0s autopkgtest [06:08:20]: starting date and time: 2024-03-24 06:08:20+0000 0s autopkgtest [06:08:20]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [06:08:20]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vvw4fn22/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:sphinx --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/7.2.6-6 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-arm64-15.secgroup --name adt-noble-arm64-tombo-20240324-060819-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 125s autopkgtest [06:10:25]: testbed dpkg architecture: arm64 125s autopkgtest [06:10:25]: testbed apt version: 2.7.12 125s autopkgtest [06:10:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 127s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 128s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4009 kB] 129s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 129s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 129s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 129s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [707 kB] 129s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 129s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 129s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 129s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4359 kB] 129s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 129s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [69.8 kB] 129s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 138s Fetched 9865 kB in 5s (2027 kB/s) 139s Reading package lists... 144s Reading package lists... 145s Building dependency tree... 145s Reading state information... 146s Calculating upgrade... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 150s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 151s sh: Attempting to set up Debian/Ubuntu apt sources automatically 151s sh: Distribution appears to be Ubuntu 154s Reading package lists... 155s Building dependency tree... 155s Reading state information... 156s eatmydata is already the newest version (131-1). 156s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 156s Reading package lists... 157s Building dependency tree... 157s Reading state information... 158s dbus is already the newest version (1.14.10-4ubuntu1). 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 161s rng-tools-debian is already the newest version (2.4). 161s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 161s Reading package lists... 162s Building dependency tree... 162s Reading state information... 163s The following packages will be REMOVED: 163s cloud-init* python3-configobj* python3-debconf* 164s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 164s After this operation, 3256 kB disk space will be freed. 164s (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 ... 75911 files and directories currently installed.) 164s Removing cloud-init (24.1.2-0ubuntu1) ... 166s Removing python3-configobj (5.0.8-3) ... 167s Removing python3-debconf (1.5.86) ... 167s Processing triggers for man-db (2.12.0-3) ... 169s (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 ... 75522 files and directories currently installed.) 169s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 171s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 171s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 171s invoke-rc.d: policy-rc.d denied execution of try-restart. 174s Reading package lists... 174s Building dependency tree... 174s Reading state information... 174s linux-generic is already the newest version (6.8.0-11.11+1). 174s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 175s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 175s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 175s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 184s Reading package lists... 184s Reading package lists... 185s Building dependency tree... 185s Reading state information... 186s Calculating upgrade... 187s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 187s Reading package lists... 188s Building dependency tree... 188s Reading state information... 190s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 190s autopkgtest [06:11:30]: rebooting testbed after setup commands that affected boot 350s autopkgtest [06:14:10]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 354s autopkgtest [06:14:14]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 361s Get:1 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (dsc) [2292 B] 361s Get:2 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (tar) [22.3 MB] 361s Get:3 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (diff) [7024 B] 361s gpgv: Signature made Sun Dec 17 19:23:46 2023 UTC 361s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 361s gpgv: issuer "tille@debian.org" 361s gpgv: Can't check signature: No public key 361s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6.dsc: no acceptable signature found 363s autopkgtest [06:14:23]: testing package tombo version 1.5.1-6 363s autopkgtest [06:14:23]: build not needed 365s autopkgtest [06:14:25]: test run-unit-test: preparing testbed 370s Reading package lists... 371s Building dependency tree... 371s Reading state information... 372s Starting pkgProblemResolver with broken count: 0 372s Starting 2 pkgProblemResolver with broken count: 0 372s Done 374s The following additional packages will be installed: 374s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 374s libhdf5-103-1 libhdf5-hl-100 libjs-jquery libjs-mathjax libjs-sphinxdoc 374s libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 python3-decorator 374s python3-h5py python3-h5py-serial python3-mappy python3-numpy python3-scipy 374s python3-tqdm sphinx-rtd-theme-common tombo tombo-doc 374s Suggested packages: 374s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 374s gfortran python3-dev python3-pytest python-scipy-doc 374s Recommended packages: 374s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 374s python3-rpy2 374s The following NEW packages will be installed: 374s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 374s libblas3 libgfortran5 libhdf5-103-1 libhdf5-hl-100 libjs-jquery 374s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 374s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 374s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 374s tombo-doc 374s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 374s Need to get 64.0 MB/64.0 MB of archives. 374s After this operation, 234 MB of additional disk space will be used. 374s Get:1 /tmp/autopkgtest.cGFhou/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 374s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-lato all 2.015-1 [2781 kB] 375s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 375s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 375s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 375s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 375s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 375s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 375s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 375s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-hl-100 arm64 1.10.10+repack-3ubuntu1 [55.5 kB] 375s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 375s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 375s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-sphinxdoc all 7.2.6-4 [149 kB] 375s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 375s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 375s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 375s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 375s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 375s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu1 [1462 kB] 376s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py all 3.10.0-1ubuntu1 [7970 B] 376s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mappy arm64 2.24+dfsg-3build2 [195 kB] 376s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-tqdm all 4.64.1-2 [95.2 kB] 376s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] 376s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 377s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 tombo arm64 1.5.1-6 [486 kB] 377s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 377s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 tombo-doc all 1.5.1-6 [21.7 MB] 379s Fetched 64.0 MB in 4s (16.0 MB/s) 379s Selecting previously unselected package fonts-lato. 380s (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 ... 75467 files and directories currently installed.) 380s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 380s Unpacking fonts-lato (2.015-1) ... 381s Selecting previously unselected package fonts-font-awesome. 381s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 381s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 381s Selecting previously unselected package fonts-mathjax. 381s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 381s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 382s Selecting previously unselected package libaec0:arm64. 382s Preparing to unpack .../03-libaec0_1.1.2-1_arm64.deb ... 382s Unpacking libaec0:arm64 (1.1.2-1) ... 382s Selecting previously unselected package libblas3:arm64. 382s Preparing to unpack .../04-libblas3_3.12.0-3_arm64.deb ... 382s Unpacking libblas3:arm64 (3.12.0-3) ... 382s Selecting previously unselected package libgfortran5:arm64. 382s Preparing to unpack .../05-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 382s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 382s Selecting previously unselected package libsz2:arm64. 382s Preparing to unpack .../06-libsz2_1.1.2-1_arm64.deb ... 382s Unpacking libsz2:arm64 (1.1.2-1) ... 382s Selecting previously unselected package libhdf5-103-1:arm64. 382s Preparing to unpack .../07-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 382s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 382s Selecting previously unselected package libhdf5-hl-100:arm64. 382s Preparing to unpack .../08-libhdf5-hl-100_1.10.10+repack-3ubuntu1_arm64.deb ... 382s Unpacking libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 382s Selecting previously unselected package libjs-jquery. 382s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 382s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 382s Selecting previously unselected package libjs-underscore. 382s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 382s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 382s Selecting previously unselected package libjs-sphinxdoc. 382s Preparing to unpack .../11-libjs-sphinxdoc_7.2.6-4_all.deb ... 382s Unpacking libjs-sphinxdoc (7.2.6-4) ... 383s Selecting previously unselected package liblapack3:arm64. 383s Preparing to unpack .../12-liblapack3_3.12.0-3_arm64.deb ... 383s Unpacking liblapack3:arm64 (3.12.0-3) ... 383s Selecting previously unselected package liblbfgsb0:arm64. 383s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 383s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 383s Selecting previously unselected package liblzf1:arm64. 383s Preparing to unpack .../14-liblzf1_3.6-4_arm64.deb ... 383s Unpacking liblzf1:arm64 (3.6-4) ... 383s Selecting previously unselected package python3-decorator. 