0s autopkgtest [10:08:10]: starting date and time: 2024-03-23 10:08:10+0000 0s autopkgtest [10:08:10]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [10:08:10]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6r4fg1b2/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-2@bos02-ppc64el-14.secgroup --name adt-noble-ppc64el-tombo-20240323-100810-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 232s autopkgtest [10:12:02]: testbed dpkg architecture: ppc64el 233s autopkgtest [10:12:03]: testbed apt version: 2.7.12 233s autopkgtest [10:12:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 234s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 234s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 234s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 234s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 234s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4029 kB] 236s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 236s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 236s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 236s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 236s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4250 kB] 237s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 237s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 237s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 240s Fetched 9687 kB in 4s (2417 kB/s) 240s Reading package lists... 244s Reading package lists... 244s Building dependency tree... 244s Reading state information... 244s Calculating upgrade... 244s The following packages will be upgraded: 244s libbsd0 libc-bin libc6 locales 244s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 244s Need to get 8313 kB of archives. 244s After this operation, 2048 B of additional disk space will be used. 244s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6 ppc64el 2.39-0ubuntu6 [3274 kB] 245s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-bin ppc64el 2.39-0ubuntu6 [751 kB] 245s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libbsd0 ppc64el 0.12.1-1 [56.9 kB] 245s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el locales all 2.39-0ubuntu6 [4232 kB] 246s Preconfiguring packages ... 246s Fetched 8313 kB in 1s (6545 kB/s) 246s (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 ... 70156 files and directories currently installed.) 246s Preparing to unpack .../libc6_2.39-0ubuntu6_ppc64el.deb ... 246s Unpacking libc6:ppc64el (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 247s Setting up libc6:ppc64el (2.39-0ubuntu6) ... 247s (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 ... 70156 files and directories currently installed.) 247s Preparing to unpack .../libc-bin_2.39-0ubuntu6_ppc64el.deb ... 247s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 247s Setting up libc-bin (2.39-0ubuntu6) ... 247s (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 ... 70156 files and directories currently installed.) 247s Preparing to unpack .../libbsd0_0.12.1-1_ppc64el.deb ... 247s Unpacking libbsd0:ppc64el (0.12.1-1) over (0.11.8-1) ... 247s Preparing to unpack .../locales_2.39-0ubuntu6_all.deb ... 247s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 247s Setting up locales (2.39-0ubuntu6) ... 248s Generating locales (this might take a while)... 249s en_US.UTF-8... done 249s Generation complete. 249s Setting up libbsd0:ppc64el (0.12.1-1) ... 249s Processing triggers for man-db (2.12.0-3) ... 250s Processing triggers for libc-bin (2.39-0ubuntu6) ... 250s Reading package lists... 251s Building dependency tree... 251s Reading state information... 251s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 252s sh: Attempting to set up Debian/Ubuntu apt sources automatically 252s sh: Distribution appears to be Ubuntu 253s Reading package lists... 253s Building dependency tree... 253s Reading state information... 253s eatmydata is already the newest version (131-1). 253s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 253s Reading package lists... 253s Building dependency tree... 253s Reading state information... 253s dbus is already the newest version (1.14.10-4ubuntu1). 253s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 253s Reading package lists... 253s Building dependency tree... 253s Reading state information... 254s rng-tools-debian is already the newest version (2.4). 254s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 254s Reading package lists... 254s Building dependency tree... 254s Reading state information... 254s The following packages will be REMOVED: 254s cloud-init* python3-configobj* python3-debconf* 254s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 254s After this operation, 3256 kB disk space will be freed. 254s (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 ... 70156 files and directories currently installed.) 254s Removing cloud-init (24.1.2-0ubuntu1) ... 255s Removing python3-configobj (5.0.8-3) ... 255s Removing python3-debconf (1.5.86) ... 255s Processing triggers for man-db (2.12.0-3) ... 255s (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 ... 69767 files and directories currently installed.) 255s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 256s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 256s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 256s invoke-rc.d: policy-rc.d denied execution of try-restart. 256s Reading package lists... 256s Building dependency tree... 256s Reading state information... 257s linux-generic is already the newest version (6.8.0-11.11+1). 257s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 259s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 259s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 259s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 262s Reading package lists... 262s Reading package lists... 262s Building dependency tree... 262s Reading state information... 262s Calculating upgrade... 262s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 262s Reading package lists... 262s Building dependency tree... 262s Reading state information... 263s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 263s autopkgtest [10:12:33]: rebooting testbed after setup commands that affected boot 434s autopkgtest [10:15:24]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 436s autopkgtest [10:15:26]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 443s Get:1 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (dsc) [2292 B] 443s Get:2 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (tar) [22.3 MB] 443s Get:3 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (diff) [7024 B] 443s gpgv: Signature made Sun Dec 17 19:23:46 2023 UTC 443s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 443s gpgv: issuer "tille@debian.org" 443s gpgv: Can't check signature: No public key 443s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6.dsc: no acceptable signature found 443s autopkgtest [10:15:33]: testing package tombo version 1.5.1-6 444s autopkgtest [10:15:34]: build not needed 449s autopkgtest [10:15:39]: test run-unit-test: preparing testbed 457s Reading package lists... 457s Building dependency tree... 457s Reading state information... 457s Starting pkgProblemResolver with broken count: 0 457s Starting 2 pkgProblemResolver with broken count: 0 457s Done 458s The following additional packages will be installed: 458s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 458s libhdf5-103-1 libhdf5-hl-100 libjs-jquery libjs-mathjax libjs-sphinxdoc 458s libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 python3-decorator 458s python3-h5py python3-h5py-serial python3-mappy python3-numpy python3-scipy 458s python3-tqdm sphinx-rtd-theme-common tombo tombo-doc 458s Suggested packages: 458s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 458s gfortran python3-dev python3-pytest python-scipy-doc 458s Recommended packages: 458s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 458s python3-rpy2 458s The following NEW packages will be installed: 458s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 458s libblas3 libgfortran5 libhdf5-103-1 libhdf5-hl-100 libjs-jquery 458s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 458s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 458s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 458s tombo-doc 458s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 458s Need to get 69.1 MB/69.1 MB of archives. 458s After this operation, 273 MB of additional disk space will be used. 458s Get:1 /tmp/autopkgtest.LnY2kY/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 458s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-lato all 2.015-1 [2781 kB] 458s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 459s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 459s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libaec0 ppc64el 1.1.2-1 [29.9 kB] 459s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 459s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 459s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsz2 ppc64el 1.1.2-1 [5472 B] 459s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-103-1 ppc64el 1.10.10+repack-3ubuntu1 [1375 kB] 459s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-hl-100 ppc64el 1.10.10+repack-3ubuntu1 [69.9 kB] 459s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 459s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 459s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-sphinxdoc all 7.2.6-4 [149 kB] 459s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 459s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1 [32.8 kB] 459s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 459s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 459s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 459s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-h5py-serial ppc64el 3.10.0-1ubuntu1 [1635 kB] 460s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-h5py all 3.10.0-1ubuntu1 [7970 B] 460s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-mappy ppc64el 2.24+dfsg-3build2 [221 kB] 460s Get:22 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-tqdm all 4.64.1-2 [95.2 kB] 460s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] 460s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-scipy ppc64el 1.11.4-6 [21.4 MB] 460s Get:25 http://ftpmaster.internal/ubuntu noble/universe ppc64el tombo ppc64el 1.5.1-6 [514 kB] 460s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 461s Get:27 http://ftpmaster.internal/ubuntu noble/universe ppc64el tombo-doc all 1.5.1-6 [21.7 MB] 461s Fetched 69.1 MB in 4s (19.7 MB/s) 461s Selecting previously unselected package fonts-lato. 462s (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 ... 69712 files and directories currently installed.) 462s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 462s Unpacking fonts-lato (2.015-1) ... 