FILE_BASENAME 335s File base name to save base by base statistics from 335s testing. Filenames will be [--statistics-file- 335s basename].[--alternate-bases]?.tombo.stats 335s --alternate-bases {dam,6mA,CpG,5mC,dcm} [{dam,6mA,CpG,5mC,dcm} ...] 335s Default non-standard base model for testing (not 335s required if user created --alternate-model-filenames 335s is provided). 335s 335s Comparison Arguments: 335s --print-available-models 335s Print available alternative models and exit. 335s --dna Explicitly select canonical DNA model. Default: 335s Automatically determine from FAST5s 335s --rna Explicitly select canonical RNA model. Default: 335s Automatically determine from FAST5s 335s 335s Significance Test Arguments: 335s --minimum-test-reads MINIMUM_TEST_READS 335s Number of reads required at a position to perform 335s significance testing or contribute to model 335s estimation. Default: 1 335s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 335s Log likelihood ratio threshold when computing fraction 335s of significant reads at each genomic position. If two 335s values are provided, statistics between these values 335s are not considered. Default thresholds: DNA:-1.5-2.5 , 335s RNA:-2.5-2.5 335s --standard-log-likelihood-ratio 335s Use a standard log likelihood ratio (LLR) statistic. 335s Default is to use an outlier-robust LLR-like 335s statistic. Detail in full online documentation. 335s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 335s Dampen fraction modified estimates for low coverage 335s sites. Two parameters are unmodified and modified 335s pseudo read counts. This is equivalent to a beta prior 335s on the fraction estimate. Set to "0 0" to disable 335s dampened fraction estimation. Default: [2, 0] 335s 335s Output Argument: 335s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 335s Base for binary files containing per-read statistics 335s from statistical testing. Filenames will be [--per- 335s read-statistics-basename].[--alternate- 335s bases]?.tombo.per_read_stats 335s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 335s Number of the most significant sites to store for 335s faster access. If a longer list of most significant 335s sites is required the list must be re-computed from 335s all batches. Very large values can increase RAM usage. 335s Default: 100000 335s 335s Multiprocessing Arguments: 335s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 335s Size of regions over which to multiprocesses statistic 335s computation. For very deep samples a smaller value is 335s recommmended in order to control memory consumption. 335s Default: 10000 335s --processes PROCESSES 335s Number of processes. Default: 1 335s 335s FAST5 Data Arguments: 335s --corrected-group CORRECTED_GROUP 335s FAST5 group created by resquiggle command. Default: 335s RawGenomeCorrected_000 335s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 335s FAST5 subgroup(s) (under /Analyses/[--basecall- 335s group]/) containing basecalls and created within 335s [--corrected-group] containing re-squiggle results. 335s Default: ['BaseCalled_template'] 335s 335s Miscellaneous Arguments: 335s --quiet, -q Don't print status information. 335s --help, -h Print this help message and exit 335s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 335s FAST5_BASEDIRS 335s [FAST5_BASEDIRS ...] 335s --statistics-file-basename 335s STATISTICS_FILE_BASENAME 335s --control-fast5-basedirs 335s CONTROL_FAST5_BASEDIRS 335s [CONTROL_FAST5_BASEDIRS ...] 335s [--sample-only-estimates] 335s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 335s [--dna] [--rna] 335s [--fishers-method-context FISHERS_METHOD_CONTEXT] 335s [--minimum-test-reads MINIMUM_TEST_READS] 335s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 335s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 335s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 335s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 335s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 335s [--processes PROCESSES] 335s [--corrected-group CORRECTED_GROUP] 335s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 335s [--quiet] [--help] 335s 335s Required Argument: 335s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 335s Directories containing fast5 files. 335s --statistics-file-basename STATISTICS_FILE_BASENAME 335s File base name to save base by base statistics from 335s testing. Filenames will be [--statistics-file- 335s basename].[--alternate-bases]?.tombo.stats 335s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 335s Set of directories containing fast5 files for control 335s reads, containing only canonical nucleotides. 335s 335s Model Prior Arguments: 335s --sample-only-estimates 335s Only use canonical sample to estimate expected signal 335s level and spread. Default: Use canonical model to 335s improve estimtates (esp. for low coverage regions) 335s using baysian posterior estimates. 335s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 335s Prior weights (one each for mean and spread) applied 335s to canonical base model for estimating posterior model 335s parameters for sample comparison. Default: [5, 40] 335s --dna Explicitly select canonical DNA model. Default: 335s Automatically determine from FAST5s 335s --rna Explicitly select canonical RNA model. Default: 335s Automatically determine from FAST5s 335s 335s Significance Test Arguments: 335s --fishers-method-context FISHERS_METHOD_CONTEXT 335s Number of context bases up and downstream over which 335s to compute Fisher's method combined p-values. Note: 335s Not applicable for alternative model likelihood ratio 335s tests. Default: 1. 335s --minimum-test-reads MINIMUM_TEST_READS 335s Number of reads required at a position to perform 335s significance testing or contribute to model 335s estimation. Default: 1 335s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 335s P-value threshold when computing fraction of 335s significant reads at each genomic position. If two 335s values are provided, statistics between these values 335s are not considered. Default thresholds: DNA:0.15-0.5 , 335s RNA:0.05-0.4 335s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 335s Dampen fraction modified estimates for low coverage 335s sites. Two parameters are unmodified and modified 335s pseudo read counts. This is equivalent to a beta prior 335s on the fraction estimate. Set to "0 0" to disable 335s dampened fraction estimation. Default: [2, 0] 335s 335s Output Argument: 335s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 335s Base for binary files containing per-read statistics 335s from statistical testing. Filenames will be [--per- 335s read-statistics-basename].[--alternate- 335s bases]?.tombo.per_read_stats 335s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 335s Number of the most significant sites to store for 335s faster access. If a longer list of most significant 335s sites is required the list must be re-computed from 335s all batches. Very large values can increase RAM usage. 335s Default: 100000 335s 335s Multiprocessing Arguments: 335s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 335s Size of regions over which to multiprocesses statistic 335s computation. For very deep samples a smaller value is 335s recommmended in order to control memory consumption. 