383s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 383s Unpacking python3-decorator (5.1.1-5) ... 383s Selecting previously unselected package python3-numpy. 383s Preparing to unpack .../16-python3-numpy_1%3a1.24.2-2_arm64.deb ... 383s Unpacking python3-numpy (1:1.24.2-2) ... 385s Selecting previously unselected package python3-h5py-serial. 385s Preparing to unpack .../17-python3-h5py-serial_3.10.0-1ubuntu1_arm64.deb ... 385s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 385s Selecting previously unselected package python3-h5py. 385s Preparing to unpack .../18-python3-h5py_3.10.0-1ubuntu1_all.deb ... 385s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 385s Selecting previously unselected package python3-mappy. 385s Preparing to unpack .../19-python3-mappy_2.24+dfsg-3build2_arm64.deb ... 385s Unpacking python3-mappy (2.24+dfsg-3build2) ... 385s Selecting previously unselected package python3-tqdm. 385s Preparing to unpack .../20-python3-tqdm_4.64.1-2_all.deb ... 385s Unpacking python3-tqdm (4.64.1-2) ... 385s Selecting previously unselected package sphinx-rtd-theme-common. 385s Preparing to unpack .../21-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... 385s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 385s Selecting previously unselected package python3-scipy. 385s Preparing to unpack .../22-python3-scipy_1.11.4-6_arm64.deb ... 385s Unpacking python3-scipy (1.11.4-6) ... 389s Selecting previously unselected package tombo. 390s Preparing to unpack .../23-tombo_1.5.1-6_arm64.deb ... 390s Unpacking tombo (1.5.1-6) ... 390s Selecting previously unselected package libjs-mathjax. 390s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 390s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 395s Selecting previously unselected package tombo-doc. 395s Preparing to unpack .../25-tombo-doc_1.5.1-6_all.deb ... 395s Unpacking tombo-doc (1.5.1-6) ... 395s Selecting previously unselected package autopkgtest-satdep. 395s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 395s Unpacking autopkgtest-satdep (0) ... 395s Setting up fonts-lato (2.015-1) ... 395s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 395s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 395s Setting up python3-tqdm (4.64.1-2) ... 396s Setting up python3-mappy (2.24+dfsg-3build2) ... 396s Setting up libaec0:arm64 (1.1.2-1) ... 396s Setting up python3-decorator (5.1.1-5) ... 397s Setting up libblas3:arm64 (3.12.0-3) ... 397s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 397s Setting up liblzf1:arm64 (3.6-4) ... 397s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 397s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 397s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 397s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 397s Setting up libsz2:arm64 (1.1.2-1) ... 397s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 397s Setting up liblapack3:arm64 (3.12.0-3) ... 397s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 397s Setting up python3-numpy (1:1.24.2-2) ... 404s Setting up libjs-sphinxdoc (7.2.6-4) ... 404s Setting up tombo-doc (1.5.1-6) ... 404s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 404s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 404s Setting up libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 404s Setting up python3-scipy (1.11.4-6) ... 415s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 415s Setting up python3-h5py (3.10.0-1ubuntu1) ... 416s Setting up tombo (1.5.1-6) ... 416s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 416s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 416s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 416s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 416s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 416s re.match('\+', fastq_rec[2]) is None): 417s Setting up autopkgtest-satdep (0) ... 417s Processing triggers for man-db (2.12.0-3) ... 418s Processing triggers for libc-bin (2.39-0ubuntu6) ... 426s (Reading database ... 82867 files and directories currently installed.) 426s Removing autopkgtest-satdep (0) ... 427s autopkgtest [06:15:27]: test run-unit-test: [----------------------- 428s ********* Testing help commands ********** 428s usage: tombo [-h] [-v] 428s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 428s ... 428s 428s ********** Tombo ********* 428s 428s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 428s 428s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 428s 428s Tombo command groups (additional help available within each command group): 428s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 428s preprocess Pre-process nanopore reads for Tombo processing. 428s filter Apply filter to Tombo index file for specified criterion. 428s detect_modifications Perform statistical testing to detect non-standard nucleotides. 428s text_output Output Tombo results in text files. 428s build_model Create canonical and alternative base Tombo models. 428s plot Save plots to visualize raw nanopore signal or testing results. 428s 428s options: 428s -h, --help show this help message and exit 428s -v, --version show Tombo version and exit. 428s usage: tombo resquiggle [--dna] [--rna] 428s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 428s [--q-score Q_SCORE] 428s [--signal-matching-score SIGNAL_MATCHING_SCORE] 428s [--processes PROCESSES] 428s [--corrected-group CORRECTED_GROUP] 428s [--basecall-group BASECALL_GROUP] 428s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 428s [--overwrite] 428s [--failed-reads-filename FAILED_READS_FILENAME] 428s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 428s [--print-advanced-arguments] [--quiet] [--help] 428s fast5s_basedir reference 428s 428s Required Arguments: 428s fast5s_basedir Directory containing fast5 files. All files ending in 428s "fast5" found recursively within this base directory 428s will be processed. 428s reference Reference genome/transcriptome FASTA file or minimap2 428s index (with "map-ont" preset) for mapping. 428s 428s Model Parameters: 428s --dna Explicitly select canonical DNA model. Default: 428s Automatically determine from FAST5s 428s --rna Explicitly select canonical RNA model. Default: 428s Automatically determine from FAST5s 428s 428s Read Filtering Argument: 428s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 428s Filter reads based on observations per base percentile 428s thresholds. Format thresholds as "percentile:thresh 428s [pctl2:thresh2 ...]". For example to filter reads with 428s 99th pctl > 200 obs/base or max > 5k obs/base use 428s "99:200 100:5000". 428s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 428s Default: 0.000000 428s --signal-matching-score SIGNAL_MATCHING_SCORE 428s Observed to expected signal matching score (higher 428s score indicates poor matching). Sample type defaults: 428s RNA : 2 || DNA : 1.1 428s 428s Multiprocessing Arguments: 428s --processes PROCESSES 428s Number of processes. Default: 1 428s 428s FAST5 Data Arguments: 428s --corrected-group CORRECTED_GROUP 428s FAST5 group created by resquiggle command. Default: 428s RawGenomeCorrected_000 428s --basecall-group BASECALL_GROUP 428s FAST5 group obtain original basecalls (under Analyses 428s group). Default: Basecall_1D_000 428s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 428s FAST5 subgroup(s) (under /Analyses/[--basecall- 428s group]/) containing basecalls and created within 428s [--corrected-group] containing re-squiggle results. 428s Default: ['BaseCalled_template'] 428s --overwrite Overwrite previous corrected group in FAST5 files. 428s Note: only effects --corrected-group or --new- 428s corrected-group. 428s 428s Input/Output Arguments: 428s --failed-reads-filename FAILED_READS_FILENAME 428s Output failed read filenames with assoicated error. 428s Default: Do not store failed reads. 428s --num-most-common-errors NUM_MOST_COMMON_ERRORS 428s Dynamically show this many most common errors so far 428s through run. Default: 0; Just show progress 428s 428s Advanced Arguments: 428s --print-advanced-arguments 428s Print advanced re-squiggle arguments and exit. 428s 428s Miscellaneous Arguments: 428s --quiet, -q Don't print status information. 428s --help, -h Print this help message and exit 429s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 429s --fastq-filenames 429s FASTQ_FILENAMES 429s [FASTQ_FILENAMES ...] 429s [--basecall-group BASECALL_GROUP] 429s [--basecall-subgroup BASECALL_SUBGROUP] 429s [--overwrite] 429s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 429s [--processes PROCESSES] 429s [--quiet] [--help] 429s 429s Required Arguments: 429s --fast5-basedir FAST5_BASEDIR 429s Directory containing fast5 files. 429s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 429s FASTQ filenames containing basecalls to be added to 429s raw FAST5 files. 429s 429s FAST5 Data Arguments: 429s --basecall-group BASECALL_GROUP 429s FAST5 group obtain original basecalls (under Analyses 429s group). Default: Basecall_1D_000 429s --basecall-subgroup BASECALL_SUBGROUP 429s FAST5 subgroup (under /Analyses/[--basecall-group]/) 429s under which to store basecalls from FASTQs. Default: 429s BaseCalled_template 429s --overwrite Overwrite previous corrected group in FAST5 files. 429s Note: only effects --corrected-group or --new- 429s corrected-group. 429s 429s Sequencing Summary Argument: 429s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 429s Sequencing summary filenames produced by albacore. 429s These can make annotation of raw FAST5 files with 429s FASTQ sequence much faster. 429s 429s Multiprocessing Argument: 429s --processes PROCESSES 429s Number of processes. Default: 1 429s 429s Miscellaneous Arguments: 429s --quiet, -q Don't print status information. 429s --help, -h Print this help message and exit 429s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 429s [FAST5_BASEDIRS ...] 429s [--corrected-group CORRECTED_GROUP] 429s [--quiet] [--help] 429s 429s Required Argument: 429s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 429s Directories containing fast5 files. 429s 429s FAST5 Data Argument: 429s --corrected-group CORRECTED_GROUP 429s FAST5 group created by resquiggle command. Default: 429s RawGenomeCorrected_000 429s 429s Miscellaneous Arguments: 429s --quiet, -q Don't print status information. 429s --help, -h Print this help message and exit 429s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 429s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 429s [--corrected-group CORRECTED_GROUP] [--quiet] 429s [--help] 429s 429s Required Argument: 429s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 429s Directories containing fast5 files. 429s 429s Read Filtering Argument: 429s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 429s Filter reads based on observations per base percentile 429s thresholds. Format thresholds as "percentile:thresh 429s [pctl2:thresh2 ...]". For example to filter reads with 429s 99th pctl > 200 obs/base or max > 5k obs/base use 429s "99:200 100:5000". 429s 429s FAST5 Data Argument: 429s --corrected-group CORRECTED_GROUP 429s FAST5 group created by resquiggle command. Default: 429s RawGenomeCorrected_000 429s 429s Miscellaneous Arguments: 429s --quiet, -q Don't print status information. 