462s Selecting previously unselected package fonts-font-awesome. 462s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 462s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 462s Selecting previously unselected package fonts-mathjax. 462s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 462s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 462s Selecting previously unselected package libaec0:ppc64el. 462s Preparing to unpack .../03-libaec0_1.1.2-1_ppc64el.deb ... 462s Unpacking libaec0:ppc64el (1.1.2-1) ... 462s Selecting previously unselected package libblas3:ppc64el. 462s Preparing to unpack .../04-libblas3_3.12.0-3_ppc64el.deb ... 462s Unpacking libblas3:ppc64el (3.12.0-3) ... 462s Selecting previously unselected package libgfortran5:ppc64el. 462s Preparing to unpack .../05-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 462s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 462s Selecting previously unselected package libsz2:ppc64el. 462s Preparing to unpack .../06-libsz2_1.1.2-1_ppc64el.deb ... 462s Unpacking libsz2:ppc64el (1.1.2-1) ... 462s Selecting previously unselected package libhdf5-103-1:ppc64el. 462s Preparing to unpack .../07-libhdf5-103-1_1.10.10+repack-3ubuntu1_ppc64el.deb ... 462s Unpacking libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 462s Selecting previously unselected package libhdf5-hl-100:ppc64el. 462s Preparing to unpack .../08-libhdf5-hl-100_1.10.10+repack-3ubuntu1_ppc64el.deb ... 462s Unpacking libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 462s Selecting previously unselected package libjs-jquery. 462s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 462s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 462s Selecting previously unselected package libjs-underscore. 462s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 462s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 462s Selecting previously unselected package libjs-sphinxdoc. 462s Preparing to unpack .../11-libjs-sphinxdoc_7.2.6-4_all.deb ... 462s Unpacking libjs-sphinxdoc (7.2.6-4) ... 462s Selecting previously unselected package liblapack3:ppc64el. 462s Preparing to unpack .../12-liblapack3_3.12.0-3_ppc64el.deb ... 462s Unpacking liblapack3:ppc64el (3.12.0-3) ... 463s Selecting previously unselected package liblbfgsb0:ppc64el. 463s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1_ppc64el.deb ... 463s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 463s Selecting previously unselected package liblzf1:ppc64el. 463s Preparing to unpack .../14-liblzf1_3.6-4_ppc64el.deb ... 463s Unpacking liblzf1:ppc64el (3.6-4) ... 463s Selecting previously unselected package python3-decorator. 463s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 463s Unpacking python3-decorator (5.1.1-5) ... 463s Selecting previously unselected package python3-numpy. 463s Preparing to unpack .../16-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 463s Unpacking python3-numpy (1:1.24.2-2) ... 463s Selecting previously unselected package python3-h5py-serial. 463s Preparing to unpack .../17-python3-h5py-serial_3.10.0-1ubuntu1_ppc64el.deb ... 463s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 463s Selecting previously unselected package python3-h5py. 463s Preparing to unpack .../18-python3-h5py_3.10.0-1ubuntu1_all.deb ... 463s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 463s Selecting previously unselected package python3-mappy. 463s Preparing to unpack .../19-python3-mappy_2.24+dfsg-3build2_ppc64el.deb ... 463s Unpacking python3-mappy (2.24+dfsg-3build2) ... 463s Selecting previously unselected package python3-tqdm. 463s Preparing to unpack .../20-python3-tqdm_4.64.1-2_all.deb ... 463s Unpacking python3-tqdm (4.64.1-2) ... 463s Selecting previously unselected package sphinx-rtd-theme-common. 463s Preparing to unpack .../21-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... 463s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 463s Selecting previously unselected package python3-scipy. 463s Preparing to unpack .../22-python3-scipy_1.11.4-6_ppc64el.deb ... 463s Unpacking python3-scipy (1.11.4-6) ... 464s Selecting previously unselected package tombo. 464s Preparing to unpack .../23-tombo_1.5.1-6_ppc64el.deb ... 464s Unpacking tombo (1.5.1-6) ... 464s Selecting previously unselected package libjs-mathjax. 464s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 464s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 465s Selecting previously unselected package tombo-doc. 465s Preparing to unpack .../25-tombo-doc_1.5.1-6_all.deb ... 465s Unpacking tombo-doc (1.5.1-6) ... 466s Selecting previously unselected package autopkgtest-satdep. 466s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 466s Unpacking autopkgtest-satdep (0) ... 466s Setting up fonts-lato (2.015-1) ... 466s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 466s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 466s Setting up python3-tqdm (4.64.1-2) ... 466s Setting up python3-mappy (2.24+dfsg-3build2) ... 466s Setting up libaec0:ppc64el (1.1.2-1) ... 466s Setting up python3-decorator (5.1.1-5) ... 466s Setting up libblas3:ppc64el (3.12.0-3) ... 466s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 466s Setting up liblzf1:ppc64el (3.6-4) ... 466s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 466s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 466s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 466s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 466s Setting up libsz2:ppc64el (1.1.2-1) ... 466s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 466s Setting up liblapack3:ppc64el (3.12.0-3) ... 466s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 466s Setting up python3-numpy (1:1.24.2-2) ... 468s Setting up libjs-sphinxdoc (7.2.6-4) ... 468s Setting up tombo-doc (1.5.1-6) ... 468s Setting up libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 468s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 468s Setting up libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 468s Setting up python3-scipy (1.11.4-6) ... 472s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 472s Setting up python3-h5py (3.10.0-1ubuntu1) ... 472s Setting up tombo (1.5.1-6) ... 472s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 472s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 472s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 472s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 472s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 472s re.match('\+', fastq_rec[2]) is None): 472s Setting up autopkgtest-satdep (0) ... 472s Processing triggers for man-db (2.12.0-3) ... 473s Processing triggers for libc-bin (2.39-0ubuntu6) ... 476s (Reading database ... 77112 files and directories currently installed.) 476s Removing autopkgtest-satdep (0) ... 477s autopkgtest [10:16:07]: test run-unit-test: [----------------------- 477s ********* Testing help commands ********** 477s usage: tombo [-h] [-v] 477s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 477s ... 477s 477s ********** Tombo ********* 477s 477s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 477s 477s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 477s 477s Tombo command groups (additional help available within each command group): 477s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 477s preprocess Pre-process nanopore reads for Tombo processing. 477s filter Apply filter to Tombo index file for specified criterion. 477s detect_modifications Perform statistical testing to detect non-standard nucleotides. 477s text_output Output Tombo results in text files. 477s build_model Create canonical and alternative base Tombo models. 477s plot Save plots to visualize raw nanopore signal or testing results. 477s 477s options: 477s -h, --help show this help message and exit 477s -v, --version show Tombo version and exit. 477s usage: tombo resquiggle [--dna] [--rna] 477s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 477s [--q-score Q_SCORE] 477s [--signal-matching-score SIGNAL_MATCHING_SCORE] 477s [--processes PROCESSES] 477s [--corrected-group CORRECTED_GROUP] 477s [--basecall-group BASECALL_GROUP] 477s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 477s [--overwrite] 477s [--failed-reads-filename FAILED_READS_FILENAME] 477s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 477s [--print-advanced-arguments] [--quiet] [--help] 477s fast5s_basedir reference 477s 477s Required Arguments: 477s fast5s_basedir Directory containing fast5 files. All files ending in 477s "fast5" found recursively within this base directory 477s will be processed. 477s reference Reference genome/transcriptome FASTA file or minimap2 477s index (with "map-ont" preset) for mapping. 477s 477s Model Parameters: 477s --dna Explicitly select canonical DNA model. Default: 477s Automatically determine from FAST5s 477s --rna Explicitly select canonical RNA model. Default: 477s Automatically determine from FAST5s 477s 477s Read Filtering Argument: 477s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 477s Filter reads based on observations per base percentile 477s thresholds. Format thresholds as "percentile:thresh 477s [pctl2:thresh2 ...]". For example to filter reads with 477s 99th pctl > 200 obs/base or max > 5k obs/base use 477s "99:200 100:5000". 477s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 477s Default: 0.000000 477s --signal-matching-score SIGNAL_MATCHING_SCORE 477s Observed to expected signal matching score (higher 477s score indicates poor matching). Sample type defaults: 477s RNA : 2 || DNA : 1.1 477s 477s Multiprocessing Arguments: 477s --processes PROCESSES 477s Number of processes. Default: 1 477s 477s FAST5 Data Arguments: 477s --corrected-group CORRECTED_GROUP 477s FAST5 group created by resquiggle command. Default: 477s RawGenomeCorrected_000 477s --basecall-group BASECALL_GROUP 477s FAST5 group obtain original basecalls (under Analyses 477s group). Default: Basecall_1D_000 477s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 477s FAST5 subgroup(s) (under /Analyses/[--basecall- 477s group]/) containing basecalls and created within 477s [--corrected-group] containing re-squiggle results. 477s Default: ['BaseCalled_template'] 477s --overwrite Overwrite previous corrected group in FAST5 files. 477s Note: only effects --corrected-group or --new- 477s corrected-group. 477s 477s Input/Output Arguments: 477s --failed-reads-filename FAILED_READS_FILENAME 477s Output failed read filenames with assoicated error. 477s Default: Do not store failed reads. 477s --num-most-common-errors NUM_MOST_COMMON_ERRORS 477s Dynamically show this many most common errors so far 477s through run. Default: 0; Just show progress 477s 477s Advanced Arguments: 477s --print-advanced-arguments 477s Print advanced re-squiggle arguments and exit. 477s 477s Miscellaneous Arguments: 477s --quiet, -q Don't print status information. 