335s Default: 10000 335s --processes PROCESSES 335s Number of processes. Default: 1 335s 335s FAST5 Data Arguments: 335s --corrected-group CORRECTED_GROUP 335s FAST5 group created by resquiggle command. Default: 335s RawGenomeCorrected_000 335s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 335s FAST5 subgroup(s) (under /Analyses/[--basecall- 335s group]/) containing basecalls and created within 335s [--corrected-group] containing re-squiggle results. 335s Default: ['BaseCalled_template'] 335s 335s Miscellaneous Arguments: 335s --quiet, -q Don't print status information. 335s --help, -h Print this help message and exit 335s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 335s FAST5_BASEDIRS 335s [FAST5_BASEDIRS ...] 335s --statistics-file-basename 335s STATISTICS_FILE_BASENAME 335s --alternate-fast5-basedirs 335s ALTERNATE_FAST5_BASEDIRS 335s [ALTERNATE_FAST5_BASEDIRS ...] 335s [--fishers-method-context FISHERS_METHOD_CONTEXT] 335s [--minimum-test-reads MINIMUM_TEST_READS] 335s [--statistic-type {ks,u,t}] 335s [--store-p-value] 335s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 335s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 335s [--processes PROCESSES] 335s [--corrected-group CORRECTED_GROUP] 335s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 335s [--quiet] [--help] 335s 335s Required Argument: 335s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 335s Directories containing fast5 files. 335s --statistics-file-basename STATISTICS_FILE_BASENAME 335s File base name to save base by base statistics from 335s testing. Filenames will be [--statistics-file- 335s basename].[--alternate-bases]?.tombo.stats 335s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 335s Set of directories containing fast5 files for 335s alternate set of reads. 335s 335s Significance Test Arguments: 335s --fishers-method-context FISHERS_METHOD_CONTEXT 335s Number of context bases up and downstream over which 335s to compute Fisher's method combined p-values. Note: 335s Not applicable for alternative model likelihood ratio 335s tests. Default: 1. 335s --minimum-test-reads MINIMUM_TEST_READS 335s Number of reads required at a position to perform 335s significance testing or contribute to model 335s estimation. Default: 50 335s --statistic-type {ks,u,t} 335s Type of statistical test to apply. Default: "ks" 335s --store-p-value Store p-value instead of effect-size statistic. 335s Statistics are D-statistic (KS-test), deviation from 335s even common language effect size (u-test), and Cohen's 335s D (t-test). 335s 335s Output Argument: 335s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 335s Number of the most significant sites to store for 335s faster access. If a longer list of most significant 335s sites is required the list must be re-computed from 335s all batches. Very large values can increase RAM usage. 335s Default: 100000 335s 335s Multiprocessing Arguments: 335s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 335s Size of regions over which to multiprocesses statistic 335s computation. For very deep samples a smaller value is 335s recommmended in order to control memory consumption. 335s Default: 10000 335s --processes PROCESSES 335s Number of processes. Default: 1 335s 335s FAST5 Data Arguments: 335s --corrected-group CORRECTED_GROUP 335s FAST5 group created by resquiggle command. Default: 335s RawGenomeCorrected_000 335s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 335s FAST5 subgroup(s) (under /Analyses/[--basecall- 335s group]/) containing basecalls and created within 335s [--corrected-group] containing re-squiggle results. 335s Default: ['BaseCalled_template'] 335s 335s Miscellaneous Arguments: 335s --quiet, -q Don't print status information. 335s --help, -h Print this help message and exit 335s usage: tombo detect_modifications aggregate_per_read_stats 335s --per-read-statistics-filename 335s PER_READ_STATISTICS_FILENAME 335s --statistics-filename 335s STATISTICS_FILENAME 335s --single-read-threshold 335s SINGLE_READ_THRESHOLD 335s [SINGLE_READ_THRESHOLD ...] 335s [--minimum-test-reads MINIMUM_TEST_READS] 335s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 335s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 335s [--processes PROCESSES] 335s [--corrected-group CORRECTED_GROUP] 335s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 335s [--quiet] [--help] 335s 335s Required Argument: 335s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 335s Binary file containing per-read statistics from 335s statistical testing. 335s --statistics-filename STATISTICS_FILENAME 335s File to save/load genomic base anchored statistics. 335s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 335s P-value or log likelihood ratio threshold when 335s computing fraction of significant reads at each 335s genomic position. If two values are provided, 335s statistics between these values are not considered. 335s 335s Significance Test Arguments: 335s --minimum-test-reads MINIMUM_TEST_READS 335s Number of reads required at a position to perform 335s significance testing or contribute to model 335s estimation. Default: 1 335s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 335s Dampen fraction modified estimates for low coverage 335s sites. Two parameters are unmodified and modified 335s pseudo read counts. This is equivalent to a beta prior 335s on the fraction estimate. Set to "0 0" to disable 335s dampened fraction estimation. Default: [2, 0] 335s 335s Output Argument: 335s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 335s Number of the most significant sites to store for 335s faster access. If a longer list of most significant 335s sites is required the list must be re-computed from 335s all batches. Very large values can increase RAM usage. 335s Default: 100000 335s 335s Multiprocessing Arguments: 335s --processes PROCESSES 335s Number of processes. Default: 1 335s 335s FAST5 Data Arguments: 335s --corrected-group CORRECTED_GROUP 335s FAST5 group created by resquiggle command. Default: 335s RawGenomeCorrected_000 335s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 335s FAST5 subgroup(s) (under /Analyses/[--basecall- 335s group]/) containing basecalls and created within 335s [--corrected-group] containing re-squiggle results. 335s Default: ['BaseCalled_template'] 335s 335s Miscellaneous Arguments: 335s --quiet, -q Don't print status information. 335s --help, -h Print this help message and exit 335s usage: tombo text_output browser_files 335s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 335s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 335s [--statistics-filename STATISTICS_FILENAME] 335s [--genome-fasta GENOME_FASTA] 335s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 335s [--browser-file-basename BROWSER_FILE_BASENAME] 335s [--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} ...]] 335s [--corrected-group CORRECTED_GROUP] 335s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 335s [--quiet] [--help] 335s 335s Data Arguments: 335s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 335s Directories containing fast5 files. 335s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 335s Set of directories containing fast5 files for control 335s reads, containing only canonical nucleotides. 335s --statistics-filename STATISTICS_FILENAME 335s File to save/load genomic base anchored statistics. 335s 335s Statistic Motif Filter Arguments: 335s --genome-fasta GENOME_FASTA 335s FASTA file used to re-squiggle. For faster sequence 335s access. 