429s --help, -h Print this help message and exit 430s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 430s [FAST5_BASEDIRS ...] 430s [--percent-to-filter PERCENT_TO_FILTER] 430s [--corrected-group CORRECTED_GROUP] 430s [--quiet] [--help] 430s 430s Required Arguments: 430s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 430s Directories containing fast5 files. 430s 430s Read Filtering Argument: 430s --percent-to-filter PERCENT_TO_FILTER 430s Percentage of all reads to filter. Reads are randomly 430s selected weighted according to the approximate 430s coverage at the mapped genomic location. This can be 430s useful in modeling and testing. Default: 10.000000 430s 430s FAST5 Data Arguments: 430s --corrected-group CORRECTED_GROUP 430s FAST5 group created by resquiggle command. Default: 430s RawGenomeCorrected_000 430s 430s Miscellaneous Arguments: 430s --quiet, -q Don't print status information. 430s --help, -h Print this help message and exit 430s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 430s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 430s [--corrected-group CORRECTED_GROUP] 430s [--basecall-group BASECALL_GROUP] [--quiet] 430s [--help] 430s 430s Required Arguments: 430s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 430s Directories containing fast5 files. 430s 430s Read Filtering Argument: 430s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 430s Default: 7.000000 430s 430s FAST5 Data Arguments: 430s --corrected-group CORRECTED_GROUP 430s FAST5 group created by resquiggle command. Default: 430s RawGenomeCorrected_000 430s --basecall-group BASECALL_GROUP 430s FAST5 group obtain original basecalls (under Analyses 430s group). Default: Basecall_1D_000 430s 430s Miscellaneous Arguments: 430s --quiet, -q Don't print status information. 430s --help, -h Print this help message and exit 430s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 430s [FAST5_BASEDIRS ...] 430s --signal-matching-score 430s SIGNAL_MATCHING_SCORE 430s [--corrected-group CORRECTED_GROUP] 430s [--quiet] [--help] 430s 430s Required Arguments: 430s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 430s Directories containing fast5 files. 430s --signal-matching-score SIGNAL_MATCHING_SCORE 430s Observed to expected signal matching score (higher 430s score indicates poor matching). Sample type defaults: 430s RNA : 2 || DNA : 1.1 430s 430s FAST5 Data Arguments: 430s --corrected-group CORRECTED_GROUP 430s FAST5 group created by resquiggle command. Default: 430s RawGenomeCorrected_000 430s 430s Miscellaneous Arguments: 430s --quiet, -q Don't print status information. 430s --help, -h Print this help message and exit 431s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 431s [FAST5_BASEDIRS ...] 431s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 431s [--include-partial-overlap] 431s [--corrected-group CORRECTED_GROUP] 431s [--quiet] [--help] 431s 431s Required Arguments: 431s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 431s Directories containing fast5 files. 431s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 431s Filter out reads not falling completely within include 431s regions. Omit start and end coordinates to include an 431s entire chromosome/sequence record. Format regions as 431s "chrm[:start-end] [chrm2[:start2-end2] ...]". 431s 431s Filter Argument: 431s --include-partial-overlap 431s Include reads that partially overlap the specified 431s region. Default: Only include reads completely 431s contained in a specified region 431s 431s FAST5 Data Argument: 431s --corrected-group CORRECTED_GROUP 431s FAST5 group created by resquiggle command. Default: 431s RawGenomeCorrected_000 431s 431s Miscellaneous Arguments: 431s --quiet, -q Don't print status information. 431s --help, -h Print this help message and exit 431s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 431s [FAST5_BASEDIRS ...] 431s --statistics-file-basename 431s STATISTICS_FILE_BASENAME [--dna] 431s [--rna] 431s [--fishers-method-context FISHERS_METHOD_CONTEXT] 431s [--minimum-test-reads MINIMUM_TEST_READS] 431s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 431s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 431s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 431s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 431s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 431s [--processes PROCESSES] 431s [--corrected-group CORRECTED_GROUP] 431s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 431s [--quiet] [--help] 431s 431s Required Argument: 431s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 431s Directories containing fast5 files. 431s --statistics-file-basename STATISTICS_FILE_BASENAME 431s File base name to save base by base statistics from 431s testing. Filenames will be [--statistics-file- 431s basename].[--alternate-bases]?.tombo.stats 431s 431s Comparison Model Arguments: 431s --dna Explicitly select canonical DNA model. Default: 431s Automatically determine from FAST5s 431s --rna Explicitly select canonical RNA model. Default: 431s Automatically determine from FAST5s 431s 431s Significance Test Arguments: 431s --fishers-method-context FISHERS_METHOD_CONTEXT 431s Number of context bases up and downstream over which 431s to compute Fisher's method combined p-values. Note: 431s Not applicable for alternative model likelihood ratio 431s tests. Default: 1. 431s --minimum-test-reads MINIMUM_TEST_READS 431s Number of reads required at a position to perform 431s significance testing or contribute to model 431s estimation. Default: 1 431s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 431s P-value threshold when computing fraction of 431s significant reads at each genomic position. If two 431s values are provided, statistics between these values 431s are not considered. Default thresholds: DNA:0.15-0.5 , 431s RNA:0.05-0.4 431s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 431s Dampen fraction modified estimates for low coverage 431s sites. Two parameters are unmodified and modified 431s pseudo read counts. This is equivalent to a beta prior 431s on the fraction estimate. Set to "0 0" to disable 431s dampened fraction estimation. Default: [2, 0] 431s 431s Output Argument: 431s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 431s Base for binary files containing per-read statistics 431s from statistical testing. Filenames will be [--per- 431s read-statistics-basename].[--alternate- 431s bases]?.tombo.per_read_stats 431s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 431s Number of the most significant sites to store for 431s faster access. If a longer list of most significant 431s sites is required the list must be re-computed from 431s all batches. Very large values can increase RAM usage. 431s Default: 100000 431s 431s Multiprocessing Arguments: 431s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 431s Size of regions over which to multiprocesses statistic 431s computation. For very deep samples a smaller value is 431s recommmended in order to control memory consumption. 431s Default: 10000 431s --processes PROCESSES 431s Number of processes. Default: 1 431s 431s FAST5 Data Arguments: 431s --corrected-group CORRECTED_GROUP 431s FAST5 group created by resquiggle command. Default: 431s RawGenomeCorrected_000 431s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 431s FAST5 subgroup(s) (under /Analyses/[--basecall- 431s group]/) containing basecalls and created within 431s [--corrected-group] containing re-squiggle results. 431s Default: ['BaseCalled_template'] 431s 431s Miscellaneous Arguments: 431s --quiet, -q Don't print status information. 431s --help, -h Print this help message and exit 431s usage: tombo detect_modifications alternative_model 431s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 431s [--statistics-file-basename STATISTICS_FILE_BASENAME] 431s [--alternate-bases {6mA,CpG,5mC,dam,dcm} [{6mA,CpG,5mC,dam,dcm} ...]] 431s [--print-available-models] 431s [--dna] [--rna] 431s [--minimum-test-reads MINIMUM_TEST_READS] 431s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 431s [--standard-log-likelihood-ratio] 431s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 431s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 431s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 431s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 431s [--processes PROCESSES] 431s [--corrected-group CORRECTED_GROUP] 431s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 431s [--quiet] [--help] 431s 431s Required Argument: 431s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 431s Directories containing fast5 files. 431s --statistics-file-basename STATISTICS_FILE_BASENAME 431s File base name to save base by base statistics from 431s testing. Filenames will be [--statistics-file- 431s basename].[--alternate-bases]?.tombo.stats 431s --alternate-bases {6mA,CpG,5mC,dam,dcm} [{6mA,CpG,5mC,dam,dcm} ...] 431s Default non-standard base model for testing (not 431s required if user created --alternate-model-filenames 431s is provided). 431s 431s Comparison Arguments: 431s --print-available-models 431s Print available alternative models and exit. 431s --dna Explicitly select canonical DNA model. Default: 431s Automatically determine from FAST5s 431s --rna Explicitly select canonical RNA model. Default: 431s Automatically determine from FAST5s 431s 431s Significance Test Arguments: 431s --minimum-test-reads MINIMUM_TEST_READS 431s Number of reads required at a position to perform 431s significance testing or contribute to model 431s estimation. Default: 1 431s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 431s Log likelihood ratio threshold when computing fraction 431s of significant reads at each genomic position. If two 431s values are provided, statistics between these values 431s are not considered. Default thresholds: DNA:-1.5-2.5 , 431s RNA:-2.5-2.5 431s --standard-log-likelihood-ratio 431s Use a standard log likelihood ratio (LLR) statistic. 431s Default is to use an outlier-robust LLR-like 431s statistic. Detail in full online documentation. 431s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 431s Dampen fraction modified estimates for low coverage 431s sites. Two parameters are unmodified and modified 431s pseudo read counts. This is equivalent to a beta prior 431s on the fraction estimate. Set to "0 0" to disable 431s dampened fraction estimation. Default: [2, 0] 431s 431s Output Argument: 431s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 431s Base for binary files containing per-read statistics 431s from statistical testing. Filenames will be [--per- 431s read-statistics-basename].[--alternate- 431s bases]?.tombo.per_read_stats 431s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 431s Number of the most significant sites to store for 431s faster access. If a longer list of most significant 431s sites is required the list must be re-computed from 431s all batches. Very large values can increase RAM usage. 431s Default: 100000 431s 431s Multiprocessing Arguments: 431s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 431s Size of regions over which to multiprocesses statistic 431s computation. For very deep samples a smaller value is 431s recommmended in order to control memory consumption. 