477s --help, -h Print this help message and exit 477s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 477s --fastq-filenames 477s FASTQ_FILENAMES 477s [FASTQ_FILENAMES ...] 477s [--basecall-group BASECALL_GROUP] 477s [--basecall-subgroup BASECALL_SUBGROUP] 477s [--overwrite] 477s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 477s [--processes PROCESSES] 477s [--quiet] [--help] 477s 477s Required Arguments: 477s --fast5-basedir FAST5_BASEDIR 477s Directory containing fast5 files. 477s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 477s FASTQ filenames containing basecalls to be added to 477s raw FAST5 files. 477s 477s FAST5 Data Arguments: 477s --basecall-group BASECALL_GROUP 477s FAST5 group obtain original basecalls (under Analyses 477s group). Default: Basecall_1D_000 477s --basecall-subgroup BASECALL_SUBGROUP 477s FAST5 subgroup (under /Analyses/[--basecall-group]/) 477s under which to store basecalls from FASTQs. Default: 477s BaseCalled_template 477s --overwrite Overwrite previous corrected group in FAST5 files. 477s Note: only effects --corrected-group or --new- 477s corrected-group. 477s 477s Sequencing Summary Argument: 477s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 477s Sequencing summary filenames produced by albacore. 477s These can make annotation of raw FAST5 files with 477s FASTQ sequence much faster. 477s 477s Multiprocessing Argument: 477s --processes PROCESSES 477s Number of processes. Default: 1 477s 477s Miscellaneous Arguments: 477s --quiet, -q Don't print status information. 477s --help, -h Print this help message and exit 477s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 477s [FAST5_BASEDIRS ...] 477s [--corrected-group CORRECTED_GROUP] 477s [--quiet] [--help] 477s 477s Required Argument: 477s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 477s Directories containing fast5 files. 477s 477s FAST5 Data Argument: 477s --corrected-group CORRECTED_GROUP 477s FAST5 group created by resquiggle command. Default: 477s RawGenomeCorrected_000 477s 477s Miscellaneous Arguments: 477s --quiet, -q Don't print status information. 477s --help, -h Print this help message and exit 477s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 477s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 477s [--corrected-group CORRECTED_GROUP] [--quiet] 477s [--help] 477s 477s Required Argument: 477s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 477s Directories containing fast5 files. 477s 477s Read Filtering Argument: 477s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 477s Filter reads based on observations per base percentile 477s thresholds. Format thresholds as "percentile:thresh 477s [pctl2:thresh2 ...]". For example to filter reads with 477s 99th pctl > 200 obs/base or max > 5k obs/base use 477s "99:200 100:5000". 477s 477s FAST5 Data Argument: 477s --corrected-group CORRECTED_GROUP 477s FAST5 group created by resquiggle command. Default: 477s RawGenomeCorrected_000 477s 477s Miscellaneous Arguments: 477s --quiet, -q Don't print status information. 477s --help, -h Print this help message and exit 477s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 477s [FAST5_BASEDIRS ...] 477s [--percent-to-filter PERCENT_TO_FILTER] 477s [--corrected-group CORRECTED_GROUP] 477s [--quiet] [--help] 477s 477s Required Arguments: 477s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 477s Directories containing fast5 files. 477s 477s Read Filtering Argument: 477s --percent-to-filter PERCENT_TO_FILTER 477s Percentage of all reads to filter. Reads are randomly 477s selected weighted according to the approximate 477s coverage at the mapped genomic location. This can be 477s useful in modeling and testing. Default: 10.000000 477s 477s FAST5 Data Arguments: 477s --corrected-group CORRECTED_GROUP 477s FAST5 group created by resquiggle command. Default: 477s RawGenomeCorrected_000 477s 477s Miscellaneous Arguments: 477s --quiet, -q Don't print status information. 477s --help, -h Print this help message and exit 477s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 477s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 477s [--corrected-group CORRECTED_GROUP] 477s [--basecall-group BASECALL_GROUP] [--quiet] 477s [--help] 477s 477s Required Arguments: 477s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 477s Directories containing fast5 files. 477s 477s Read Filtering Argument: 477s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 477s Default: 7.000000 477s 477s FAST5 Data Arguments: 477s --corrected-group CORRECTED_GROUP 477s FAST5 group created by resquiggle command. Default: 477s RawGenomeCorrected_000 477s --basecall-group BASECALL_GROUP 477s FAST5 group obtain original basecalls (under Analyses 477s group). Default: Basecall_1D_000 477s 477s Miscellaneous Arguments: 477s --quiet, -q Don't print status information. 477s --help, -h Print this help message and exit 478s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 478s [FAST5_BASEDIRS ...] 478s --signal-matching-score 478s SIGNAL_MATCHING_SCORE 478s [--corrected-group CORRECTED_GROUP] 478s [--quiet] [--help] 478s 478s Required Arguments: 478s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 478s Directories containing fast5 files. 478s --signal-matching-score SIGNAL_MATCHING_SCORE 478s Observed to expected signal matching score (higher 478s score indicates poor matching). Sample type defaults: 478s RNA : 2 || DNA : 1.1 478s 478s FAST5 Data Arguments: 478s --corrected-group CORRECTED_GROUP 478s FAST5 group created by resquiggle command. Default: 478s RawGenomeCorrected_000 478s 478s Miscellaneous Arguments: 478s --quiet, -q Don't print status information. 478s --help, -h Print this help message and exit 478s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 478s [FAST5_BASEDIRS ...] 478s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 478s [--include-partial-overlap] 478s [--corrected-group CORRECTED_GROUP] 478s [--quiet] [--help] 478s 478s Required Arguments: 478s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 478s Directories containing fast5 files. 478s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 478s Filter out reads not falling completely within include 478s regions. Omit start and end coordinates to include an 478s entire chromosome/sequence record. Format regions as 478s "chrm[:start-end] [chrm2[:start2-end2] ...]". 478s 478s Filter Argument: 478s --include-partial-overlap 478s Include reads that partially overlap the specified 478s region. Default: Only include reads completely 478s contained in a specified region 478s 478s FAST5 Data Argument: 478s --corrected-group CORRECTED_GROUP 478s FAST5 group created by resquiggle command. Default: 478s RawGenomeCorrected_000 478s 478s Miscellaneous Arguments: 478s --quiet, -q Don't print status information. 478s --help, -h Print this help message and exit 478s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 478s [FAST5_BASEDIRS ...] 478s --statistics-file-basename 478s STATISTICS_FILE_BASENAME [--dna] 478s [--rna] 478s [--fishers-method-context FISHERS_METHOD_CONTEXT] 478s [--minimum-test-reads MINIMUM_TEST_READS] 478s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 478s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 478s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 478s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 478s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 478s [--processes PROCESSES] 478s [--corrected-group CORRECTED_GROUP] 478s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 478s [--quiet] [--help] 478s 478s Required Argument: 478s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 478s Directories containing fast5 files. 478s --statistics-file-basename STATISTICS_FILE_BASENAME 478s File base name to save base by base statistics from 478s testing. Filenames will be [--statistics-file- 478s basename].[--alternate-bases]?.tombo.stats 478s 478s Comparison Model Arguments: 478s --dna Explicitly select canonical DNA model. Default: 478s Automatically determine from FAST5s 478s --rna Explicitly select canonical RNA model. Default: 478s Automatically determine from FAST5s 478s 478s Significance Test Arguments: 478s --fishers-method-context FISHERS_METHOD_CONTEXT 478s Number of context bases up and downstream over which 478s to compute Fisher's method combined p-values. Note: 478s Not applicable for alternative model likelihood ratio 478s tests. Default: 1. 478s --minimum-test-reads MINIMUM_TEST_READS 478s Number of reads required at a position to perform 478s significance testing or contribute to model 478s estimation. Default: 1 478s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 478s P-value threshold when computing fraction of 478s significant reads at each genomic position. If two 478s values are provided, statistics between these values 478s are not considered. Default thresholds: DNA:0.15-0.5 , 478s RNA:0.05-0.4 478s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 478s Dampen fraction modified estimates for low coverage 478s sites. Two parameters are unmodified and modified 478s pseudo read counts. This is equivalent to a beta prior 478s on the fraction estimate. Set to "0 0" to disable 478s dampened fraction estimation. Default: [2, 0] 478s 478s Output Argument: 478s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 478s Base for binary files containing per-read statistics 478s from statistical testing. Filenames will be [--per- 478s read-statistics-basename].[--alternate- 478s bases]?.tombo.per_read_stats 478s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 478s Number of the most significant sites to store for 478s faster access. If a longer list of most significant 478s sites is required the list must be re-computed from 478s all batches. Very large values can increase RAM usage. 478s Default: 100000 478s 478s Multiprocessing Arguments: 478s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 478s Size of regions over which to multiprocesses statistic 478s computation. For very deep samples a smaller value is 478s recommmended in order to control memory consumption. 478s Default: 10000 478s --processes PROCESSES 478s Number of processes. Default: 1 478s 478s FAST5 Data Arguments: 478s --corrected-group CORRECTED_GROUP 478s FAST5 group created by resquiggle command. Default: 478s RawGenomeCorrected_000 478s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 478s FAST5 subgroup(s) (under /Analyses/[--basecall- 478s group]/) containing basecalls and created within 478s [--corrected-group] containing re-squiggle results. 478s Default: ['BaseCalled_template'] 478s 478s Miscellaneous Arguments: 478s --quiet, -q Don't print status information. 478s --help, -h Print this help message and exit 478s usage: tombo detect_modifications alternative_model 478s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 478s [--statistics-file-basename STATISTICS_FILE_BASENAME] 478s [--alternate-bases {5mC,dcm,6mA,dam,CpG} [{5mC,dcm,6mA,dam,CpG} ...]] 