335s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 335s Ground truth, motif centered, modified base 335s descriptions for output filtering. Format descriptions 335s as: "motif:mod_pos:name". The mod_pos indicates the 335s modified base within the motif (1-based index). 335s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 335s output for identification of E. coli dam and dcm 335s methylation. 335s 335s Output Arguments: 335s --browser-file-basename BROWSER_FILE_BASENAME 335s Basename for output browser files. Two files (plus and 335s minus strand) will be produced for each --file-types 335s supplied. Filenames formatted as "[browser-file- 335s basename].[file- 335s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 335s Default: tombo_results 335s --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} ...] 335s Data types of genome browser files to produce. 335s Produced coverage files are in bedGraph format, while 335s all other file types will be in wiggle format 335s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 335s Default: "coverage" 335s 335s FAST5 Data Arguments: 335s --corrected-group CORRECTED_GROUP 335s FAST5 group created by resquiggle command. Default: 335s RawGenomeCorrected_000 335s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 335s FAST5 subgroup(s) (under /Analyses/[--basecall- 335s group]/) containing basecalls and created within 335s [--corrected-group] containing re-squiggle results. 335s Default: ['BaseCalled_template'] 335s 335s Miscellaneous Arguments: 335s --quiet, -q Don't print status information. 335s --help, -h Print this help message and exit 335s usage: tombo text_output signif_sequence_context --statistics-filename 335s STATISTICS_FILENAME 335s [--genome-fasta GENOME_FASTA] 335s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 335s [--num-regions NUM_REGIONS] 335s [--num-bases NUM_BASES] 335s [--sequences-filename SEQUENCES_FILENAME] 335s [--corrected-group CORRECTED_GROUP] 335s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 335s [--quiet] [--help] 335s 335s Required Argument: 335s --statistics-filename STATISTICS_FILENAME 335s File to save/load genomic base anchored statistics. 335s 335s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 335s --genome-fasta GENOME_FASTA 335s FASTA file used to re-squiggle. For faster sequence 335s access. 335s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 335s Directories containing fast5 files. 335s 335s Region Selection Arguments: 335s --num-regions NUM_REGIONS 335s Number of regions to plot. Default: 100 335s --num-bases NUM_BASES 335s Number of bases to plot/output. Default: 15 335s 335s Output Arguments: 335s --sequences-filename SEQUENCES_FILENAME 335s File for sequences from selected regions. Sequences 335s will be stored in FASTA format. Default: 335s tombo_results.significant_regions.fasta. 335s 335s FAST5 Data Arguments: 335s --corrected-group CORRECTED_GROUP 335s FAST5 group created by resquiggle command. Default: 335s RawGenomeCorrected_000 335s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 335s FAST5 subgroup(s) (under /Analyses/[--basecall- 335s group]/) containing basecalls and created within 335s [--corrected-group] containing re-squiggle results. 335s Default: ['BaseCalled_template'] 335s 335s Miscellaneous Arguments: 335s --quiet, -q Don't print status information. 335s --help, -h Print this help message and exit 335s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 335s [FAST5_BASEDIRS ...] 335s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 335s [--plot-standard-model] 335s [--plot-alternate-model {dam,CpG,6mA,dcm,5mC}] 335s [--overplot-threshold OVERPLOT_THRESHOLD] 335s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 335s [--num-regions NUM_REGIONS] 335s [--num-bases NUM_BASES] 335s [--pdf-filename PDF_FILENAME] 335s [--corrected-group CORRECTED_GROUP] 335s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 335s [--quiet] [--help] 335s 335s Required Argument: 335s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 335s Directories containing fast5 files. 335s 335s Comparison Arguments: 335s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 335s Set of directories containing fast5 files for control 335s reads, containing only canonical nucleotides. 335s --plot-standard-model 335s Add default standard model distribution to the plot. 335s --plot-alternate-model {dam,CpG,6mA,dcm,5mC} 335s Add alternative model distribution to the plot. 335s 335s Overplotting Arguments: 335s --overplot-threshold OVERPLOT_THRESHOLD 335s Coverage level to trigger alternative plot type 335s instead of raw signal. Default: 50 335s --overplot-type {Downsample,Boxplot,Quantile,Density} 335s Plot type for regions with higher coverage. Default: 335s Downsample 335s 335s Plotting Region Arguments: 335s --num-regions NUM_REGIONS 335s Number of regions to plot. Default: 10 335s --num-bases NUM_BASES 335s Number of bases to plot/output. Default: 21 335s 335s Output Argument: 335s --pdf-filename PDF_FILENAME 335s PDF filename to store plot(s). Default: 335s tombo_results.max_coverage.pdf 335s 335s FAST5 Data Arguments: 335s --corrected-group CORRECTED_GROUP 335s FAST5 group created by resquiggle command. Default: 335s RawGenomeCorrected_000 335s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 335s FAST5 subgroup(s) (under /Analyses/[--basecall- 335s group]/) containing basecalls and created within 335s [--corrected-group] containing re-squiggle results. 335s Default: ['BaseCalled_template'] 335s 335s Miscellaneous Arguments: 335s --quiet, -q Don't print status information. 335s --help, -h Print this help message and exit 335s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 335s [FAST5_BASEDIRS ...] --genome-locations 335s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 335s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 335s [--plot-standard-model] 335s [--plot-alternate-model {CpG,6mA,dam,dcm,5mC}] 335s [--overplot-threshold OVERPLOT_THRESHOLD] 335s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 335s [--num-bases NUM_BASES] 335s [--pdf-filename PDF_FILENAME] 335s [--corrected-group CORRECTED_GROUP] 335s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 335s [--quiet] [--help] 335s 335s Required Arguments: 335s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 335s Directories containing fast5 files. 335s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 335s Genomic locations at which to plot signal. Format 335s locations as "chrm:position[:strand] 335s [chrm2:position2[:strand2] ...]" (strand not 335s applicable for all applications) 335s 335s Comparison Arguments: 335s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 335s Set of directories containing fast5 files for control 335s reads, containing only canonical nucleotides. 335s --plot-standard-model 335s Add default standard model distribution to the plot. 335s --plot-alternate-model {CpG,6mA,dam,dcm,5mC} 335s Add alternative model distribution to the plot. 335s 335s Overplotting Arguments: 335s --overplot-threshold OVERPLOT_THRESHOLD 335s Coverage level to trigger alternative plot type 335s instead of raw signal. Default: 50 335s --overplot-type {Downsample,Boxplot,Quantile,Density} 335s Plot type for regions with higher coverage. Default: 335s Downsample 335s 335s Plotting Region Argument: 335s --num-bases NUM_BASES 335s Number of bases to plot/output. Default: 21 335s 335s Output Argument: 335s --pdf-filename PDF_FILENAME 335s PDF filename to store plot(s). Default: 335s tombo_results.genome_locations.pdf 335s 335s FAST5 Data Arguments: 335s --corrected-group CORRECTED_GROUP 335s FAST5 group created by resquiggle command. Default: 335s RawGenomeCorrected_000 335s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 335s FAST5 subgroup(s) (under /Analyses/[--basecall- 335s group]/) containing basecalls and created within 335s [--corrected-group] containing re-squiggle results. 