431s Default: 10000 431s --processes PROCESSES 431s Number of processes. Default: 1 431s 431s FAST5 Data Arguments: 431s --corrected-group CORRECTED_GROUP 431s FAST5 group created by resquiggle command. Default: 431s RawGenomeCorrected_000 431s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 431s FAST5 subgroup(s) (under /Analyses/[--basecall- 431s group]/) containing basecalls and created within 431s [--corrected-group] containing re-squiggle results. 431s Default: ['BaseCalled_template'] 431s 431s Miscellaneous Arguments: 431s --quiet, -q Don't print status information. 431s --help, -h Print this help message and exit 432s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 432s FAST5_BASEDIRS 432s [FAST5_BASEDIRS ...] 432s --statistics-file-basename 432s STATISTICS_FILE_BASENAME 432s --control-fast5-basedirs 432s CONTROL_FAST5_BASEDIRS 432s [CONTROL_FAST5_BASEDIRS ...] 432s [--sample-only-estimates] 432s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 432s [--dna] [--rna] 432s [--fishers-method-context FISHERS_METHOD_CONTEXT] 432s [--minimum-test-reads MINIMUM_TEST_READS] 432s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 432s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 432s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 432s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 432s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 432s [--processes PROCESSES] 432s [--corrected-group CORRECTED_GROUP] 432s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 432s [--quiet] [--help] 432s 432s Required Argument: 432s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 432s Directories containing fast5 files. 432s --statistics-file-basename STATISTICS_FILE_BASENAME 432s File base name to save base by base statistics from 432s testing. Filenames will be [--statistics-file- 432s basename].[--alternate-bases]?.tombo.stats 432s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 432s Set of directories containing fast5 files for control 432s reads, containing only canonical nucleotides. 432s 432s Model Prior Arguments: 432s --sample-only-estimates 432s Only use canonical sample to estimate expected signal 432s level and spread. Default: Use canonical model to 432s improve estimtates (esp. for low coverage regions) 432s using baysian posterior estimates. 432s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 432s Prior weights (one each for mean and spread) applied 432s to canonical base model for estimating posterior model 432s parameters for sample comparison. Default: [5, 40] 432s --dna Explicitly select canonical DNA model. Default: 432s Automatically determine from FAST5s 432s --rna Explicitly select canonical RNA model. Default: 432s Automatically determine from FAST5s 432s 432s Significance Test Arguments: 432s --fishers-method-context FISHERS_METHOD_CONTEXT 432s Number of context bases up and downstream over which 432s to compute Fisher's method combined p-values. Note: 432s Not applicable for alternative model likelihood ratio 432s tests. Default: 1. 432s --minimum-test-reads MINIMUM_TEST_READS 432s Number of reads required at a position to perform 432s significance testing or contribute to model 432s estimation. Default: 1 432s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 432s P-value threshold when computing fraction of 432s significant reads at each genomic position. If two 432s values are provided, statistics between these values 432s are not considered. Default thresholds: DNA:0.15-0.5 , 432s RNA:0.05-0.4 432s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 432s Dampen fraction modified estimates for low coverage 432s sites. Two parameters are unmodified and modified 432s pseudo read counts. This is equivalent to a beta prior 432s on the fraction estimate. Set to "0 0" to disable 432s dampened fraction estimation. Default: [2, 0] 432s 432s Output Argument: 432s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 432s Base for binary files containing per-read statistics 432s from statistical testing. Filenames will be [--per- 432s read-statistics-basename].[--alternate- 432s bases]?.tombo.per_read_stats 432s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 432s Number of the most significant sites to store for 432s faster access. If a longer list of most significant 432s sites is required the list must be re-computed from 432s all batches. Very large values can increase RAM usage. 432s Default: 100000 432s 432s Multiprocessing Arguments: 432s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 432s Size of regions over which to multiprocesses statistic 432s computation. For very deep samples a smaller value is 432s recommmended in order to control memory consumption. 432s Default: 10000 432s --processes PROCESSES 432s Number of processes. Default: 1 432s 432s FAST5 Data Arguments: 432s --corrected-group CORRECTED_GROUP 432s FAST5 group created by resquiggle command. Default: 432s RawGenomeCorrected_000 432s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 432s FAST5 subgroup(s) (under /Analyses/[--basecall- 432s group]/) containing basecalls and created within 432s [--corrected-group] containing re-squiggle results. 432s Default: ['BaseCalled_template'] 432s 432s Miscellaneous Arguments: 432s --quiet, -q Don't print status information. 432s --help, -h Print this help message and exit 432s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 432s FAST5_BASEDIRS 432s [FAST5_BASEDIRS ...] 432s --statistics-file-basename 432s STATISTICS_FILE_BASENAME 432s --alternate-fast5-basedirs 432s ALTERNATE_FAST5_BASEDIRS 432s [ALTERNATE_FAST5_BASEDIRS ...] 432s [--fishers-method-context FISHERS_METHOD_CONTEXT] 432s [--minimum-test-reads MINIMUM_TEST_READS] 432s [--statistic-type {ks,u,t}] 432s [--store-p-value] 432s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 432s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 432s [--processes PROCESSES] 432s [--corrected-group CORRECTED_GROUP] 432s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 432s [--quiet] [--help] 432s 432s Required Argument: 432s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 432s Directories containing fast5 files. 432s --statistics-file-basename STATISTICS_FILE_BASENAME 432s File base name to save base by base statistics from 432s testing. Filenames will be [--statistics-file- 432s basename].[--alternate-bases]?.tombo.stats 432s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 432s Set of directories containing fast5 files for 432s alternate set of reads. 432s 432s Significance Test Arguments: 432s --fishers-method-context FISHERS_METHOD_CONTEXT 432s Number of context bases up and downstream over which 432s to compute Fisher's method combined p-values. Note: 432s Not applicable for alternative model likelihood ratio 432s tests. Default: 1. 432s --minimum-test-reads MINIMUM_TEST_READS 432s Number of reads required at a position to perform 432s significance testing or contribute to model 432s estimation. Default: 50 432s --statistic-type {ks,u,t} 432s Type of statistical test to apply. Default: "ks" 432s --store-p-value Store p-value instead of effect-size statistic. 432s Statistics are D-statistic (KS-test), deviation from 432s even common language effect size (u-test), and Cohen's 432s D (t-test). 432s 432s Output Argument: 432s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 432s Number of the most significant sites to store for 432s faster access. If a longer list of most significant 432s sites is required the list must be re-computed from 432s all batches. Very large values can increase RAM usage. 432s Default: 100000 432s 432s Multiprocessing Arguments: 432s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 432s Size of regions over which to multiprocesses statistic 432s computation. For very deep samples a smaller value is 432s recommmended in order to control memory consumption. 432s Default: 10000 432s --processes PROCESSES 432s Number of processes. Default: 1 432s 432s FAST5 Data Arguments: 432s --corrected-group CORRECTED_GROUP 432s FAST5 group created by resquiggle command. Default: 432s RawGenomeCorrected_000 432s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 432s FAST5 subgroup(s) (under /Analyses/[--basecall- 432s group]/) containing basecalls and created within 432s [--corrected-group] containing re-squiggle results. 432s Default: ['BaseCalled_template'] 432s 432s Miscellaneous Arguments: 432s --quiet, -q Don't print status information. 432s --help, -h Print this help message and exit 433s usage: tombo detect_modifications aggregate_per_read_stats 433s --per-read-statistics-filename 433s PER_READ_STATISTICS_FILENAME 433s --statistics-filename 433s STATISTICS_FILENAME 433s --single-read-threshold 433s SINGLE_READ_THRESHOLD 433s [SINGLE_READ_THRESHOLD ...] 433s [--minimum-test-reads MINIMUM_TEST_READS] 433s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 433s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 433s [--processes PROCESSES] 433s [--corrected-group CORRECTED_GROUP] 433s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 433s [--quiet] [--help] 433s 433s Required Argument: 433s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 433s Binary file containing per-read statistics from 433s statistical testing. 433s --statistics-filename STATISTICS_FILENAME 433s File to save/load genomic base anchored statistics. 433s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 433s P-value or log likelihood ratio threshold when 433s computing fraction of significant reads at each 433s genomic position. If two values are provided, 433s statistics between these values are not considered. 433s 433s Significance Test Arguments: 433s --minimum-test-reads MINIMUM_TEST_READS 433s Number of reads required at a position to perform 433s significance testing or contribute to model 433s estimation. Default: 1 433s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 433s Dampen fraction modified estimates for low coverage 433s sites. Two parameters are unmodified and modified 433s pseudo read counts. This is equivalent to a beta prior 433s on the fraction estimate. Set to "0 0" to disable 433s dampened fraction estimation. Default: [2, 0] 433s 433s Output Argument: 433s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 433s Number of the most significant sites to store for 433s faster access. If a longer list of most significant 433s sites is required the list must be re-computed from 433s all batches. Very large values can increase RAM usage. 433s Default: 100000 433s 433s Multiprocessing Arguments: 433s --processes PROCESSES 433s Number of processes. Default: 1 433s 433s FAST5 Data Arguments: 433s --corrected-group CORRECTED_GROUP 433s FAST5 group created by resquiggle command. Default: 433s RawGenomeCorrected_000 433s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 433s FAST5 subgroup(s) (under /Analyses/[--basecall- 433s group]/) containing basecalls and created within 433s [--corrected-group] containing re-squiggle results. 433s Default: ['BaseCalled_template'] 433s 433s Miscellaneous Arguments: 433s --quiet, -q Don't print status information. 433s --help, -h Print this help message and exit 433s usage: tombo text_output browser_files 433s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 433s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 433s [--statistics-filename STATISTICS_FILENAME] 433s [--genome-fasta GENOME_FASTA] 433s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 433s [--browser-file-basename BROWSER_FILE_BASENAME] 433s [--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} ...]] 