478s [--print-available-models] 478s [--dna] [--rna] 478s [--minimum-test-reads MINIMUM_TEST_READS] 478s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 478s [--standard-log-likelihood-ratio] 478s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 478s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 478s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 478s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 478s [--processes PROCESSES] 478s [--corrected-group CORRECTED_GROUP] 478s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 478s [--quiet] [--help] 478s 478s Required Argument: 478s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 478s Directories containing fast5 files. 478s --statistics-file-basename STATISTICS_FILE_BASENAME 478s File base name to save base by base statistics from 478s testing. Filenames will be [--statistics-file- 478s basename].[--alternate-bases]?.tombo.stats 478s --alternate-bases {5mC,dcm,6mA,dam,CpG} [{5mC,dcm,6mA,dam,CpG} ...] 478s Default non-standard base model for testing (not 478s required if user created --alternate-model-filenames 478s is provided). 478s 478s Comparison Arguments: 478s --print-available-models 478s Print available alternative models and exit. 478s --dna Explicitly select canonical DNA model. Default: 478s Automatically determine from FAST5s 478s --rna Explicitly select canonical RNA model. Default: 478s Automatically determine from FAST5s 478s 478s Significance Test Arguments: 478s --minimum-test-reads MINIMUM_TEST_READS 478s Number of reads required at a position to perform 478s significance testing or contribute to model 478s estimation. Default: 1 478s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 478s Log likelihood ratio threshold when computing fraction 478s of significant reads at each genomic position. If two 478s values are provided, statistics between these values 478s are not considered. Default thresholds: DNA:-1.5-2.5 , 478s RNA:-2.5-2.5 478s --standard-log-likelihood-ratio 478s Use a standard log likelihood ratio (LLR) statistic. 478s Default is to use an outlier-robust LLR-like 478s statistic. Detail in full online documentation. 478s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 478s Dampen fraction modified estimates for low coverage 478s sites. Two parameters are unmodified and modified 478s pseudo read counts. This is equivalent to a beta prior 478s on the fraction estimate. Set to "0 0" to disable 478s dampened fraction estimation. Default: [2, 0] 478s 478s Output Argument: 478s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 478s Base for binary files containing per-read statistics 478s from statistical testing. Filenames will be [--per- 478s read-statistics-basename].[--alternate- 478s bases]?.tombo.per_read_stats 478s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 478s Number of the most significant sites to store for 478s faster access. If a longer list of most significant 478s sites is required the list must be re-computed from 478s all batches. Very large values can increase RAM usage. 478s Default: 100000 478s 478s Multiprocessing Arguments: 478s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 478s Size of regions over which to multiprocesses statistic 478s computation. For very deep samples a smaller value is 478s recommmended in order to control memory consumption. 478s Default: 10000 478s --processes PROCESSES 478s Number of processes. Default: 1 478s 478s FAST5 Data Arguments: 478s --corrected-group CORRECTED_GROUP 478s FAST5 group created by resquiggle command. Default: 478s RawGenomeCorrected_000 478s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 478s FAST5 subgroup(s) (under /Analyses/[--basecall- 478s group]/) containing basecalls and created within 478s [--corrected-group] containing re-squiggle results. 478s Default: ['BaseCalled_template'] 478s 478s Miscellaneous Arguments: 478s --quiet, -q Don't print status information. 478s --help, -h Print this help message and exit 478s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 478s FAST5_BASEDIRS 478s [FAST5_BASEDIRS ...] 478s --statistics-file-basename 478s STATISTICS_FILE_BASENAME 478s --control-fast5-basedirs 478s CONTROL_FAST5_BASEDIRS 478s [CONTROL_FAST5_BASEDIRS ...] 478s [--sample-only-estimates] 478s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 478s [--dna] [--rna] 478s [--fishers-method-context FISHERS_METHOD_CONTEXT] 478s [--minimum-test-reads MINIMUM_TEST_READS] 478s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 478s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 478s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 478s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 478s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 478s [--processes PROCESSES] 478s [--corrected-group CORRECTED_GROUP] 478s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 478s [--quiet] [--help] 478s 478s Required Argument: 478s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 478s Directories containing fast5 files. 478s --statistics-file-basename STATISTICS_FILE_BASENAME 478s File base name to save base by base statistics from 478s testing. Filenames will be [--statistics-file- 478s basename].[--alternate-bases]?.tombo.stats 478s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 478s Set of directories containing fast5 files for control 478s reads, containing only canonical nucleotides. 478s 478s Model Prior Arguments: 478s --sample-only-estimates 478s Only use canonical sample to estimate expected signal 478s level and spread. Default: Use canonical model to 478s improve estimtates (esp. for low coverage regions) 478s using baysian posterior estimates. 478s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 478s Prior weights (one each for mean and spread) applied 478s to canonical base model for estimating posterior model 478s parameters for sample comparison. Default: [5, 40] 478s --dna Explicitly select canonical DNA model. Default: 478s Automatically determine from FAST5s 478s --rna Explicitly select canonical RNA model. Default: 478s Automatically determine from FAST5s 478s 478s Significance Test Arguments: 478s --fishers-method-context FISHERS_METHOD_CONTEXT 478s Number of context bases up and downstream over which 478s to compute Fisher's method combined p-values. Note: 478s Not applicable for alternative model likelihood ratio 478s tests. Default: 1. 478s --minimum-test-reads MINIMUM_TEST_READS 478s Number of reads required at a position to perform 478s significance testing or contribute to model 478s estimation. Default: 1 478s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 478s P-value threshold when computing fraction of 478s significant reads at each genomic position. If two 478s values are provided, statistics between these values 478s are not considered. Default thresholds: DNA:0.15-0.5 , 478s RNA:0.05-0.4 478s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 478s Dampen fraction modified estimates for low coverage 478s sites. Two parameters are unmodified and modified 478s pseudo read counts. This is equivalent to a beta prior 478s on the fraction estimate. Set to "0 0" to disable 478s dampened fraction estimation. Default: [2, 0] 478s 478s Output Argument: 478s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 478s Base for binary files containing per-read statistics 478s from statistical testing. Filenames will be [--per- 478s read-statistics-basename].[--alternate- 478s bases]?.tombo.per_read_stats 478s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 478s Number of the most significant sites to store for 478s faster access. If a longer list of most significant 478s sites is required the list must be re-computed from 478s all batches. Very large values can increase RAM usage. 478s Default: 100000 478s 478s Multiprocessing Arguments: 478s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 478s Size of regions over which to multiprocesses statistic 478s computation. For very deep samples a smaller value is 478s recommmended in order to control memory consumption. 478s Default: 10000 478s --processes PROCESSES 478s Number of processes. Default: 1 478s 478s FAST5 Data Arguments: 478s --corrected-group CORRECTED_GROUP 478s FAST5 group created by resquiggle command. Default: 478s RawGenomeCorrected_000 478s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 478s FAST5 subgroup(s) (under /Analyses/[--basecall- 478s group]/) containing basecalls and created within 478s [--corrected-group] containing re-squiggle results. 478s Default: ['BaseCalled_template'] 478s 478s Miscellaneous Arguments: 478s --quiet, -q Don't print status information. 478s --help, -h Print this help message and exit 478s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 478s FAST5_BASEDIRS 478s [FAST5_BASEDIRS ...] 478s --statistics-file-basename 478s STATISTICS_FILE_BASENAME 478s --alternate-fast5-basedirs 478s ALTERNATE_FAST5_BASEDIRS 478s [ALTERNATE_FAST5_BASEDIRS ...] 478s [--fishers-method-context FISHERS_METHOD_CONTEXT] 478s [--minimum-test-reads MINIMUM_TEST_READS] 478s [--statistic-type {ks,u,t}] 478s [--store-p-value] 478s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 478s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 478s [--processes PROCESSES] 478s [--corrected-group CORRECTED_GROUP] 478s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 478s [--quiet] [--help] 478s 478s Required Argument: 478s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 478s Directories containing fast5 files. 478s --statistics-file-basename STATISTICS_FILE_BASENAME 478s File base name to save base by base statistics from 478s testing. Filenames will be [--statistics-file- 478s basename].[--alternate-bases]?.tombo.stats 478s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 478s Set of directories containing fast5 files for 478s alternate set of reads. 478s 478s Significance Test Arguments: 478s --fishers-method-context FISHERS_METHOD_CONTEXT 478s Number of context bases up and downstream over which 478s to compute Fisher's method combined p-values. Note: 478s Not applicable for alternative model likelihood ratio 478s tests. Default: 1. 478s --minimum-test-reads MINIMUM_TEST_READS 478s Number of reads required at a position to perform 478s significance testing or contribute to model 478s estimation. Default: 50 478s --statistic-type {ks,u,t} 478s Type of statistical test to apply. Default: "ks" 478s --store-p-value Store p-value instead of effect-size statistic. 478s Statistics are D-statistic (KS-test), deviation from 478s even common language effect size (u-test), and Cohen's 478s D (t-test). 478s 478s Output Argument: 478s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 478s Number of the most significant sites to store for 478s faster access. If a longer list of most significant 478s sites is required the list must be re-computed from 478s all batches. Very large values can increase RAM usage. 