335s Default: ['BaseCalled_template'] 335s 335s Miscellaneous Arguments: 335s --quiet, -q Don't print status information. 335s --help, -h Print this help message and exit 335s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 335s [FAST5_BASEDIRS ...] --motif MOTIF 335s --genome-fasta GENOME_FASTA 335s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 335s [--plot-standard-model] 335s [--plot-alternate-model {dcm,dam,CpG,6mA,5mC}] 335s [--overplot-threshold OVERPLOT_THRESHOLD] 335s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 335s [--num-regions NUM_REGIONS] 335s [--num-bases NUM_BASES] [--deepest-coverage] 335s [--pdf-filename PDF_FILENAME] 335s [--corrected-group CORRECTED_GROUP] 335s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 335s [--quiet] [--help] 335s 335s Required Arguments: 335s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 335s Directories containing fast5 files. 335s --motif MOTIF Motif of interest at which to plot signal and 335s statsitics. Supports IUPAC single letter codes (use T 335s for RNA). 335s --genome-fasta GENOME_FASTA 335s FASTA file used to re-squiggle. For faster sequence 335s access. 335s 335s Comparison Arguments: 335s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 335s Set of directories containing fast5 files for control 335s reads, containing only canonical nucleotides. 335s --plot-standard-model 335s Add default standard model distribution to the plot. 335s --plot-alternate-model {dcm,dam,CpG,6mA,5mC} 335s Add alternative model distribution to the plot. 335s 335s Overplotting Arguments: 335s --overplot-threshold OVERPLOT_THRESHOLD 335s Coverage level to trigger alternative plot type 335s instead of raw signal. Default: 50 335s --overplot-type {Downsample,Boxplot,Quantile,Density} 335s Plot type for regions with higher coverage. Default: 335s Downsample 335s 335s Plotting Region Arguments: 335s --num-regions NUM_REGIONS 335s Number of regions to plot. Default: 10 335s --num-bases NUM_BASES 335s Number of bases to plot/output. Default: 21 335s --deepest-coverage Plot the deepest coverage regions. 335s 335s Output Argument: 335s --pdf-filename PDF_FILENAME 335s PDF filename to store plot(s). Default: 335s tombo_results.motif_centered.pdf 335s 335s FAST5 Data Arguments: 335s --corrected-group CORRECTED_GROUP 335s FAST5 group created by resquiggle command. Default: 335s RawGenomeCorrected_000 335s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 335s FAST5 subgroup(s) (under /Analyses/[--basecall- 335s group]/) containing basecalls and created within 335s [--corrected-group] containing re-squiggle results. 335s Default: ['BaseCalled_template'] 335s 335s Miscellaneous Arguments: 335s --quiet, -q Don't print status information. 335s --help, -h Print this help message and exit 335s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 335s [FAST5_BASEDIRS ...] --control-fast5-basedirs 335s CONTROL_FAST5_BASEDIRS 335s [CONTROL_FAST5_BASEDIRS ...] 335s [--overplot-threshold OVERPLOT_THRESHOLD] 335s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 335s [--num-regions NUM_REGIONS] 335s [--num-bases NUM_BASES] 335s [--pdf-filename PDF_FILENAME] 335s [--sequences-filename SEQUENCES_FILENAME] 335s [--corrected-group CORRECTED_GROUP] 335s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 335s [--quiet] [--help] 335s 335s Required Arguments: 335s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 335s Directories containing fast5 files. 335s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 335s Set of directories containing fast5 files for control 335s reads, containing only canonical nucleotides. 335s 335s Overplotting Arguments: 335s --overplot-threshold OVERPLOT_THRESHOLD 335s Coverage level to trigger alternative plot type 335s instead of raw signal. Default: 50 335s --overplot-type {Downsample,Boxplot,Quantile,Density} 335s Plot type for regions with higher coverage. Default: 335s Downsample 335s 335s Plotting Region Arguments: 335s --num-regions NUM_REGIONS 335s Number of regions to plot. Default: 10 335s --num-bases NUM_BASES 335s Number of bases to plot/output. Default: 21 335s 335s Output Arguments: 335s --pdf-filename PDF_FILENAME 335s PDF filename to store plot(s). Default: 335s tombo_results.max_difference.pdf 335s --sequences-filename SEQUENCES_FILENAME 335s File for sequences from selected regions. Sequences 335s will be stored in FASTA format. Default: None. 335s 335s FAST5 Data Arguments: 335s --corrected-group CORRECTED_GROUP 335s FAST5 group created by resquiggle command. Default: 335s RawGenomeCorrected_000 335s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 335s FAST5 subgroup(s) (under /Analyses/[--basecall- 335s group]/) containing basecalls and created within 335s [--corrected-group] containing re-squiggle results. 335s Default: ['BaseCalled_template'] 335s 335s Miscellaneous Arguments: 335s --quiet, -q Don't print status information. 335s --help, -h Print this help message and exit 336s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 336s [FAST5_BASEDIRS ...] --statistics-filename 336s STATISTICS_FILENAME 336s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 336s [--plot-standard-model] 336s [--plot-alternate-model {CpG,6mA,dcm,dam,5mC}] 336s [--overplot-threshold OVERPLOT_THRESHOLD] 336s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 336s [--num-regions NUM_REGIONS] 336s [--num-bases NUM_BASES] 336s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 336s [--pdf-filename PDF_FILENAME] 336s [--sequences-filename SEQUENCES_FILENAME] 336s [--corrected-group CORRECTED_GROUP] 336s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 336s [--quiet] [--help] 336s 336s Required Arguments: 336s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 336s Directories containing fast5 files. 336s --statistics-filename STATISTICS_FILENAME 336s File to save/load genomic base anchored statistics. 336s 336s Comparison Arguments: 336s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 336s Set of directories containing fast5 files for control 336s reads, containing only canonical nucleotides. 