433s [--corrected-group CORRECTED_GROUP] 433s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 433s [--quiet] [--help] 433s 433s Data Arguments: 433s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 433s Directories containing fast5 files. 433s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 433s Set of directories containing fast5 files for control 433s reads, containing only canonical nucleotides. 433s --statistics-filename STATISTICS_FILENAME 433s File to save/load genomic base anchored statistics. 433s 433s Statistic Motif Filter Arguments: 433s --genome-fasta GENOME_FASTA 433s FASTA file used to re-squiggle. For faster sequence 433s access. 433s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 433s Ground truth, motif centered, modified base 433s descriptions for output filtering. Format descriptions 433s as: "motif:mod_pos:name". The mod_pos indicates the 433s modified base within the motif (1-based index). 433s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 433s output for identification of E. coli dam and dcm 433s methylation. 433s 433s Output Arguments: 433s --browser-file-basename BROWSER_FILE_BASENAME 433s Basename for output browser files. Two files (plus and 433s minus strand) will be produced for each --file-types 433s supplied. Filenames formatted as "[browser-file- 433s basename].[file- 433s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 433s Default: tombo_results 433s --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} ...] 433s Data types of genome browser files to produce. 433s Produced coverage files are in bedGraph format, while 433s all other file types will be in wiggle format 433s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 433s Default: "coverage" 433s 433s FAST5 Data Arguments: 433s --corrected-group CORRECTED_GROUP 433s FAST5 group created by resquiggle command. Default: 433s RawGenomeCorrected_000 433s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 433s FAST5 subgroup(s) (under /Analyses/[--basecall- 433s group]/) containing basecalls and created within 433s [--corrected-group] containing re-squiggle results. 433s Default: ['BaseCalled_template'] 433s 433s Miscellaneous Arguments: 433s --quiet, -q Don't print status information. 433s --help, -h Print this help message and exit 433s usage: tombo text_output signif_sequence_context --statistics-filename 433s STATISTICS_FILENAME 433s [--genome-fasta GENOME_FASTA] 433s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 433s [--num-regions NUM_REGIONS] 433s [--num-bases NUM_BASES] 433s [--sequences-filename SEQUENCES_FILENAME] 433s [--corrected-group CORRECTED_GROUP] 433s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 433s [--quiet] [--help] 433s 433s Required Argument: 433s --statistics-filename STATISTICS_FILENAME 433s File to save/load genomic base anchored statistics. 433s 433s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 433s --genome-fasta GENOME_FASTA 433s FASTA file used to re-squiggle. For faster sequence 433s access. 433s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 433s Directories containing fast5 files. 433s 433s Region Selection Arguments: 433s --num-regions NUM_REGIONS 433s Number of regions to plot. Default: 100 433s --num-bases NUM_BASES 433s Number of bases to plot/output. Default: 15 433s 433s Output Arguments: 433s --sequences-filename SEQUENCES_FILENAME 433s File for sequences from selected regions. Sequences 433s will be stored in FASTA format. Default: 433s tombo_results.significant_regions.fasta. 433s 433s FAST5 Data Arguments: 433s --corrected-group CORRECTED_GROUP 433s FAST5 group created by resquiggle command. Default: 433s RawGenomeCorrected_000 433s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 433s FAST5 subgroup(s) (under /Analyses/[--basecall- 433s group]/) containing basecalls and created within 433s [--corrected-group] containing re-squiggle results. 433s Default: ['BaseCalled_template'] 433s 433s Miscellaneous Arguments: 433s --quiet, -q Don't print status information. 433s --help, -h Print this help message and exit 434s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 434s [FAST5_BASEDIRS ...] 434s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 434s [--plot-standard-model] 434s [--plot-alternate-model {6mA,dcm,dam,5mC,CpG}] 434s [--overplot-threshold OVERPLOT_THRESHOLD] 434s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 434s [--num-regions NUM_REGIONS] 434s [--num-bases NUM_BASES] 434s [--pdf-filename PDF_FILENAME] 434s [--corrected-group CORRECTED_GROUP] 434s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 434s [--quiet] [--help] 434s 434s Required Argument: 434s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 434s Directories containing fast5 files. 434s 434s Comparison Arguments: 434s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 434s Set of directories containing fast5 files for control 434s reads, containing only canonical nucleotides. 434s --plot-standard-model 434s Add default standard model distribution to the plot. 434s --plot-alternate-model {6mA,dcm,dam,5mC,CpG} 434s Add alternative model distribution to the plot. 434s 434s Overplotting Arguments: 434s --overplot-threshold OVERPLOT_THRESHOLD 434s Coverage level to trigger alternative plot type 434s instead of raw signal. Default: 50 434s --overplot-type {Downsample,Boxplot,Quantile,Density} 434s Plot type for regions with higher coverage. Default: 434s Downsample 434s 434s Plotting Region Arguments: 434s --num-regions NUM_REGIONS 434s Number of regions to plot. Default: 10 434s --num-bases NUM_BASES 434s Number of bases to plot/output. Default: 21 434s 434s Output Argument: 434s --pdf-filename PDF_FILENAME 434s PDF filename to store plot(s). Default: 434s tombo_results.max_coverage.pdf 434s 434s FAST5 Data Arguments: 434s --corrected-group CORRECTED_GROUP 434s FAST5 group created by resquiggle command. Default: 434s RawGenomeCorrected_000 434s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 434s FAST5 subgroup(s) (under /Analyses/[--basecall- 434s group]/) containing basecalls and created within 434s [--corrected-group] containing re-squiggle results. 434s Default: ['BaseCalled_template'] 434s 434s Miscellaneous Arguments: 434s --quiet, -q Don't print status information. 434s --help, -h Print this help message and exit 434s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 434s [FAST5_BASEDIRS ...] --genome-locations 434s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 434s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 434s [--plot-standard-model] 434s [--plot-alternate-model {CpG,dam,6mA,5mC,dcm}] 434s [--overplot-threshold OVERPLOT_THRESHOLD] 434s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 434s [--num-bases NUM_BASES] 434s [--pdf-filename PDF_FILENAME] 434s [--corrected-group CORRECTED_GROUP] 434s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 434s [--quiet] [--help] 434s 434s Required Arguments: 434s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 434s Directories containing fast5 files. 434s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 434s Genomic locations at which to plot signal. Format 434s locations as "chrm:position[:strand] 434s [chrm2:position2[:strand2] ...]" (strand not 434s applicable for all applications) 434s 434s Comparison Arguments: 434s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 434s Set of directories containing fast5 files for control 434s reads, containing only canonical nucleotides. 434s --plot-standard-model 434s Add default standard model distribution to the plot. 434s --plot-alternate-model {CpG,dam,6mA,5mC,dcm} 434s Add alternative model distribution to the plot. 434s 434s Overplotting Arguments: 434s --overplot-threshold OVERPLOT_THRESHOLD 434s Coverage level to trigger alternative plot type 434s instead of raw signal. Default: 50 434s --overplot-type {Downsample,Boxplot,Quantile,Density} 434s Plot type for regions with higher coverage. Default: 434s Downsample 434s 434s Plotting Region Argument: 434s --num-bases NUM_BASES 434s Number of bases to plot/output. Default: 21 434s 434s Output Argument: 434s --pdf-filename PDF_FILENAME 434s PDF filename to store plot(s). Default: 434s tombo_results.genome_locations.pdf 434s 434s FAST5 Data Arguments: 434s --corrected-group CORRECTED_GROUP 434s FAST5 group created by resquiggle command. Default: 434s RawGenomeCorrected_000 434s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 434s FAST5 subgroup(s) (under /Analyses/[--basecall- 434s group]/) containing basecalls and created within 434s [--corrected-group] containing re-squiggle results. 434s Default: ['BaseCalled_template'] 434s 434s Miscellaneous Arguments: 434s --quiet, -q Don't print status information. 434s --help, -h Print this help message and exit 434s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 434s [FAST5_BASEDIRS ...] --motif MOTIF 434s --genome-fasta GENOME_FASTA 434s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 434s [--plot-standard-model] 434s [--plot-alternate-model {6mA,CpG,dcm,dam,5mC}] 434s [--overplot-threshold OVERPLOT_THRESHOLD] 434s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 434s [--num-regions NUM_REGIONS] 434s [--num-bases NUM_BASES] [--deepest-coverage] 434s [--pdf-filename PDF_FILENAME] 434s [--corrected-group CORRECTED_GROUP] 434s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 434s [--quiet] [--help] 434s 434s Required Arguments: 434s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 434s Directories containing fast5 files. 434s --motif MOTIF Motif of interest at which to plot signal and 434s statsitics. Supports IUPAC single letter codes (use T 434s for RNA). 434s --genome-fasta GENOME_FASTA 434s FASTA file used to re-squiggle. For faster sequence 434s access. 434s 434s Comparison Arguments: 434s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 434s Set of directories containing fast5 files for control 434s reads, containing only canonical nucleotides. 434s --plot-standard-model 434s Add default standard model distribution to the plot. 434s --plot-alternate-model {6mA,CpG,dcm,dam,5mC} 434s Add alternative model distribution to the plot. 434s 434s Overplotting Arguments: 434s --overplot-threshold OVERPLOT_THRESHOLD 434s Coverage level to trigger alternative plot type 434s instead of raw signal. Default: 50 434s --overplot-type {Downsample,Boxplot,Quantile,Density} 434s Plot type for regions with higher coverage. Default: 434s Downsample 434s 434s Plotting Region Arguments: 434s --num-regions NUM_REGIONS 434s Number of regions to plot. Default: 10 434s --num-bases NUM_BASES 434s Number of bases to plot/output. Default: 21 434s --deepest-coverage Plot the deepest coverage regions. 434s 434s Output Argument: 434s --pdf-filename PDF_FILENAME 434s PDF filename to store plot(s). Default: 434s tombo_results.motif_centered.pdf 434s 434s FAST5 Data Arguments: 434s --corrected-group CORRECTED_GROUP 434s FAST5 group created by resquiggle command. Default: 434s RawGenomeCorrected_000 434s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 434s FAST5 subgroup(s) (under /Analyses/[--basecall- 434s group]/) containing basecalls and created within 434s [--corrected-group] containing re-squiggle results. 