478s Default: 100000 478s 478s Multiprocessing Arguments: 478s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 478s Size of regions over which to multiprocesses statistic 478s computation. For very deep samples a smaller value is 478s recommmended in order to control memory consumption. 478s Default: 10000 478s --processes PROCESSES 478s Number of processes. Default: 1 478s 478s FAST5 Data Arguments: 478s --corrected-group CORRECTED_GROUP 478s FAST5 group created by resquiggle command. Default: 478s RawGenomeCorrected_000 478s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 478s FAST5 subgroup(s) (under /Analyses/[--basecall- 478s group]/) containing basecalls and created within 478s [--corrected-group] containing re-squiggle results. 478s Default: ['BaseCalled_template'] 478s 478s Miscellaneous Arguments: 478s --quiet, -q Don't print status information. 478s --help, -h Print this help message and exit 478s usage: tombo detect_modifications aggregate_per_read_stats 478s --per-read-statistics-filename 478s PER_READ_STATISTICS_FILENAME 478s --statistics-filename 478s STATISTICS_FILENAME 478s --single-read-threshold 478s SINGLE_READ_THRESHOLD 478s [SINGLE_READ_THRESHOLD ...] 478s [--minimum-test-reads MINIMUM_TEST_READS] 478s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 478s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 478s [--processes PROCESSES] 478s [--corrected-group CORRECTED_GROUP] 478s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 478s [--quiet] [--help] 478s 478s Required Argument: 478s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 478s Binary file containing per-read statistics from 478s statistical testing. 478s --statistics-filename STATISTICS_FILENAME 478s File to save/load genomic base anchored statistics. 478s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 478s P-value or log likelihood ratio threshold when 478s computing fraction of significant reads at each 478s genomic position. If two values are provided, 478s statistics between these values are not considered. 478s 478s Significance Test Arguments: 478s --minimum-test-reads MINIMUM_TEST_READS 478s Number of reads required at a position to perform 478s significance testing or contribute to model 478s estimation. Default: 1 478s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 478s Dampen fraction modified estimates for low coverage 478s sites. Two parameters are unmodified and modified 478s pseudo read counts. This is equivalent to a beta prior 478s on the fraction estimate. Set to "0 0" to disable 478s dampened fraction estimation. Default: [2, 0] 478s 478s Output Argument: 478s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 478s Number of the most significant sites to store for 478s faster access. If a longer list of most significant 478s sites is required the list must be re-computed from 478s all batches. Very large values can increase RAM usage. 478s Default: 100000 478s 478s Multiprocessing Arguments: 478s --processes PROCESSES 478s Number of processes. Default: 1 478s 478s FAST5 Data Arguments: 478s --corrected-group CORRECTED_GROUP 478s FAST5 group created by resquiggle command. Default: 478s RawGenomeCorrected_000 478s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 478s FAST5 subgroup(s) (under /Analyses/[--basecall- 478s group]/) containing basecalls and created within 478s [--corrected-group] containing re-squiggle results. 478s Default: ['BaseCalled_template'] 478s 478s Miscellaneous Arguments: 478s --quiet, -q Don't print status information. 478s --help, -h Print this help message and exit 478s usage: tombo text_output browser_files 478s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 478s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 478s [--statistics-filename STATISTICS_FILENAME] 478s [--genome-fasta GENOME_FASTA] 478s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 478s [--browser-file-basename BROWSER_FILE_BASENAME] 478s [--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} ...]] 478s [--corrected-group CORRECTED_GROUP] 478s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 478s [--quiet] [--help] 478s 478s Data Arguments: 478s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 478s Directories containing fast5 files. 478s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 478s Set of directories containing fast5 files for control 478s reads, containing only canonical nucleotides. 478s --statistics-filename STATISTICS_FILENAME 478s File to save/load genomic base anchored statistics. 478s 478s Statistic Motif Filter Arguments: 478s --genome-fasta GENOME_FASTA 478s FASTA file used to re-squiggle. For faster sequence 478s access. 478s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 478s Ground truth, motif centered, modified base 478s descriptions for output filtering. Format descriptions 478s as: "motif:mod_pos:name". The mod_pos indicates the 478s modified base within the motif (1-based index). 478s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 478s output for identification of E. coli dam and dcm 478s methylation. 478s 478s Output Arguments: 478s --browser-file-basename BROWSER_FILE_BASENAME 478s Basename for output browser files. Two files (plus and 478s minus strand) will be produced for each --file-types 478s supplied. Filenames formatted as "[browser-file- 478s basename].[file- 478s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 478s Default: tombo_results 478s --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} ...] 478s Data types of genome browser files to produce. 478s Produced coverage files are in bedGraph format, while 478s all other file types will be in wiggle format 478s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 478s Default: "coverage" 478s 478s FAST5 Data Arguments: 478s --corrected-group CORRECTED_GROUP 478s FAST5 group created by resquiggle command. Default: 478s RawGenomeCorrected_000 478s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 478s FAST5 subgroup(s) (under /Analyses/[--basecall- 478s group]/) containing basecalls and created within 478s [--corrected-group] containing re-squiggle results. 478s Default: ['BaseCalled_template'] 478s 478s Miscellaneous Arguments: 478s --quiet, -q Don't print status information. 478s --help, -h Print this help message and exit 478s usage: tombo text_output signif_sequence_context --statistics-filename 478s STATISTICS_FILENAME 478s [--genome-fasta GENOME_FASTA] 478s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 478s [--num-regions NUM_REGIONS] 478s [--num-bases NUM_BASES] 478s [--sequences-filename SEQUENCES_FILENAME] 478s [--corrected-group CORRECTED_GROUP] 478s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 478s [--quiet] [--help] 478s 478s Required Argument: 478s --statistics-filename STATISTICS_FILENAME 478s File to save/load genomic base anchored statistics. 478s 478s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 478s --genome-fasta GENOME_FASTA 478s FASTA file used to re-squiggle. For faster sequence 478s access. 478s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 478s Directories containing fast5 files. 478s 478s Region Selection Arguments: 478s --num-regions NUM_REGIONS 478s Number of regions to plot. Default: 100 478s --num-bases NUM_BASES 478s Number of bases to plot/output. Default: 15 478s 478s Output Arguments: 478s --sequences-filename SEQUENCES_FILENAME 478s File for sequences from selected regions. Sequences 478s will be stored in FASTA format. Default: 478s tombo_results.significant_regions.fasta. 478s 478s FAST5 Data Arguments: 478s --corrected-group CORRECTED_GROUP 478s FAST5 group created by resquiggle command. Default: 478s RawGenomeCorrected_000 478s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 478s FAST5 subgroup(s) (under /Analyses/[--basecall- 478s group]/) containing basecalls and created within 478s [--corrected-group] containing re-squiggle results. 478s Default: ['BaseCalled_template'] 478s 478s Miscellaneous Arguments: 478s --quiet, -q Don't print status information. 478s --help, -h Print this help message and exit 478s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 478s [FAST5_BASEDIRS ...] 478s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 478s [--plot-standard-model] 478s [--plot-alternate-model {dam,5mC,CpG,6mA,dcm}] 478s [--overplot-threshold OVERPLOT_THRESHOLD] 478s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 478s [--num-regions NUM_REGIONS] 478s [--num-bases NUM_BASES] 478s [--pdf-filename PDF_FILENAME] 478s [--corrected-group CORRECTED_GROUP] 478s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 478s [--quiet] [--help] 478s 478s Required Argument: 478s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 478s Directories containing fast5 files. 478s 478s Comparison Arguments: 478s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 478s Set of directories containing fast5 files for control 478s reads, containing only canonical nucleotides. 478s --plot-standard-model 478s Add default standard model distribution to the plot. 478s --plot-alternate-model {dam,5mC,CpG,6mA,dcm} 478s Add alternative model distribution to the plot. 478s 478s Overplotting Arguments: 478s --overplot-threshold OVERPLOT_THRESHOLD 478s Coverage level to trigger alternative plot type 478s instead of raw signal. Default: 50 478s --overplot-type {Downsample,Boxplot,Quantile,Density} 478s Plot type for regions with higher coverage. Default: 478s Downsample 478s 478s Plotting Region Arguments: 478s --num-regions NUM_REGIONS 478s Number of regions to plot. Default: 10 478s --num-bases NUM_BASES 478s Number of bases to plot/output. Default: 21 478s 478s Output Argument: 478s --pdf-filename PDF_FILENAME 478s PDF filename to store plot(s). Default: 478s tombo_results.max_coverage.pdf 478s 478s FAST5 Data Arguments: 478s --corrected-group CORRECTED_GROUP 478s FAST5 group created by resquiggle command. Default: 478s RawGenomeCorrected_000 478s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 478s FAST5 subgroup(s) (under /Analyses/[--basecall- 478s group]/) containing basecalls and created within 478s [--corrected-group] containing re-squiggle results. 478s Default: ['BaseCalled_template'] 478s 478s Miscellaneous Arguments: 478s --quiet, -q Don't print status information. 478s --help, -h Print this help message and exit 479s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 479s [FAST5_BASEDIRS ...] --genome-locations 479s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 479s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 479s [--plot-standard-model] 479s [--plot-alternate-model {5mC,CpG,6mA,dam,dcm}] 479s [--overplot-threshold OVERPLOT_THRESHOLD] 479s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 479s [--num-bases NUM_BASES] 479s [--pdf-filename PDF_FILENAME] 479s [--corrected-group CORRECTED_GROUP] 479s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 479s [--quiet] [--help] 479s 479s Required Arguments: 479s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 479s Directories containing fast5 files. 