336s --plot-standard-model 336s Add default standard model distribution to the plot. 336s --plot-alternate-model {CpG,6mA,dcm,dam,5mC} 336s Add alternative model distribution to the plot. 336s 336s Overplotting Arguments: 336s --overplot-threshold OVERPLOT_THRESHOLD 336s Coverage level to trigger alternative plot type 336s instead of raw signal. Default: 50 336s --overplot-type {Downsample,Boxplot,Quantile,Density} 336s Plot type for regions with higher coverage. Default: 336s Downsample 336s 336s Plotting Region Arguments: 336s --num-regions NUM_REGIONS 336s Number of regions to plot. Default: 10 336s --num-bases NUM_BASES 336s Number of bases to plot/output. Default: 21 336s 336s Statistical Argument: 336s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 336s Dampen fraction modified estimates for low coverage 336s sites. Two parameters are unmodified and modified 336s pseudo read counts. This is equivalent to a beta prior 336s on the fraction estimate. Set to "0 0" to disable 336s dampened fraction estimation. Default: [2, 0] 336s 336s Output Arguments: 336s --pdf-filename PDF_FILENAME 336s PDF filename to store plot(s). Default: 336s tombo_results.significant_difference.pdf 336s --sequences-filename SEQUENCES_FILENAME 336s File for sequences from selected regions. Sequences 336s will be stored in FASTA format. Default: None. 336s 336s FAST5 Data Arguments: 336s --corrected-group CORRECTED_GROUP 336s FAST5 group created by resquiggle command. Default: 336s RawGenomeCorrected_000 336s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 336s FAST5 subgroup(s) (under /Analyses/[--basecall- 336s group]/) containing basecalls and created within 336s [--corrected-group] containing re-squiggle results. 336s Default: ['BaseCalled_template'] 336s 336s Miscellaneous Arguments: 336s --quiet, -q Don't print status information. 336s --help, -h Print this help message and exit 336s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 336s [FAST5_BASEDIRS ...] --motif MOTIF 336s --statistics-filename STATISTICS_FILENAME 336s --genome-fasta GENOME_FASTA 336s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 336s [--plot-standard-model] 336s [--plot-alternate-model {dam,6mA,dcm,5mC,CpG}] 336s [--overplot-threshold OVERPLOT_THRESHOLD] 336s [--num-regions NUM_REGIONS] 336s [--num-context NUM_CONTEXT] 336s [--num-statistics NUM_STATISTICS] 336s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 336s [--pdf-filename PDF_FILENAME] 336s [--corrected-group CORRECTED_GROUP] 336s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 336s [--quiet] [--help] 336s 336s Required Arguments: 336s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 336s Directories containing fast5 files. 336s --motif MOTIF Motif of interest at which to plot signal and 336s statsitics. Supports IUPAC single letter codes (use T 336s for RNA). 336s --statistics-filename STATISTICS_FILENAME 336s File to save/load genomic base anchored statistics. 336s --genome-fasta GENOME_FASTA 336s FASTA file used to re-squiggle. For faster sequence 336s access. 336s 336s Comparison Arguments: 336s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 336s Set of directories containing fast5 files for control 336s reads, containing only canonical nucleotides. 336s --plot-standard-model 336s Add default standard model distribution to the plot. 336s --plot-alternate-model {dam,6mA,dcm,5mC,CpG} 336s Add alternative model distribution to the plot. 336s 336s Overplotting Argument: 336s --overplot-threshold OVERPLOT_THRESHOLD 336s Coverage level to trigger alternative plot type 336s instead of raw signal. Default: 50 336s 336s Plotting Region Arguments: 336s --num-regions NUM_REGIONS 336s Number of regions to plot. Default: 3 336s --num-context NUM_CONTEXT 336s Number of context bases around motif. Default: 5 336s --num-statistics NUM_STATISTICS 336s Number of motif centered regions to include in 336s statistic distributions. Default: 200 336s 336s Statistical Argument: 336s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 336s Dampen fraction modified estimates for low coverage 336s sites. Two parameters are unmodified and modified 336s pseudo read counts. This is equivalent to a beta prior 336s on the fraction estimate. Set to "0 0" to disable 336s dampened fraction estimation. Default: [2, 0] 336s 336s Output Argument: 336s --pdf-filename PDF_FILENAME 336s PDF filename to store plot(s). Default: 336s tombo_results.motif_statistics.pdf 336s 336s FAST5 Data Arguments: 336s --corrected-group CORRECTED_GROUP 336s FAST5 group created by resquiggle command. Default: 336s RawGenomeCorrected_000 336s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 336s FAST5 subgroup(s) (under /Analyses/[--basecall- 336s group]/) containing basecalls and created within 336s [--corrected-group] containing re-squiggle results. 336s Default: ['BaseCalled_template'] 336s 336s Miscellaneous Arguments: 336s --quiet, -q Don't print status information. 336s --help, -h Print this help message and exit 336s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 336s [GENOME_LOCATIONS ...] 336s --per-read-statistics-filename 336s PER_READ_STATISTICS_FILENAME 336s [--genome-fasta GENOME_FASTA] 336s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 336s [--num-reads NUM_READS] [--num-bases NUM_BASES] 336s [--box-center] [--pdf-filename PDF_FILENAME] 336s [--corrected-group CORRECTED_GROUP] 336s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 336s [--quiet] [--help] 336s 336s Required Arguments: 336s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 336s Genomic locations at which to plot signal. Format 336s locations as "chrm:position[:strand] 336s [chrm2:position2[:strand2] ...]" (strand not 336s applicable for all applications) 336s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 336s Binary file containing per-read statistics from 336s statistical testing. 336s 336s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 336s --genome-fasta GENOME_FASTA 336s FASTA file used to re-squiggle. For faster sequence 336s access. 336s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 336s Directories containing fast5 files. 336s 336s Plotting Region Arguments: 336s --num-reads NUM_READS 336s Number of reads to plot. Default: 100 336s --num-bases NUM_BASES 336s Number of bases to plot/output. Default: 51 336s --box-center Plot a box around the central base. 336s 336s Output Argument: 336s --pdf-filename PDF_FILENAME 336s PDF filename to store plot(s). Default: 336s tombo_results.per_read_stats.pdf 336s 336s FAST5 Data Arguments: 336s --corrected-group CORRECTED_GROUP 336s FAST5 group created by resquiggle command. Default: 336s RawGenomeCorrected_000 336s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 336s FAST5 subgroup(s) (under /Analyses/[--basecall- 336s group]/) containing basecalls and created within 336s [--corrected-group] containing re-squiggle results. 336s Default: ['BaseCalled_template'] 336s 336s Miscellaneous Arguments: 336s --quiet, -q Don't print status information. 336s --help, -h Print this help message and exit 336s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 336s [STATISTICS_FILENAMES ...] 336s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 336s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 336s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 336s [--genome-fasta GENOME_FASTA] 336s [--pdf-filename PDF_FILENAME] 336s [--statistics-per-block STATISTICS_PER_BLOCK] 336s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 336s [--quiet] [--help] 336s 336s Required Argument: 336s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 336s Files to load genomic base anchored statistics. 336s 336s Ground Truth Arguments (provide bed files or motifs): 336s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 336s Modification description and bed format files 336s containing single base locations of ground truth 336s modified sites. Bed files should contain 6 fields 336s including strand. Format descriptions as 336s "mod_name:locs.bed". Example: "CpG 336s bisulfite":bisulfite_locs.bed 336s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 336s Bed format files containing single base locations of 336s ground truth unmodified sites. Bed files should 336s contain 6 fields including strand. 