434s Default: ['BaseCalled_template'] 434s 434s Miscellaneous Arguments: 434s --quiet, -q Don't print status information. 434s --help, -h Print this help message and exit 435s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 435s [FAST5_BASEDIRS ...] --control-fast5-basedirs 435s CONTROL_FAST5_BASEDIRS 435s [CONTROL_FAST5_BASEDIRS ...] 435s [--overplot-threshold OVERPLOT_THRESHOLD] 435s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 435s [--num-regions NUM_REGIONS] 435s [--num-bases NUM_BASES] 435s [--pdf-filename PDF_FILENAME] 435s [--sequences-filename SEQUENCES_FILENAME] 435s [--corrected-group CORRECTED_GROUP] 435s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 435s [--quiet] [--help] 435s 435s Required Arguments: 435s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 435s Directories containing fast5 files. 435s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 435s Set of directories containing fast5 files for control 435s reads, containing only canonical nucleotides. 435s 435s Overplotting Arguments: 435s --overplot-threshold OVERPLOT_THRESHOLD 435s Coverage level to trigger alternative plot type 435s instead of raw signal. Default: 50 435s --overplot-type {Downsample,Boxplot,Quantile,Density} 435s Plot type for regions with higher coverage. Default: 435s Downsample 435s 435s Plotting Region Arguments: 435s --num-regions NUM_REGIONS 435s Number of regions to plot. Default: 10 435s --num-bases NUM_BASES 435s Number of bases to plot/output. Default: 21 435s 435s Output Arguments: 435s --pdf-filename PDF_FILENAME 435s PDF filename to store plot(s). Default: 435s tombo_results.max_difference.pdf 435s --sequences-filename SEQUENCES_FILENAME 435s File for sequences from selected regions. Sequences 435s will be stored in FASTA format. Default: None. 435s 435s FAST5 Data Arguments: 435s --corrected-group CORRECTED_GROUP 435s FAST5 group created by resquiggle command. Default: 435s RawGenomeCorrected_000 435s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 435s FAST5 subgroup(s) (under /Analyses/[--basecall- 435s group]/) containing basecalls and created within 435s [--corrected-group] containing re-squiggle results. 435s Default: ['BaseCalled_template'] 435s 435s Miscellaneous Arguments: 435s --quiet, -q Don't print status information. 435s --help, -h Print this help message and exit 435s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 435s [FAST5_BASEDIRS ...] --statistics-filename 435s STATISTICS_FILENAME 435s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 435s [--plot-standard-model] 435s [--plot-alternate-model {CpG,5mC,6mA,dcm,dam}] 435s [--overplot-threshold OVERPLOT_THRESHOLD] 435s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 435s [--num-regions NUM_REGIONS] 435s [--num-bases NUM_BASES] 435s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 435s [--pdf-filename PDF_FILENAME] 435s [--sequences-filename SEQUENCES_FILENAME] 435s [--corrected-group CORRECTED_GROUP] 435s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 435s [--quiet] [--help] 435s 435s Required Arguments: 435s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 435s Directories containing fast5 files. 435s --statistics-filename STATISTICS_FILENAME 435s File to save/load genomic base anchored statistics. 435s 435s Comparison Arguments: 435s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 435s Set of directories containing fast5 files for control 435s reads, containing only canonical nucleotides. 435s --plot-standard-model 435s Add default standard model distribution to the plot. 435s --plot-alternate-model {CpG,5mC,6mA,dcm,dam} 435s Add alternative model distribution to the plot. 435s 435s Overplotting Arguments: 435s --overplot-threshold OVERPLOT_THRESHOLD 435s Coverage level to trigger alternative plot type 435s instead of raw signal. Default: 50 435s --overplot-type {Downsample,Boxplot,Quantile,Density} 435s Plot type for regions with higher coverage. Default: 435s Downsample 435s 435s Plotting Region Arguments: 435s --num-regions NUM_REGIONS 435s Number of regions to plot. Default: 10 435s --num-bases NUM_BASES 435s Number of bases to plot/output. Default: 21 435s 435s Statistical Argument: 435s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 435s Dampen fraction modified estimates for low coverage 435s sites. Two parameters are unmodified and modified 435s pseudo read counts. This is equivalent to a beta prior 435s on the fraction estimate. Set to "0 0" to disable 435s dampened fraction estimation. Default: [2, 0] 435s 435s Output Arguments: 435s --pdf-filename PDF_FILENAME 435s PDF filename to store plot(s). Default: 435s tombo_results.significant_difference.pdf 435s --sequences-filename SEQUENCES_FILENAME 435s File for sequences from selected regions. Sequences 435s will be stored in FASTA format. Default: None. 435s 435s FAST5 Data Arguments: 435s --corrected-group CORRECTED_GROUP 435s FAST5 group created by resquiggle command. Default: 435s RawGenomeCorrected_000 435s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 435s FAST5 subgroup(s) (under /Analyses/[--basecall- 435s group]/) containing basecalls and created within 435s [--corrected-group] containing re-squiggle results. 435s Default: ['BaseCalled_template'] 435s 435s Miscellaneous Arguments: 435s --quiet, -q Don't print status information. 435s --help, -h Print this help message and exit 435s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 435s [FAST5_BASEDIRS ...] --motif MOTIF 435s --statistics-filename STATISTICS_FILENAME 435s --genome-fasta GENOME_FASTA 435s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 435s [--plot-standard-model] 435s [--plot-alternate-model {5mC,dam,CpG,dcm,6mA}] 435s [--overplot-threshold OVERPLOT_THRESHOLD] 435s [--num-regions NUM_REGIONS] 435s [--num-context NUM_CONTEXT] 435s [--num-statistics NUM_STATISTICS] 435s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 435s [--pdf-filename PDF_FILENAME] 435s [--corrected-group CORRECTED_GROUP] 435s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 435s [--quiet] [--help] 435s 435s Required Arguments: 435s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 435s Directories containing fast5 files. 435s --motif MOTIF Motif of interest at which to plot signal and 435s statsitics. Supports IUPAC single letter codes (use T 435s for RNA). 435s --statistics-filename STATISTICS_FILENAME 435s File to save/load genomic base anchored statistics. 435s --genome-fasta GENOME_FASTA 435s FASTA file used to re-squiggle. For faster sequence 435s access. 435s 435s Comparison Arguments: 435s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 435s Set of directories containing fast5 files for control 435s reads, containing only canonical nucleotides. 435s --plot-standard-model 435s Add default standard model distribution to the plot. 435s --plot-alternate-model {5mC,dam,CpG,dcm,6mA} 435s Add alternative model distribution to the plot. 435s 435s Overplotting Argument: 435s --overplot-threshold OVERPLOT_THRESHOLD 435s Coverage level to trigger alternative plot type 435s instead of raw signal. Default: 50 435s 435s Plotting Region Arguments: 435s --num-regions NUM_REGIONS 435s Number of regions to plot. Default: 3 435s --num-context NUM_CONTEXT 435s Number of context bases around motif. Default: 5 435s --num-statistics NUM_STATISTICS 435s Number of motif centered regions to include in 435s statistic distributions. Default: 200 435s 435s Statistical Argument: 435s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 435s Dampen fraction modified estimates for low coverage 435s sites. Two parameters are unmodified and modified 435s pseudo read counts. This is equivalent to a beta prior 435s on the fraction estimate. Set to "0 0" to disable 435s dampened fraction estimation. Default: [2, 0] 435s 435s Output Argument: 435s --pdf-filename PDF_FILENAME 435s PDF filename to store plot(s). Default: 435s tombo_results.motif_statistics.pdf 435s 435s FAST5 Data Arguments: 435s --corrected-group CORRECTED_GROUP 435s FAST5 group created by resquiggle command. Default: 435s RawGenomeCorrected_000 435s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 435s FAST5 subgroup(s) (under /Analyses/[--basecall- 435s group]/) containing basecalls and created within 435s [--corrected-group] containing re-squiggle results. 435s Default: ['BaseCalled_template'] 435s 435s Miscellaneous Arguments: 435s --quiet, -q Don't print status information. 435s --help, -h Print this help message and exit 436s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 436s [GENOME_LOCATIONS ...] 436s --per-read-statistics-filename 436s PER_READ_STATISTICS_FILENAME 436s [--genome-fasta GENOME_FASTA] 436s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 436s [--num-reads NUM_READS] [--num-bases NUM_BASES] 436s [--box-center] [--pdf-filename PDF_FILENAME] 436s [--corrected-group CORRECTED_GROUP] 436s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 436s [--quiet] [--help] 436s 436s Required Arguments: 436s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 436s Genomic locations at which to plot signal. Format 436s locations as "chrm:position[:strand] 436s [chrm2:position2[:strand2] ...]" (strand not 436s applicable for all applications) 436s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 436s Binary file containing per-read statistics from 436s statistical testing. 436s 436s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 436s --genome-fasta GENOME_FASTA 436s FASTA file used to re-squiggle. For faster sequence 436s access. 436s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 436s Directories containing fast5 files. 436s 436s Plotting Region Arguments: 436s --num-reads NUM_READS 436s Number of reads to plot. Default: 100 436s --num-bases NUM_BASES 436s Number of bases to plot/output. Default: 51 436s --box-center Plot a box around the central base. 436s 436s Output Argument: 436s --pdf-filename PDF_FILENAME 436s PDF filename to store plot(s). Default: 436s tombo_results.per_read_stats.pdf 436s 436s FAST5 Data Arguments: 436s --corrected-group CORRECTED_GROUP 436s FAST5 group created by resquiggle command. Default: 436s RawGenomeCorrected_000 436s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 436s FAST5 subgroup(s) (under /Analyses/[--basecall- 436s group]/) containing basecalls and created within 436s [--corrected-group] containing re-squiggle results. 436s Default: ['BaseCalled_template'] 436s 436s Miscellaneous Arguments: 436s --quiet, -q Don't print status information. 436s --help, -h Print this help message and exit 436s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 436s [STATISTICS_FILENAMES ...] 436s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 436s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 436s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 436s [--genome-fasta GENOME_FASTA] 436s [--pdf-filename PDF_FILENAME] 436s [--statistics-per-block STATISTICS_PER_BLOCK] 436s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 436s [--quiet] [--help] 436s 436s Required Argument: 436s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 436s Files to load genomic base anchored statistics. 