479s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 479s Genomic locations at which to plot signal. Format 479s locations as "chrm:position[:strand] 479s [chrm2:position2[:strand2] ...]" (strand not 479s applicable for all applications) 479s 479s Comparison Arguments: 479s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 479s Set of directories containing fast5 files for control 479s reads, containing only canonical nucleotides. 479s --plot-standard-model 479s Add default standard model distribution to the plot. 479s --plot-alternate-model {5mC,CpG,6mA,dam,dcm} 479s Add alternative model distribution to the plot. 479s 479s Overplotting Arguments: 479s --overplot-threshold OVERPLOT_THRESHOLD 479s Coverage level to trigger alternative plot type 479s instead of raw signal. Default: 50 479s --overplot-type {Downsample,Boxplot,Quantile,Density} 479s Plot type for regions with higher coverage. Default: 479s Downsample 479s 479s Plotting Region Argument: 479s --num-bases NUM_BASES 479s Number of bases to plot/output. Default: 21 479s 479s Output Argument: 479s --pdf-filename PDF_FILENAME 479s PDF filename to store plot(s). Default: 479s tombo_results.genome_locations.pdf 479s 479s FAST5 Data Arguments: 479s --corrected-group CORRECTED_GROUP 479s FAST5 group created by resquiggle command. Default: 479s RawGenomeCorrected_000 479s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 479s FAST5 subgroup(s) (under /Analyses/[--basecall- 479s group]/) containing basecalls and created within 479s [--corrected-group] containing re-squiggle results. 479s Default: ['BaseCalled_template'] 479s 479s Miscellaneous Arguments: 479s --quiet, -q Don't print status information. 479s --help, -h Print this help message and exit 479s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 479s [FAST5_BASEDIRS ...] --motif MOTIF 479s --genome-fasta GENOME_FASTA 479s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 479s [--plot-standard-model] 479s [--plot-alternate-model {5mC,dam,dcm,CpG,6mA}] 479s [--overplot-threshold OVERPLOT_THRESHOLD] 479s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 479s [--num-regions NUM_REGIONS] 479s [--num-bases NUM_BASES] [--deepest-coverage] 479s [--pdf-filename PDF_FILENAME] 479s [--corrected-group CORRECTED_GROUP] 479s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 479s [--quiet] [--help] 479s 479s Required Arguments: 479s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 479s Directories containing fast5 files. 479s --motif MOTIF Motif of interest at which to plot signal and 479s statsitics. Supports IUPAC single letter codes (use T 479s for RNA). 479s --genome-fasta GENOME_FASTA 479s FASTA file used to re-squiggle. For faster sequence 479s access. 479s 479s Comparison Arguments: 479s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 479s Set of directories containing fast5 files for control 479s reads, containing only canonical nucleotides. 479s --plot-standard-model 479s Add default standard model distribution to the plot. 479s --plot-alternate-model {5mC,dam,dcm,CpG,6mA} 479s Add alternative model distribution to the plot. 479s 479s Overplotting Arguments: 479s --overplot-threshold OVERPLOT_THRESHOLD 479s Coverage level to trigger alternative plot type 479s instead of raw signal. Default: 50 479s --overplot-type {Downsample,Boxplot,Quantile,Density} 479s Plot type for regions with higher coverage. Default: 479s Downsample 479s 479s Plotting Region Arguments: 479s --num-regions NUM_REGIONS 479s Number of regions to plot. Default: 10 479s --num-bases NUM_BASES 479s Number of bases to plot/output. Default: 21 479s --deepest-coverage Plot the deepest coverage regions. 479s 479s Output Argument: 479s --pdf-filename PDF_FILENAME 479s PDF filename to store plot(s). Default: 479s tombo_results.motif_centered.pdf 479s 479s FAST5 Data Arguments: 479s --corrected-group CORRECTED_GROUP 479s FAST5 group created by resquiggle command. Default: 479s RawGenomeCorrected_000 479s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 479s FAST5 subgroup(s) (under /Analyses/[--basecall- 479s group]/) containing basecalls and created within 479s [--corrected-group] containing re-squiggle results. 479s Default: ['BaseCalled_template'] 479s 479s Miscellaneous Arguments: 479s --quiet, -q Don't print status information. 479s --help, -h Print this help message and exit 479s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 479s [FAST5_BASEDIRS ...] --control-fast5-basedirs 479s CONTROL_FAST5_BASEDIRS 479s [CONTROL_FAST5_BASEDIRS ...] 479s [--overplot-threshold OVERPLOT_THRESHOLD] 479s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 479s [--num-regions NUM_REGIONS] 479s [--num-bases NUM_BASES] 479s [--pdf-filename PDF_FILENAME] 479s [--sequences-filename SEQUENCES_FILENAME] 479s [--corrected-group CORRECTED_GROUP] 479s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 479s [--quiet] [--help] 479s 479s Required Arguments: 479s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 479s Directories containing fast5 files. 479s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 479s Set of directories containing fast5 files for control 479s reads, containing only canonical nucleotides. 479s 479s Overplotting Arguments: 479s --overplot-threshold OVERPLOT_THRESHOLD 479s Coverage level to trigger alternative plot type 479s instead of raw signal. Default: 50 479s --overplot-type {Downsample,Boxplot,Quantile,Density} 479s Plot type for regions with higher coverage. Default: 479s Downsample 479s 479s Plotting Region Arguments: 479s --num-regions NUM_REGIONS 479s Number of regions to plot. Default: 10 479s --num-bases NUM_BASES 479s Number of bases to plot/output. Default: 21 479s 479s Output Arguments: 479s --pdf-filename PDF_FILENAME 479s PDF filename to store plot(s). Default: 479s tombo_results.max_difference.pdf 479s --sequences-filename SEQUENCES_FILENAME 479s File for sequences from selected regions. Sequences 479s will be stored in FASTA format. Default: None. 479s 479s FAST5 Data Arguments: 479s --corrected-group CORRECTED_GROUP 479s FAST5 group created by resquiggle command. Default: 479s RawGenomeCorrected_000 479s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 479s FAST5 subgroup(s) (under /Analyses/[--basecall- 479s group]/) containing basecalls and created within 479s [--corrected-group] containing re-squiggle results. 479s Default: ['BaseCalled_template'] 479s 479s Miscellaneous Arguments: 479s --quiet, -q Don't print status information. 479s --help, -h Print this help message and exit 479s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 479s [FAST5_BASEDIRS ...] --statistics-filename 479s STATISTICS_FILENAME 479s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 479s [--plot-standard-model] 479s [--plot-alternate-model {CpG,6mA,5mC,dcm,dam}] 479s [--overplot-threshold OVERPLOT_THRESHOLD] 479s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 479s [--num-regions NUM_REGIONS] 479s [--num-bases NUM_BASES] 479s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 479s [--pdf-filename PDF_FILENAME] 479s [--sequences-filename SEQUENCES_FILENAME] 479s [--corrected-group CORRECTED_GROUP] 479s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 479s [--quiet] [--help] 479s 479s Required Arguments: 479s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 479s Directories containing fast5 files. 479s --statistics-filename STATISTICS_FILENAME 479s File to save/load genomic base anchored statistics. 479s 479s Comparison Arguments: 479s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 479s Set of directories containing fast5 files for control 479s reads, containing only canonical nucleotides. 479s --plot-standard-model 479s Add default standard model distribution to the plot. 479s --plot-alternate-model {CpG,6mA,5mC,dcm,dam} 479s Add alternative model distribution to the plot. 479s 479s Overplotting Arguments: 479s --overplot-threshold OVERPLOT_THRESHOLD 479s Coverage level to trigger alternative plot type 479s instead of raw signal. Default: 50 479s --overplot-type {Downsample,Boxplot,Quantile,Density} 479s Plot type for regions with higher coverage. Default: 479s Downsample 479s 479s Plotting Region Arguments: 479s --num-regions NUM_REGIONS 479s Number of regions to plot. Default: 10 479s --num-bases NUM_BASES 479s Number of bases to plot/output. Default: 21 479s 479s Statistical Argument: 479s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 479s Dampen fraction modified estimates for low coverage 479s sites. Two parameters are unmodified and modified 479s pseudo read counts. This is equivalent to a beta prior 479s on the fraction estimate. Set to "0 0" to disable 479s dampened fraction estimation. Default: [2, 0] 479s 479s Output Arguments: 479s --pdf-filename PDF_FILENAME 479s PDF filename to store plot(s). Default: 479s tombo_results.significant_difference.pdf 479s --sequences-filename SEQUENCES_FILENAME 479s File for sequences from selected regions. Sequences 479s will be stored in FASTA format. Default: None. 479s 479s FAST5 Data Arguments: 479s --corrected-group CORRECTED_GROUP 479s FAST5 group created by resquiggle command. Default: 479s RawGenomeCorrected_000 479s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 479s FAST5 subgroup(s) (under /Analyses/[--basecall- 479s group]/) containing basecalls and created within 479s [--corrected-group] containing re-squiggle results. 479s Default: ['BaseCalled_template'] 479s 479s Miscellaneous Arguments: 479s --quiet, -q Don't print status information. 479s --help, -h Print this help message and exit 479s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 479s [FAST5_BASEDIRS ...] --motif MOTIF 479s --statistics-filename STATISTICS_FILENAME 479s --genome-fasta GENOME_FASTA 479s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 479s [--plot-standard-model] 479s [--plot-alternate-model {6mA,dcm,dam,5mC,CpG}] 479s [--overplot-threshold OVERPLOT_THRESHOLD] 479s [--num-regions NUM_REGIONS] 479s [--num-context NUM_CONTEXT] 479s [--num-statistics NUM_STATISTICS] 479s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 479s [--pdf-filename PDF_FILENAME] 479s [--corrected-group CORRECTED_GROUP] 479s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 479s [--quiet] [--help] 479s 479s Required Arguments: 479s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 479s Directories containing fast5 files. 479s --motif MOTIF Motif of interest at which to plot signal and 479s statsitics. Supports IUPAC single letter codes (use T 479s for RNA). 479s --statistics-filename STATISTICS_FILENAME 479s File to save/load genomic base anchored statistics. 