336s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 336s Ground truth, motif centered, modified base 336s descriptions for computing ROC and PR curves. Each 336s statistics file is associated with a set of motif 336s descriptions. Format descriptions as: 336s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 336s mod_pos indicates the alternate-base within the motif 336s (1-based index). Example: CCWGG:2:"dcm 336s 5mC"::GATC:2:"dam 6mA" would assess the performance of 336s a single Tombo statistics file for identification of 336s E. coli dam and dcm methylation. 336s --genome-fasta GENOME_FASTA 336s FASTA file used to re-squiggle. For faster sequence 336s access. 336s 336s Output Arguments: 336s --pdf-filename PDF_FILENAME 336s PDF filename to store plot(s). Default: 336s tombo_results.roc.pdf 336s 336s Down-sampling Arguments: 336s --statistics-per-block STATISTICS_PER_BLOCK 336s Number of randomly selected per-read, per-base 336s statistics to extract from each genomic block for 336s plotting. Default: Include all stats 336s --total-statistics-limit TOTAL_STATISTICS_LIMIT 336s Total per-read statistics to be extracted for 336s plotting. Avoids memory overflow for large runs. 336s Default: 5000000 336s 336s Miscellaneous Arguments: 336s --quiet, -q Don't print status information. 336s --help, -h Print this help message and exit 336s usage: tombo plot per_read_roc --per-read-statistics-filenames 336s PER_READ_STATISTICS_FILENAMES 336s [PER_READ_STATISTICS_FILENAMES ...] 336s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 336s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 336s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 336s [--genome-fasta GENOME_FASTA] 336s [--statistics-per-block STATISTICS_PER_BLOCK] 336s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 336s [--pdf-filename PDF_FILENAME] [--quiet] 336s [--help] 336s 336s Required Argument: 336s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 336s Binary files containing per-read statistics from 336s statistical testing. 336s 336s Ground Truth Arguments (provide bed files or motifs): 336s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 336s Modification description and bed format files 336s containing single base locations of ground truth 336s modified sites. Bed files should contain 6 fields 336s including strand. Format descriptions as 336s "mod_name:locs.bed". Example: "CpG 336s bisulfite":bisulfite_locs.bed 336s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 336s Bed format files containing single base locations of 336s ground truth unmodified sites. Bed files should 336s contain 6 fields including strand. 336s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 336s Ground truth, motif centered, modified base 336s descriptions for computing ROC and PR curves. Each 336s statistics file is associated with a set of motif 336s descriptions. Format descriptions as: 336s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 336s mod_pos indicates the alternate-base within the motif 336s (1-based index). Example: CCWGG:2:"dcm 336s 5mC"::GATC:2:"dam 6mA" would assess the performance of 336s a single Tombo statistics file for identification of 336s E. coli dam and dcm methylation. 336s --genome-fasta GENOME_FASTA 336s FASTA file used to re-squiggle. For faster sequence 336s access. 336s 336s Down-sampling Arguments: 336s --statistics-per-block STATISTICS_PER_BLOCK 336s Number of randomly selected per-read, per-base 336s statistics to extract from each genomic block for 336s plotting. Default: 100000 336s --total-statistics-limit TOTAL_STATISTICS_LIMIT 336s Total per-read statistics to be extracted for 336s plotting. Avoids memory overflow for large runs. 336s Default: 5000000 336s 336s Output Arguments: 336s --pdf-filename PDF_FILENAME 336s PDF filename to store plot(s). Default: 336s tombo_results.per_reads_roc.pdf 336s 336s Miscellaneous Arguments: 336s --quiet, -q Don't print status information. 336s --help, -h Print this help message and exit 336s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 336s [--upstream-bases {0,1,2,3,4}] 336s [--downstream-bases {0,1,2,3,4}] [--read-mean] 336s [--num-kmer-threshold NUM_KMER_THRESHOLD] 336s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 336s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 336s [--corrected-group CORRECTED_GROUP] 336s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 336s [--quiet] [--help] 336s 336s Required Argument: 336s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 336s Directories containing fast5 files. 336s 336s Data Processing Arguments: 336s --upstream-bases {0,1,2,3,4} 336s Upstream bases in k-mer. Default: 1 336s --downstream-bases {0,1,2,3,4} 336s Downstream bases in k-mer. Default: 2 336s --read-mean Plot k-mer means across whole reads as opposed to 336s individual k-mer event levels. 336s --num-kmer-threshold NUM_KMER_THRESHOLD 336s Observations of each k-mer required to include a read 336s in read level averages. Default: 1 336s 336s Plotting Region Arguments: 336s --num-reads NUM_READS 336s Number of reads to plot. Default: 100 336s 336s Output Arguments: 336s --pdf-filename PDF_FILENAME 336s PDF filename to store plot(s). Default: 336s tombo_results.kmer_distribution.pdf 336s --r-data-filename R_DATA_FILENAME 336s Filename to save R data structure. Default: Don't save 336s --dont-plot Don't plot result. Useful to produce only R data file. 336s 336s FAST5 Data Arguments: 336s --corrected-group CORRECTED_GROUP 336s FAST5 group created by resquiggle command. Default: 336s RawGenomeCorrected_000 336s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 336s FAST5 subgroup(s) (under /Analyses/[--basecall- 336s group]/) containing basecalls and created within 336s [--corrected-group] containing re-squiggle results. 336s Default: ['BaseCalled_template'] 336s 336s Miscellaneous Arguments: 336s --quiet, -q Don't print status information. 336s --help, -h Print this help message and exit 336s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 336s [FAST5_BASEDIRS ...] 336s --control-fast5-basedirs 336s CONTROL_FAST5_BASEDIRS 336s [CONTROL_FAST5_BASEDIRS ...] 336s --statistics-filename 336s STATISTICS_FILENAME 336s [--genome-fasta GENOME_FASTA] 336s [--processes PROCESSES] 336s [--num-regions NUM_REGIONS] 336s [--num-bases NUM_BASES] 336s [--slide-span SLIDE_SPAN] 336s [--pdf-filename PDF_FILENAME] 336s [--r-data-filename R_DATA_FILENAME] 336s [--corrected-group CORRECTED_GROUP] 336s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 336s [--quiet] [--help] 336s 336s Required Arguments: 336s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 336s Directories containing fast5 files. 336s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 336s Set of directories containing fast5 files for control 336s reads, containing only canonical nucleotides. 336s --statistics-filename STATISTICS_FILENAME 336s File to save/load genomic base anchored statistics. 336s 336s FASTA Sequence Argument: 336s --genome-fasta GENOME_FASTA 336s FASTA file used to re-squiggle. For faster sequence 336s access. 