436s 436s Ground Truth Arguments (provide bed files or motifs): 436s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 436s Modification description and bed format files 436s containing single base locations of ground truth 436s modified sites. Bed files should contain 6 fields 436s including strand. Format descriptions as 436s "mod_name:locs.bed". Example: "CpG 436s bisulfite":bisulfite_locs.bed 436s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 436s Bed format files containing single base locations of 436s ground truth unmodified sites. Bed files should 436s contain 6 fields including strand. 436s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 436s Ground truth, motif centered, modified base 436s descriptions for computing ROC and PR curves. Each 436s statistics file is associated with a set of motif 436s descriptions. Format descriptions as: 436s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 436s mod_pos indicates the alternate-base within the motif 436s (1-based index). Example: CCWGG:2:"dcm 436s 5mC"::GATC:2:"dam 6mA" would assess the performance of 436s a single Tombo statistics file for identification of 436s E. coli dam and dcm methylation. 436s --genome-fasta GENOME_FASTA 436s FASTA file used to re-squiggle. For faster sequence 436s access. 436s 436s Output Arguments: 436s --pdf-filename PDF_FILENAME 436s PDF filename to store plot(s). Default: 436s tombo_results.roc.pdf 436s 436s Down-sampling Arguments: 436s --statistics-per-block STATISTICS_PER_BLOCK 436s Number of randomly selected per-read, per-base 436s statistics to extract from each genomic block for 436s plotting. Default: Include all stats 436s --total-statistics-limit TOTAL_STATISTICS_LIMIT 436s Total per-read statistics to be extracted for 436s plotting. Avoids memory overflow for large runs. 436s Default: 5000000 436s 436s Miscellaneous Arguments: 436s --quiet, -q Don't print status information. 436s --help, -h Print this help message and exit 436s usage: tombo plot per_read_roc --per-read-statistics-filenames 436s PER_READ_STATISTICS_FILENAMES 436s [PER_READ_STATISTICS_FILENAMES ...] 436s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 436s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 436s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 436s [--genome-fasta GENOME_FASTA] 436s [--statistics-per-block STATISTICS_PER_BLOCK] 436s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 436s [--pdf-filename PDF_FILENAME] [--quiet] 436s [--help] 436s 436s Required Argument: 436s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 436s Binary files containing per-read statistics from 436s statistical testing. 436s 436s Ground Truth Arguments (provide bed files or motifs): 436s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 436s Modification description and bed format files 436s containing single base locations of ground truth 436s modified sites. Bed files should contain 6 fields 436s including strand. Format descriptions as 436s "mod_name:locs.bed". Example: "CpG 436s bisulfite":bisulfite_locs.bed 436s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 436s Bed format files containing single base locations of 436s ground truth unmodified sites. Bed files should 436s contain 6 fields including strand. 436s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 436s Ground truth, motif centered, modified base 436s descriptions for computing ROC and PR curves. Each 436s statistics file is associated with a set of motif 436s descriptions. Format descriptions as: 436s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 436s mod_pos indicates the alternate-base within the motif 436s (1-based index). Example: CCWGG:2:"dcm 436s 5mC"::GATC:2:"dam 6mA" would assess the performance of 436s a single Tombo statistics file for identification of 436s E. coli dam and dcm methylation. 436s --genome-fasta GENOME_FASTA 436s FASTA file used to re-squiggle. For faster sequence 436s access. 436s 436s Down-sampling Arguments: 436s --statistics-per-block STATISTICS_PER_BLOCK 436s Number of randomly selected per-read, per-base 436s statistics to extract from each genomic block for 436s plotting. Default: 100000 436s --total-statistics-limit TOTAL_STATISTICS_LIMIT 436s Total per-read statistics to be extracted for 436s plotting. Avoids memory overflow for large runs. 436s Default: 5000000 436s 436s Output Arguments: 436s --pdf-filename PDF_FILENAME 436s PDF filename to store plot(s). Default: 436s tombo_results.per_reads_roc.pdf 436s 436s Miscellaneous Arguments: 436s --quiet, -q Don't print status information. 436s --help, -h Print this help message and exit 437s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 437s [--upstream-bases {0,1,2,3,4}] 437s [--downstream-bases {0,1,2,3,4}] [--read-mean] 437s [--num-kmer-threshold NUM_KMER_THRESHOLD] 437s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 437s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 437s [--corrected-group CORRECTED_GROUP] 437s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 437s [--quiet] [--help] 437s 437s Required Argument: 437s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 437s Directories containing fast5 files. 437s 437s Data Processing Arguments: 437s --upstream-bases {0,1,2,3,4} 437s Upstream bases in k-mer. Default: 1 437s --downstream-bases {0,1,2,3,4} 437s Downstream bases in k-mer. Default: 2 437s --read-mean Plot k-mer means across whole reads as opposed to 437s individual k-mer event levels. 437s --num-kmer-threshold NUM_KMER_THRESHOLD 437s Observations of each k-mer required to include a read 437s in read level averages. Default: 1 437s 437s Plotting Region Arguments: 437s --num-reads NUM_READS 437s Number of reads to plot. Default: 100 437s 437s Output Arguments: 437s --pdf-filename PDF_FILENAME 437s PDF filename to store plot(s). Default: 437s tombo_results.kmer_distribution.pdf 437s --r-data-filename R_DATA_FILENAME 437s Filename to save R data structure. Default: Don't save 437s --dont-plot Don't plot result. Useful to produce only R data file. 437s 437s FAST5 Data Arguments: 437s --corrected-group CORRECTED_GROUP 437s FAST5 group created by resquiggle command. Default: 437s RawGenomeCorrected_000 437s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 437s FAST5 subgroup(s) (under /Analyses/[--basecall- 437s group]/) containing basecalls and created within 437s [--corrected-group] containing re-squiggle results. 437s Default: ['BaseCalled_template'] 437s 437s Miscellaneous Arguments: 437s --quiet, -q Don't print status information. 437s --help, -h Print this help message and exit 437s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 437s [FAST5_BASEDIRS ...] 437s --control-fast5-basedirs 437s CONTROL_FAST5_BASEDIRS 437s [CONTROL_FAST5_BASEDIRS ...] 437s --statistics-filename 437s STATISTICS_FILENAME 437s [--genome-fasta GENOME_FASTA] 437s [--processes PROCESSES] 437s [--num-regions NUM_REGIONS] 437s [--num-bases NUM_BASES] 437s [--slide-span SLIDE_SPAN] 437s [--pdf-filename PDF_FILENAME] 437s [--r-data-filename R_DATA_FILENAME] 437s [--corrected-group CORRECTED_GROUP] 437s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 437s [--quiet] [--help] 437s 437s Required Arguments: 437s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 437s Directories containing fast5 files. 437s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 437s Set of directories containing fast5 files for control 437s reads, containing only canonical nucleotides. 437s --statistics-filename STATISTICS_FILENAME 437s File to save/load genomic base anchored statistics. 437s 437s FASTA Sequence Argument: 437s --genome-fasta GENOME_FASTA 437s FASTA file used to re-squiggle. For faster sequence 437s access. 437s 437s Multiprocessing Argument: 437s --processes PROCESSES 437s Number of processes. Default: 1 437s 437s Plotting Region Arguments: 437s --num-regions NUM_REGIONS 437s Number of regions to plot. Default: 10 437s --num-bases NUM_BASES 437s Number of bases to plot/output. Default: 21 437s --slide-span SLIDE_SPAN 437s Number of bases offset over which to search when 437s computing distances for signal cluster plotting. 437s Default: 0 (exact position) 437s 437s Output Arguments: 437s --pdf-filename PDF_FILENAME 437s PDF filename to store plot(s). Default: 437s tombo_results.signal_clusters.pdf 437s --r-data-filename R_DATA_FILENAME 437s Filename to save R data structure. Default: Don't save 437s 437s FAST5 Data Arguments: 437s --corrected-group CORRECTED_GROUP 437s FAST5 group created by resquiggle command. Default: 437s RawGenomeCorrected_000 437s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 437s FAST5 subgroup(s) (under /Analyses/[--basecall- 437s group]/) containing basecalls and created within 437s [--corrected-group] containing re-squiggle results. 437s Default: ['BaseCalled_template'] 437s 437s Miscellaneous Arguments: 437s --quiet, -q Don't print status information. 437s --help, -h Print this help message and exit 437s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 437s 437s Required Arguments: 437s fast5s_basedir Directory containing fast5 files. All files ending in 437s "fast5" found recursively within this base directory will be 437s processed. 437s 437s Miscellaneous Arguments: 437s --quiet, -q Don't print status information. 437s --help, -h Print this help message and exit 438s usage: tombo build_model event_resquiggle 438s [--minimap2-executable MINIMAP2_EXECUTABLE] 438s [--minimap2-index MINIMAP2_INDEX] 438s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 438s [--graphmap-executable GRAPHMAP_EXECUTABLE] 438s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 438s [--normalization-type {median,pA,pA_raw,none}] 438s [--pore-model-filename PORE_MODEL_FILENAME] 438s [--outlier-threshold OUTLIER_THRESHOLD] 438s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 438s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 438s [--timeout TIMEOUT] 438s [--cpts-limit CPTS_LIMIT] 438s [--skip-index] [--overwrite] 438s [--failed-reads-filename FAILED_READS_FILENAME] 438s [--include-event-stdev] 438s [--corrected-group CORRECTED_GROUP] 438s [--basecall-group BASECALL_GROUP] 438s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 438s [--processes PROCESSES] 438s [--align-processes ALIGN_PROCESSES] 438s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 438s [--resquiggle-processes RESQUIGGLE_PROCESSES] 438s [--quiet] [--help] 438s fast5s_basedir reference_fasta 438s 438s Required Arguments: 438s fast5s_basedir Directory containing fast5 files. All files ending in 438s "fast5" found recursively within this base directory 438s will be processed. 438s reference_fasta Reference genome/transcriptome FASTA file for mapping. 438s 438s Mapper Arguments (One mapper is required): 438s --minimap2-executable MINIMAP2_EXECUTABLE 438s Path to minimap2 executable. 438s --minimap2-index MINIMAP2_INDEX 438s Path to minimap2 index (with map-ont preset) file 438s corresponding to the [genome_fasta] provided. 438s --bwa-mem-executable BWA_MEM_EXECUTABLE 438s Path to bwa-mem executable. 438s --graphmap-executable GRAPHMAP_EXECUTABLE 438s Path to graphmap executable. 