479s --genome-fasta GENOME_FASTA 479s FASTA file used to re-squiggle. For faster sequence 479s access. 479s 479s Comparison Arguments: 479s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 479s Set of directories containing fast5 files for control 479s reads, containing only canonical nucleotides. 479s --plot-standard-model 479s Add default standard model distribution to the plot. 479s --plot-alternate-model {6mA,dcm,dam,5mC,CpG} 479s Add alternative model distribution to the plot. 479s 479s Overplotting Argument: 479s --overplot-threshold OVERPLOT_THRESHOLD 479s Coverage level to trigger alternative plot type 479s instead of raw signal. Default: 50 479s 479s Plotting Region Arguments: 479s --num-regions NUM_REGIONS 479s Number of regions to plot. Default: 3 479s --num-context NUM_CONTEXT 479s Number of context bases around motif. Default: 5 479s --num-statistics NUM_STATISTICS 479s Number of motif centered regions to include in 479s statistic distributions. Default: 200 479s 479s Statistical Argument: 479s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 479s Dampen fraction modified estimates for low coverage 479s sites. Two parameters are unmodified and modified 479s pseudo read counts. This is equivalent to a beta prior 479s on the fraction estimate. Set to "0 0" to disable 479s dampened fraction estimation. Default: [2, 0] 479s 479s Output Argument: 479s --pdf-filename PDF_FILENAME 479s PDF filename to store plot(s). Default: 479s tombo_results.motif_statistics.pdf 479s 479s FAST5 Data Arguments: 479s --corrected-group CORRECTED_GROUP 479s FAST5 group created by resquiggle command. Default: 479s RawGenomeCorrected_000 479s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 479s FAST5 subgroup(s) (under /Analyses/[--basecall- 479s group]/) containing basecalls and created within 479s [--corrected-group] containing re-squiggle results. 479s Default: ['BaseCalled_template'] 479s 479s Miscellaneous Arguments: 479s --quiet, -q Don't print status information. 479s --help, -h Print this help message and exit 479s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 479s [GENOME_LOCATIONS ...] 479s --per-read-statistics-filename 479s PER_READ_STATISTICS_FILENAME 479s [--genome-fasta GENOME_FASTA] 479s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 479s [--num-reads NUM_READS] [--num-bases NUM_BASES] 479s [--box-center] [--pdf-filename PDF_FILENAME] 479s [--corrected-group CORRECTED_GROUP] 479s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 479s [--quiet] [--help] 479s 479s Required Arguments: 479s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 479s Genomic locations at which to plot signal. Format 479s locations as "chrm:position[:strand] 479s [chrm2:position2[:strand2] ...]" (strand not 479s applicable for all applications) 479s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 479s Binary file containing per-read statistics from 479s statistical testing. 479s 479s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 479s --genome-fasta GENOME_FASTA 479s FASTA file used to re-squiggle. For faster sequence 479s access. 479s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 479s Directories containing fast5 files. 479s 479s Plotting Region Arguments: 479s --num-reads NUM_READS 479s Number of reads to plot. Default: 100 479s --num-bases NUM_BASES 479s Number of bases to plot/output. Default: 51 479s --box-center Plot a box around the central base. 479s 479s Output Argument: 479s --pdf-filename PDF_FILENAME 479s PDF filename to store plot(s). Default: 479s tombo_results.per_read_stats.pdf 479s 479s FAST5 Data Arguments: 479s --corrected-group CORRECTED_GROUP 479s FAST5 group created by resquiggle command. Default: 479s RawGenomeCorrected_000 479s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 479s FAST5 subgroup(s) (under /Analyses/[--basecall- 479s group]/) containing basecalls and created within 479s [--corrected-group] containing re-squiggle results. 479s Default: ['BaseCalled_template'] 479s 479s Miscellaneous Arguments: 479s --quiet, -q Don't print status information. 479s --help, -h Print this help message and exit 479s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 479s [STATISTICS_FILENAMES ...] 479s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 479s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 479s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 479s [--genome-fasta GENOME_FASTA] 479s [--pdf-filename PDF_FILENAME] 479s [--statistics-per-block STATISTICS_PER_BLOCK] 479s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 479s [--quiet] [--help] 479s 479s Required Argument: 479s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 479s Files to load genomic base anchored statistics. 479s 479s Ground Truth Arguments (provide bed files or motifs): 479s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 479s Modification description and bed format files 479s containing single base locations of ground truth 479s modified sites. Bed files should contain 6 fields 479s including strand. Format descriptions as 479s "mod_name:locs.bed". Example: "CpG 479s bisulfite":bisulfite_locs.bed 479s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 479s Bed format files containing single base locations of 479s ground truth unmodified sites. Bed files should 479s contain 6 fields including strand. 479s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 479s Ground truth, motif centered, modified base 479s descriptions for computing ROC and PR curves. Each 479s statistics file is associated with a set of motif 479s descriptions. Format descriptions as: 479s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 479s mod_pos indicates the alternate-base within the motif 479s (1-based index). Example: CCWGG:2:"dcm 479s 5mC"::GATC:2:"dam 6mA" would assess the performance of 479s a single Tombo statistics file for identification of 479s E. coli dam and dcm methylation. 479s --genome-fasta GENOME_FASTA 479s FASTA file used to re-squiggle. For faster sequence 479s access. 479s 479s Output Arguments: 479s --pdf-filename PDF_FILENAME 479s PDF filename to store plot(s). Default: 479s tombo_results.roc.pdf 479s 479s Down-sampling Arguments: 479s --statistics-per-block STATISTICS_PER_BLOCK 479s Number of randomly selected per-read, per-base 479s statistics to extract from each genomic block for 479s plotting. Default: Include all stats 479s --total-statistics-limit TOTAL_STATISTICS_LIMIT 479s Total per-read statistics to be extracted for 479s plotting. Avoids memory overflow for large runs. 479s Default: 5000000 479s 479s Miscellaneous Arguments: 479s --quiet, -q Don't print status information. 479s --help, -h Print this help message and exit 479s usage: tombo plot per_read_roc --per-read-statistics-filenames 479s PER_READ_STATISTICS_FILENAMES 479s [PER_READ_STATISTICS_FILENAMES ...] 479s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 479s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 479s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 479s [--genome-fasta GENOME_FASTA] 479s [--statistics-per-block STATISTICS_PER_BLOCK] 479s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 479s [--pdf-filename PDF_FILENAME] [--quiet] 479s [--help] 479s 479s Required Argument: 479s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 479s Binary files containing per-read statistics from 479s statistical testing. 479s 479s Ground Truth Arguments (provide bed files or motifs): 479s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 479s Modification description and bed format files 479s containing single base locations of ground truth 479s modified sites. Bed files should contain 6 fields 479s including strand. Format descriptions as 479s "mod_name:locs.bed". Example: "CpG 479s bisulfite":bisulfite_locs.bed 479s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 479s Bed format files containing single base locations of 479s ground truth unmodified sites. Bed files should 479s contain 6 fields including strand. 479s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 479s Ground truth, motif centered, modified base 479s descriptions for computing ROC and PR curves. Each 479s statistics file is associated with a set of motif 479s descriptions. Format descriptions as: 479s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 479s mod_pos indicates the alternate-base within the motif 479s (1-based index). Example: CCWGG:2:"dcm 479s 5mC"::GATC:2:"dam 6mA" would assess the performance of 479s a single Tombo statistics file for identification of 479s E. coli dam and dcm methylation. 479s --genome-fasta GENOME_FASTA 479s FASTA file used to re-squiggle. For faster sequence 479s access. 479s 479s Down-sampling Arguments: 479s --statistics-per-block STATISTICS_PER_BLOCK 479s Number of randomly selected per-read, per-base 479s statistics to extract from each genomic block for 479s plotting. Default: 100000 479s --total-statistics-limit TOTAL_STATISTICS_LIMIT 479s Total per-read statistics to be extracted for 479s plotting. Avoids memory overflow for large runs. 479s Default: 5000000 479s 479s Output Arguments: 479s --pdf-filename PDF_FILENAME 479s PDF filename to store plot(s). Default: 479s tombo_results.per_reads_roc.pdf 479s 479s Miscellaneous Arguments: 479s --quiet, -q Don't print status information. 479s --help, -h Print this help message and exit 479s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 479s [--upstream-bases {0,1,2,3,4}] 479s [--downstream-bases {0,1,2,3,4}] [--read-mean] 479s [--num-kmer-threshold NUM_KMER_THRESHOLD] 479s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 479s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 479s [--corrected-group CORRECTED_GROUP] 479s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 479s [--quiet] [--help] 479s 479s Required Argument: 479s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 479s Directories containing fast5 files. 479s 479s Data Processing Arguments: 479s --upstream-bases {0,1,2,3,4} 479s Upstream bases in k-mer. Default: 1 479s --downstream-bases {0,1,2,3,4} 479s Downstream bases in k-mer. Default: 2 479s --read-mean Plot k-mer means across whole reads as opposed to 479s individual k-mer event levels. 479s --num-kmer-threshold NUM_KMER_THRESHOLD 479s Observations of each k-mer required to include a read 479s in read level averages. Default: 1 479s 479s Plotting Region Arguments: 479s --num-reads NUM_READS 479s Number of reads to plot. Default: 100 479s 479s Output Arguments: 479s --pdf-filename PDF_FILENAME 479s PDF filename to store plot(s). Default: 479s tombo_results.kmer_distribution.pdf 479s --r-data-filename R_DATA_FILENAME 479s Filename to save R data structure. Default: Don't save 479s --dont-plot Don't plot result. Useful to produce only R data file. 479s 479s FAST5 Data Arguments: 479s --corrected-group CORRECTED_GROUP 479s FAST5 group created by resquiggle command. Default: 479s RawGenomeCorrected_000 479s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 479s FAST5 subgroup(s) (under /Analyses/[--basecall- 479s group]/) containing basecalls and created within 479s [--corrected-group] containing re-squiggle results. 