336s 336s Multiprocessing Argument: 336s --processes PROCESSES 336s Number of processes. Default: 1 336s 336s Plotting Region Arguments: 336s --num-regions NUM_REGIONS 336s Number of regions to plot. Default: 10 336s --num-bases NUM_BASES 336s Number of bases to plot/output. Default: 21 336s --slide-span SLIDE_SPAN 336s Number of bases offset over which to search when 336s computing distances for signal cluster plotting. 336s Default: 0 (exact position) 336s 336s Output Arguments: 336s --pdf-filename PDF_FILENAME 336s PDF filename to store plot(s). Default: 336s tombo_results.signal_clusters.pdf 336s --r-data-filename R_DATA_FILENAME 336s Filename to save R data structure. Default: Don't save 336s 336s FAST5 Data Arguments: 336s --corrected-group CORRECTED_GROUP 336s FAST5 group created by resquiggle command. Default: 336s RawGenomeCorrected_000 336s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 336s FAST5 subgroup(s) (under /Analyses/[--basecall- 336s group]/) containing basecalls and created within 336s [--corrected-group] containing re-squiggle results. 336s Default: ['BaseCalled_template'] 336s 336s Miscellaneous Arguments: 336s --quiet, -q Don't print status information. 336s --help, -h Print this help message and exit 336s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 336s 336s Required Arguments: 336s fast5s_basedir Directory containing fast5 files. All files ending in 336s "fast5" found recursively within this base directory will be 336s processed. 336s 336s Miscellaneous Arguments: 336s --quiet, -q Don't print status information. 336s --help, -h Print this help message and exit 336s usage: tombo build_model event_resquiggle 336s [--minimap2-executable MINIMAP2_EXECUTABLE] 336s [--minimap2-index MINIMAP2_INDEX] 336s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 336s [--graphmap-executable GRAPHMAP_EXECUTABLE] 336s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 336s [--normalization-type {median,pA,pA_raw,none}] 336s [--pore-model-filename PORE_MODEL_FILENAME] 336s [--outlier-threshold OUTLIER_THRESHOLD] 336s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 336s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 336s [--timeout TIMEOUT] 336s [--cpts-limit CPTS_LIMIT] 336s [--skip-index] [--overwrite] 336s [--failed-reads-filename FAILED_READS_FILENAME] 336s [--include-event-stdev] 336s [--corrected-group CORRECTED_GROUP] 336s [--basecall-group BASECALL_GROUP] 336s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 336s [--processes PROCESSES] 336s [--align-processes ALIGN_PROCESSES] 336s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 336s [--resquiggle-processes RESQUIGGLE_PROCESSES] 336s [--quiet] [--help] 336s fast5s_basedir reference_fasta 336s 336s Required Arguments: 336s fast5s_basedir Directory containing fast5 files. All files ending in 336s "fast5" found recursively within this base directory 336s will be processed. 336s reference_fasta Reference genome/transcriptome FASTA file for mapping. 336s 336s Mapper Arguments (One mapper is required): 336s --minimap2-executable MINIMAP2_EXECUTABLE 336s Path to minimap2 executable. 336s --minimap2-index MINIMAP2_INDEX 336s Path to minimap2 index (with map-ont preset) file 336s corresponding to the [genome_fasta] provided. 336s --bwa-mem-executable BWA_MEM_EXECUTABLE 336s Path to bwa-mem executable. 336s --graphmap-executable GRAPHMAP_EXECUTABLE 336s Path to graphmap executable. 336s --alignment-batch-size ALIGNMENT_BATCH_SIZE 336s Number of reads included in each alignment call. Note: 336s A new system mapping call is made for each batch 336s (including loading of the genome), so it is advised to 336s use larger values for larger genomes. Default: 1000 336s 336s Signal Processing Arguments: 336s --normalization-type {median,pA,pA_raw,none} 336s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 336s as in the ONT events (using offset, range and 336s digitization), "pA": k-mer-based correction for pA 336s drift as in nanopolish (requires [--pore-model- 336s filename]), "median": median and MAD from raw signal. 336s Default: median 336s --pore-model-filename PORE_MODEL_FILENAME 336s File containing kmer model parameters (level_mean and 336s level_stdv) used in order to compute kmer-based 336s corrected pA values. E.g. https://github.com/jts/nanop 336s olish/blob/master/etc/r9- 336s models/template_median68pA.5mers.model 336s --outlier-threshold OUTLIER_THRESHOLD 336s Windosrize the signal at this number of scale values. 336s Negative value disables outlier clipping. Default: 336s 5.000000 336s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 336s Specify the 2 parameters for segmentation 1) running 336s neighboring windows width 2) minimum raw observations 336s per genomic base. Sample type defaults: RNA : 12 6 || 336s DNA : 5 3 336s 336s Read Filtering Arguments: 336s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 336s Filter reads based on observations per base percentile 336s thresholds. Format thresholds as "percentile:thresh 336s [pctl2:thresh2 ...]". For example to filter reads with 336s 99th pctl > 200 obs/base or max > 5k obs/base use 336s "99:200 100:5000". 336s --timeout TIMEOUT Timeout in seconds for processing a single read. 336s Default: No timeout. 336s --cpts-limit CPTS_LIMIT 336s Maximum number of changepoints to find within a single 336s indel group. Default: No limit. 336s 336s Input/Output Arguments: 336s --skip-index Skip creation of tombo index. This drastically slows 336s downstream tombo commands. Default stores tombo index 336s named ".[--fast5-basedir].[--corrected- 336s group].tombo.index" to be loaded automatically for 336s downstream commands. 336s --overwrite Overwrite previous corrected group in FAST5 files. 336s Note: only effects --corrected-group or --new- 336s corrected-group. 336s --failed-reads-filename FAILED_READS_FILENAME 336s Output failed read filenames with assoicated error. 336s Default: Do not store failed reads. 336s --include-event-stdev 336s Include corrected event standard deviation in output 336s FAST5 data. 336s 336s FAST5 Data Arguments: 336s --corrected-group CORRECTED_GROUP 336s FAST5 group created by resquiggle command. Default: 336s RawGenomeCorrected_000 336s --basecall-group BASECALL_GROUP 336s FAST5 group obtain original basecalls (under Analyses 336s group). Default: Basecall_1D_000 336s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 336s FAST5 subgroup(s) (under /Analyses/[--basecall- 336s group]/) containing basecalls and created within 336s [--corrected-group] containing re-squiggle results. 336s Default: ['BaseCalled_template'] 336s 336s Multiprocessing Arguments: 336s --processes PROCESSES 336s Number of processes. Default: 2 336s --align-processes ALIGN_PROCESSES 336s Number of processes to use for parsing and aligning 336s original basecalls. Each process will independently 336s load the genome into memory, so use caution with 336s larger genomes (e.g. human). Default: 1 336s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 336s Number of threads to use for aligner system call. 336s Default: [--processes] / (2 * [--align-processes)] 336s --resquiggle-processes RESQUIGGLE_PROCESSES 336s Number of processes to use for resquiggle algorithm. 336s Default: [--processes] / 2 336s 336s Miscellaneous Arguments: 336s --quiet, -q Don't print status information. 336s --help, -h Print this help message and exit 336s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 336s [FAST5_BASEDIRS ...] 