438s --alignment-batch-size ALIGNMENT_BATCH_SIZE 438s Number of reads included in each alignment call. Note: 438s A new system mapping call is made for each batch 438s (including loading of the genome), so it is advised to 438s use larger values for larger genomes. Default: 1000 438s 438s Signal Processing Arguments: 438s --normalization-type {median,pA,pA_raw,none} 438s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 438s as in the ONT events (using offset, range and 438s digitization), "pA": k-mer-based correction for pA 438s drift as in nanopolish (requires [--pore-model- 438s filename]), "median": median and MAD from raw signal. 438s Default: median 438s --pore-model-filename PORE_MODEL_FILENAME 438s File containing kmer model parameters (level_mean and 438s level_stdv) used in order to compute kmer-based 438s corrected pA values. E.g. https://github.com/jts/nanop 438s olish/blob/master/etc/r9- 438s models/template_median68pA.5mers.model 438s --outlier-threshold OUTLIER_THRESHOLD 438s Windosrize the signal at this number of scale values. 438s Negative value disables outlier clipping. Default: 438s 5.000000 438s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 438s Specify the 2 parameters for segmentation 1) running 438s neighboring windows width 2) minimum raw observations 438s per genomic base. Sample type defaults: RNA : 12 6 || 438s DNA : 5 3 438s 438s Read Filtering Arguments: 438s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 438s Filter reads based on observations per base percentile 438s thresholds. Format thresholds as "percentile:thresh 438s [pctl2:thresh2 ...]". For example to filter reads with 438s 99th pctl > 200 obs/base or max > 5k obs/base use 438s "99:200 100:5000". 438s --timeout TIMEOUT Timeout in seconds for processing a single read. 438s Default: No timeout. 438s --cpts-limit CPTS_LIMIT 438s Maximum number of changepoints to find within a single 438s indel group. Default: No limit. 438s 438s Input/Output Arguments: 438s --skip-index Skip creation of tombo index. This drastically slows 438s downstream tombo commands. Default stores tombo index 438s named ".[--fast5-basedir].[--corrected- 438s group].tombo.index" to be loaded automatically for 438s downstream commands. 438s --overwrite Overwrite previous corrected group in FAST5 files. 438s Note: only effects --corrected-group or --new- 438s corrected-group. 438s --failed-reads-filename FAILED_READS_FILENAME 438s Output failed read filenames with assoicated error. 438s Default: Do not store failed reads. 438s --include-event-stdev 438s Include corrected event standard deviation in output 438s FAST5 data. 438s 438s FAST5 Data Arguments: 438s --corrected-group CORRECTED_GROUP 438s FAST5 group created by resquiggle command. Default: 438s RawGenomeCorrected_000 438s --basecall-group BASECALL_GROUP 438s FAST5 group obtain original basecalls (under Analyses 438s group). Default: Basecall_1D_000 438s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 438s FAST5 subgroup(s) (under /Analyses/[--basecall- 438s group]/) containing basecalls and created within 438s [--corrected-group] containing re-squiggle results. 438s Default: ['BaseCalled_template'] 438s 438s Multiprocessing Arguments: 438s --processes PROCESSES 438s Number of processes. Default: 2 438s --align-processes ALIGN_PROCESSES 438s Number of processes to use for parsing and aligning 438s original basecalls. Each process will independently 438s load the genome into memory, so use caution with 438s larger genomes (e.g. human). Default: 1 438s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 438s Number of threads to use for aligner system call. 438s Default: [--processes] / (2 * [--align-processes)] 438s --resquiggle-processes RESQUIGGLE_PROCESSES 438s Number of processes to use for resquiggle algorithm. 438s Default: [--processes] / 2 438s 438s Miscellaneous Arguments: 438s --quiet, -q Don't print status information. 438s --help, -h Print this help message and exit 438s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 438s [FAST5_BASEDIRS ...] 438s --tombo-model-filename 438s TOMBO_MODEL_FILENAME 438s [--estimate-mean] 438s [--kmer-specific-sd] 438s [--upstream-bases {0,1,2,3,4}] 438s [--downstream-bases {0,1,2,3,4}] 438s [--minimum-test-reads MINIMUM_TEST_READS] 438s [--coverage-threshold COVERAGE_THRESHOLD] 438s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 438s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 438s [--processes PROCESSES] 438s [--corrected-group CORRECTED_GROUP] 438s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 438s [--quiet] [--help] 438s 438s Required Arguments: 438s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 438s Directories containing fast5 files. 438s --tombo-model-filename TOMBO_MODEL_FILENAME 438s Filename to save Tombo model. 438s 438s Modeling Arguments: 438s --estimate-mean Use the mean instead of median for model level 438s estimation. Note: This can cause poor fits due to 438s outliers 438s --kmer-specific-sd Estimate standard deviation for each k-mers 438s individually. 438s --upstream-bases {0,1,2,3,4} 438s Upstream bases in k-mer. Default: 1 438s --downstream-bases {0,1,2,3,4} 438s Downstream bases in k-mer. Default: 2 438s 438s Filtering Arguments: 438s --minimum-test-reads MINIMUM_TEST_READS 438s Number of reads required at a position to perform 438s significance testing or contribute to model 438s estimation. Default: 10 438s --coverage-threshold COVERAGE_THRESHOLD 438s Maximum mean coverage per region when estimating k-mer 438s model (limits compute time for deep samples). Default: 438s 100 438s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 438s Number of each k-mer observations required in order to 438s produce a reference (genomic locations for standard 438s reference and per-read for alternative reference). 438s Default: 5 438s 438s Multiprocessing Arguments: 438s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 438s Size of regions over which to multiprocesses statistic 438s computation. For very deep samples a smaller value is 438s recommmended in order to control memory consumption. 438s Default: 10000 438s --processes PROCESSES 438s Number of processes. Default: 1 438s 438s FAST5 Data Arguments: 438s --corrected-group CORRECTED_GROUP 438s FAST5 group created by resquiggle command. Default: 438s RawGenomeCorrected_000 438s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 438s FAST5 subgroup(s) (under /Analyses/[--basecall- 438s group]/) containing basecalls and created within 438s [--corrected-group] containing re-squiggle results. 438s Default: ['BaseCalled_template'] 438s 438s Miscellaneous Arguments: 438s --quiet, -q Don't print status information. 438s --help, -h Print this help message and exit 438s usage: tombo build_model estimate_alt_reference --alternate-model-filename 438s ALTERNATE_MODEL_FILENAME 438s --alternate-model-name 438s ALTERNATE_MODEL_NAME 438s --alternate-model-base 438s {A,C,G,T} 438s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 438s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 438s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 438s [--control-density-filename CONTROL_DENSITY_FILENAME] 438s [--dna] [--rna] 438s [--tombo-model-filename TOMBO_MODEL_FILENAME] 438s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 438s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 438s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 438s [--save-density-basename SAVE_DENSITY_BASENAME] 438s [--processes PROCESSES] 438s [--corrected-group CORRECTED_GROUP] 438s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 438s [--quiet] [--help] 438s 438s Required Arguments: 438s --alternate-model-filename ALTERNATE_MODEL_FILENAME 438s Tombo model for alternative likelihood ratio 438s significance testing. 438s --alternate-model-name ALTERNATE_MODEL_NAME 438s A short name to associate with this alternate model 438s (e.g. 5mC, 6mA, etc.). This text will be included in 438s output filenames when this model is used for testing. 438s --alternate-model-base {A,C,G,T} 438s Non-standard base is an alternative to this base. 438s 438s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 438s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 438s Directories containing fast5 files. 438s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 438s Set of directories containing fast5 files for control 438s reads, containing only canonical nucleotides. 438s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 438s File containing k-mer level kernel density estimates 438s for the alternative sample saved using --save-density- 438s basename. 438s --control-density-filename CONTROL_DENSITY_FILENAME 438s File containing k-mer level kernel density estimates 438s for the control sample saved using --save-density- 438s basename. 438s 438s Standard Model Arguments: 438s --dna Explicitly select canonical DNA model. Default: 438s Automatically determine from FAST5s 438s --rna Explicitly select canonical RNA model. Default: 438s Automatically determine from FAST5s 438s --tombo-model-filename TOMBO_MODEL_FILENAME 438s Tombo model filename. If no file is provided, the 438s default DNA or RNA Tombo model will be used. 438s 438s Model Fitting Arguments: 438s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 438s When esitmating the alternative base incorporation 438s rate, this percent of k-mers are assumed to have 438s significantly shifted signal so the alternative 438s distribution minimally overlaps the standard base 438s distribution. Default: 5.000000 438s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 438s Bandwidth applied when performing Gaussian kernal 438s density esitmation on standard and alternative base 438s signal distributions. Default: 0.050000 438s 438s Filtering Argument: 438s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 438s Number of each k-mer observations required in order to 438s produce a reference (genomic locations for standard 438s reference and per-read for alternative reference). 438s Default: 1000 438s 438s Output Argument: 438s --save-density-basename SAVE_DENSITY_BASENAME 438s Basename to save alternative model estimation density 438s estimation information. See scripts/debug_est_alt.R 438s for info use example. Default: Don't save. 438s 438s Multiprocessing Arguments: 438s --processes PROCESSES 438s Number of processes. Default: 1 438s 438s FAST5 Data Arguments: 438s --corrected-group CORRECTED_GROUP 438s FAST5 group created by resquiggle command. Default: 438s RawGenomeCorrected_000 438s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 438s FAST5 subgroup(s) (under /Analyses/[--basecall- 438s group]/) containing basecalls and created within 438s [--corrected-group] containing re-squiggle results. 438s Default: ['BaseCalled_template'] 438s 438s Miscellaneous Arguments: 438s --quiet, -q Don't print status information. 438s --help, -h Print this help message and exit 439s This test only tests the help system 439s There is an extensive test in 439s 439s tombo/tests/shell_tests.sh 439s 439s but this requires to download larger data 439s sets which is not done for the moment. 439s autopkgtest [06:15:39]: test run-unit-test: -----------------------] 440s autopkgtest [06:15:40]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 440s run-unit-test PASS 440s autopkgtest [06:15:40]: @@@@@@@@@@@@@@@@@@@@ summary 440s run-unit-test PASS 452s Creating nova instance adt-noble-arm64-tombo-20240324-060819-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 86f9118c-691d-4fd3-ac71-bf5396ee0d8a)...