336s --tombo-model-filename 336s TOMBO_MODEL_FILENAME 336s [--estimate-mean] 336s [--kmer-specific-sd] 336s [--upstream-bases {0,1,2,3,4}] 336s [--downstream-bases {0,1,2,3,4}] 336s [--minimum-test-reads MINIMUM_TEST_READS] 336s [--coverage-threshold COVERAGE_THRESHOLD] 336s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 336s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 336s [--processes PROCESSES] 336s [--corrected-group CORRECTED_GROUP] 336s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 336s [--quiet] [--help] 336s 336s Required Arguments: 336s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 336s Directories containing fast5 files. 336s --tombo-model-filename TOMBO_MODEL_FILENAME 336s Filename to save Tombo model. 336s 336s Modeling Arguments: 336s --estimate-mean Use the mean instead of median for model level 336s estimation. Note: This can cause poor fits due to 336s outliers 336s --kmer-specific-sd Estimate standard deviation for each k-mers 336s individually. 336s --upstream-bases {0,1,2,3,4} 336s Upstream bases in k-mer. Default: 1 336s --downstream-bases {0,1,2,3,4} 336s Downstream bases in k-mer. Default: 2 336s 336s Filtering Arguments: 336s --minimum-test-reads MINIMUM_TEST_READS 336s Number of reads required at a position to perform 336s significance testing or contribute to model 336s estimation. Default: 10 336s --coverage-threshold COVERAGE_THRESHOLD 336s Maximum mean coverage per region when estimating k-mer 336s model (limits compute time for deep samples). Default: 336s 100 336s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 336s Number of each k-mer observations required in order to 336s produce a reference (genomic locations for standard 336s reference and per-read for alternative reference). 336s Default: 5 336s 336s Multiprocessing Arguments: 336s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 336s Size of regions over which to multiprocesses statistic 336s computation. For very deep samples a smaller value is 336s recommmended in order to control memory consumption. 336s Default: 10000 336s --processes PROCESSES 336s Number of processes. Default: 1 336s 336s FAST5 Data Arguments: 336s --corrected-group CORRECTED_GROUP 336s FAST5 group created by resquiggle command. Default: 336s RawGenomeCorrected_000 336s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 336s FAST5 subgroup(s) (under /Analyses/[--basecall- 336s group]/) containing basecalls and created within 336s [--corrected-group] containing re-squiggle results. 336s Default: ['BaseCalled_template'] 336s 336s Miscellaneous Arguments: 336s --quiet, -q Don't print status information. 336s --help, -h Print this help message and exit 337s usage: tombo build_model estimate_alt_reference --alternate-model-filename 337s ALTERNATE_MODEL_FILENAME 337s --alternate-model-name 337s ALTERNATE_MODEL_NAME 337s --alternate-model-base 337s {A,C,G,T} 337s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 337s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 337s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 337s [--control-density-filename CONTROL_DENSITY_FILENAME] 337s [--dna] [--rna] 337s [--tombo-model-filename TOMBO_MODEL_FILENAME] 337s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 337s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 337s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 337s [--save-density-basename SAVE_DENSITY_BASENAME] 337s [--processes PROCESSES] 337s [--corrected-group CORRECTED_GROUP] 337s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 337s [--quiet] [--help] 337s 337s Required Arguments: 337s --alternate-model-filename ALTERNATE_MODEL_FILENAME 337s Tombo model for alternative likelihood ratio 337s significance testing. 337s --alternate-model-name ALTERNATE_MODEL_NAME 337s A short name to associate with this alternate model 337s (e.g. 5mC, 6mA, etc.). This text will be included in 337s output filenames when this model is used for testing. 337s --alternate-model-base {A,C,G,T} 337s Non-standard base is an alternative to this base. 337s 337s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 337s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 337s Directories containing fast5 files. 337s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 337s Set of directories containing fast5 files for control 337s reads, containing only canonical nucleotides. 337s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 337s File containing k-mer level kernel density estimates 337s for the alternative sample saved using --save-density- 337s basename. 337s --control-density-filename CONTROL_DENSITY_FILENAME 337s File containing k-mer level kernel density estimates 337s for the control sample saved using --save-density- 337s basename. 337s 337s Standard Model Arguments: 337s --dna Explicitly select canonical DNA model. Default: 337s Automatically determine from FAST5s 337s --rna Explicitly select canonical RNA model. Default: 337s Automatically determine from FAST5s 337s --tombo-model-filename TOMBO_MODEL_FILENAME 337s Tombo model filename. If no file is provided, the 337s default DNA or RNA Tombo model will be used. 337s 337s Model Fitting Arguments: 337s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 337s When esitmating the alternative base incorporation 337s rate, this percent of k-mers are assumed to have 337s significantly shifted signal so the alternative 337s distribution minimally overlaps the standard base 337s distribution. Default: 5.000000 337s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 337s Bandwidth applied when performing Gaussian kernal 337s density esitmation on standard and alternative base 337s signal distributions. Default: 0.050000 337s 337s Filtering Argument: 337s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 337s Number of each k-mer observations required in order to 337s produce a reference (genomic locations for standard 337s reference and per-read for alternative reference). 337s Default: 1000 337s 337s Output Argument: 337s --save-density-basename SAVE_DENSITY_BASENAME 337s Basename to save alternative model estimation density 337s estimation information. See scripts/debug_est_alt.R 337s for info use example. Default: Don't save. 337s 337s Multiprocessing Arguments: 337s --processes PROCESSES 337s Number of processes. Default: 1 337s 337s FAST5 Data Arguments: 337s --corrected-group CORRECTED_GROUP 337s FAST5 group created by resquiggle command. Default: 337s RawGenomeCorrected_000 337s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 337s FAST5 subgroup(s) (under /Analyses/[--basecall- 337s group]/) containing basecalls and created within 337s [--corrected-group] containing re-squiggle results. 337s Default: ['BaseCalled_template'] 337s 337s Miscellaneous Arguments: 337s --quiet, -q Don't print status information. 337s --help, -h Print this help message and exit 337s This test only tests the help system 337s There is an extensive test in 337s 337s tombo/tests/shell_tests.sh 337s 337s but this requires to download larger data 337s sets which is not done for the moment. 337s autopkgtest [00:14:41]: test run-unit-test: -----------------------] 338s autopkgtest [00:14:42]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 338s run-unit-test PASS 338s autopkgtest [00:14:42]: @@@@@@@@@@@@@@@@@@@@ summary 338s run-unit-test PASS 358s Creating nova instance adt-noble-ppc64el-tombo-20240320-000904-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240319.img (UUID 6e7a6c13-d651-45a1-a24f-48d9d59effd9)...