479s Default: ['BaseCalled_template'] 479s 479s Miscellaneous Arguments: 479s --quiet, -q Don't print status information. 479s --help, -h Print this help message and exit 479s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 479s [FAST5_BASEDIRS ...] 479s --control-fast5-basedirs 479s CONTROL_FAST5_BASEDIRS 479s [CONTROL_FAST5_BASEDIRS ...] 479s --statistics-filename 479s STATISTICS_FILENAME 479s [--genome-fasta GENOME_FASTA] 479s [--processes PROCESSES] 479s [--num-regions NUM_REGIONS] 479s [--num-bases NUM_BASES] 479s [--slide-span SLIDE_SPAN] 479s [--pdf-filename PDF_FILENAME] 479s [--r-data-filename R_DATA_FILENAME] 479s [--corrected-group CORRECTED_GROUP] 479s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 479s [--quiet] [--help] 479s 479s Required Arguments: 479s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 479s Directories containing fast5 files. 479s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 479s Set of directories containing fast5 files for control 479s reads, containing only canonical nucleotides. 479s --statistics-filename STATISTICS_FILENAME 479s File to save/load genomic base anchored statistics. 479s 479s FASTA Sequence Argument: 479s --genome-fasta GENOME_FASTA 479s FASTA file used to re-squiggle. For faster sequence 479s access. 479s 479s Multiprocessing Argument: 479s --processes PROCESSES 479s Number of processes. Default: 1 479s 479s Plotting Region Arguments: 479s --num-regions NUM_REGIONS 479s Number of regions to plot. Default: 10 479s --num-bases NUM_BASES 479s Number of bases to plot/output. Default: 21 479s --slide-span SLIDE_SPAN 479s Number of bases offset over which to search when 479s computing distances for signal cluster plotting. 479s Default: 0 (exact position) 479s 479s Output Arguments: 479s --pdf-filename PDF_FILENAME 479s PDF filename to store plot(s). Default: 479s tombo_results.signal_clusters.pdf 479s --r-data-filename R_DATA_FILENAME 479s Filename to save R data structure. Default: Don't save 479s 479s FAST5 Data Arguments: 479s --corrected-group CORRECTED_GROUP 479s FAST5 group created by resquiggle command. Default: 479s RawGenomeCorrected_000 479s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 479s FAST5 subgroup(s) (under /Analyses/[--basecall- 479s group]/) containing basecalls and created within 479s [--corrected-group] containing re-squiggle results. 479s Default: ['BaseCalled_template'] 479s 479s Miscellaneous Arguments: 479s --quiet, -q Don't print status information. 479s --help, -h Print this help message and exit 480s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 480s 480s Required Arguments: 480s fast5s_basedir Directory containing fast5 files. All files ending in 480s "fast5" found recursively within this base directory will be 480s processed. 480s 480s Miscellaneous Arguments: 480s --quiet, -q Don't print status information. 480s --help, -h Print this help message and exit 480s usage: tombo build_model event_resquiggle 480s [--minimap2-executable MINIMAP2_EXECUTABLE] 480s [--minimap2-index MINIMAP2_INDEX] 480s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 480s [--graphmap-executable GRAPHMAP_EXECUTABLE] 480s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 480s [--normalization-type {median,pA,pA_raw,none}] 480s [--pore-model-filename PORE_MODEL_FILENAME] 480s [--outlier-threshold OUTLIER_THRESHOLD] 480s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 480s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 480s [--timeout TIMEOUT] 480s [--cpts-limit CPTS_LIMIT] 480s [--skip-index] [--overwrite] 480s [--failed-reads-filename FAILED_READS_FILENAME] 480s [--include-event-stdev] 480s [--corrected-group CORRECTED_GROUP] 480s [--basecall-group BASECALL_GROUP] 480s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 480s [--processes PROCESSES] 480s [--align-processes ALIGN_PROCESSES] 480s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 480s [--resquiggle-processes RESQUIGGLE_PROCESSES] 480s [--quiet] [--help] 480s fast5s_basedir reference_fasta 480s 480s Required Arguments: 480s fast5s_basedir Directory containing fast5 files. All files ending in 480s "fast5" found recursively within this base directory 480s will be processed. 480s reference_fasta Reference genome/transcriptome FASTA file for mapping. 480s 480s Mapper Arguments (One mapper is required): 480s --minimap2-executable MINIMAP2_EXECUTABLE 480s Path to minimap2 executable. 480s --minimap2-index MINIMAP2_INDEX 480s Path to minimap2 index (with map-ont preset) file 480s corresponding to the [genome_fasta] provided. 480s --bwa-mem-executable BWA_MEM_EXECUTABLE 480s Path to bwa-mem executable. 480s --graphmap-executable GRAPHMAP_EXECUTABLE 480s Path to graphmap executable. 480s --alignment-batch-size ALIGNMENT_BATCH_SIZE 480s Number of reads included in each alignment call. Note: 480s A new system mapping call is made for each batch 480s (including loading of the genome), so it is advised to 480s use larger values for larger genomes. Default: 1000 480s 480s Signal Processing Arguments: 480s --normalization-type {median,pA,pA_raw,none} 480s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 480s as in the ONT events (using offset, range and 480s digitization), "pA": k-mer-based correction for pA 480s drift as in nanopolish (requires [--pore-model- 480s filename]), "median": median and MAD from raw signal. 480s Default: median 480s --pore-model-filename PORE_MODEL_FILENAME 480s File containing kmer model parameters (level_mean and 480s level_stdv) used in order to compute kmer-based 480s corrected pA values. E.g. https://github.com/jts/nanop 480s olish/blob/master/etc/r9- 480s models/template_median68pA.5mers.model 480s --outlier-threshold OUTLIER_THRESHOLD 480s Windosrize the signal at this number of scale values. 480s Negative value disables outlier clipping. Default: 480s 5.000000 480s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 480s Specify the 2 parameters for segmentation 1) running 480s neighboring windows width 2) minimum raw observations 480s per genomic base. Sample type defaults: RNA : 12 6 || 480s DNA : 5 3 480s 480s Read Filtering Arguments: 480s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 480s Filter reads based on observations per base percentile 480s thresholds. Format thresholds as "percentile:thresh 480s [pctl2:thresh2 ...]". For example to filter reads with 480s 99th pctl > 200 obs/base or max > 5k obs/base use 480s "99:200 100:5000". 480s --timeout TIMEOUT Timeout in seconds for processing a single read. 480s Default: No timeout. 480s --cpts-limit CPTS_LIMIT 480s Maximum number of changepoints to find within a single 480s indel group. Default: No limit. 480s 480s Input/Output Arguments: 480s --skip-index Skip creation of tombo index. This drastically slows 480s downstream tombo commands. Default stores tombo index 480s named ".[--fast5-basedir].[--corrected- 480s group].tombo.index" to be loaded automatically for 480s downstream commands. 480s --overwrite Overwrite previous corrected group in FAST5 files. 480s Note: only effects --corrected-group or --new- 480s corrected-group. 480s --failed-reads-filename FAILED_READS_FILENAME 480s Output failed read filenames with assoicated error. 480s Default: Do not store failed reads. 480s --include-event-stdev 480s Include corrected event standard deviation in output 480s FAST5 data. 480s 480s FAST5 Data Arguments: 480s --corrected-group CORRECTED_GROUP 480s FAST5 group created by resquiggle command. Default: 480s RawGenomeCorrected_000 480s --basecall-group BASECALL_GROUP 480s FAST5 group obtain original basecalls (under Analyses 480s group). Default: Basecall_1D_000 480s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 480s FAST5 subgroup(s) (under /Analyses/[--basecall- 480s group]/) containing basecalls and created within 480s [--corrected-group] containing re-squiggle results. 480s Default: ['BaseCalled_template'] 480s 480s Multiprocessing Arguments: 480s --processes PROCESSES 480s Number of processes. Default: 2 480s --align-processes ALIGN_PROCESSES 480s Number of processes to use for parsing and aligning 480s original basecalls. Each process will independently 480s load the genome into memory, so use caution with 480s larger genomes (e.g. human). Default: 1 480s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 480s Number of threads to use for aligner system call. 480s Default: [--processes] / (2 * [--align-processes)] 480s --resquiggle-processes RESQUIGGLE_PROCESSES 480s Number of processes to use for resquiggle algorithm. 480s Default: [--processes] / 2 480s 480s Miscellaneous Arguments: 480s --quiet, -q Don't print status information. 480s --help, -h Print this help message and exit 480s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 480s [FAST5_BASEDIRS ...] 480s --tombo-model-filename 480s TOMBO_MODEL_FILENAME 480s [--estimate-mean] 480s [--kmer-specific-sd] 480s [--upstream-bases {0,1,2,3,4}] 480s [--downstream-bases {0,1,2,3,4}] 480s [--minimum-test-reads MINIMUM_TEST_READS] 480s [--coverage-threshold COVERAGE_THRESHOLD] 480s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 480s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 480s [--processes PROCESSES] 480s [--corrected-group CORRECTED_GROUP] 480s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 480s [--quiet] [--help] 480s 480s Required Arguments: 480s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 480s Directories containing fast5 files. 480s --tombo-model-filename TOMBO_MODEL_FILENAME 480s Filename to save Tombo model. 480s 480s Modeling Arguments: 480s --estimate-mean Use the mean instead of median for model level 480s estimation. Note: This can cause poor fits due to 480s outliers 480s --kmer-specific-sd Estimate standard deviation for each k-mers 480s individually. 480s --upstream-bases {0,1,2,3,4} 480s Upstream bases in k-mer. Default: 1 480s --downstream-bases {0,1,2,3,4} 480s Downstream bases in k-mer. Default: 2 480s 480s Filtering Arguments: 480s --minimum-test-reads MINIMUM_TEST_READS 480s Number of reads required at a position to perform 480s significance testing or contribute to model 480s estimation. Default: 10 480s --coverage-threshold COVERAGE_THRESHOLD 480s Maximum mean coverage per region when estimating k-mer 480s model (limits compute time for deep samples). Default: 480s 100 480s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 480s Number of each k-mer observations required in order to 480s produce a reference (genomic locations for standard 480s reference and per-read for alternative reference). 480s Default: 5 480s 480s Multiprocessing Arguments: 480s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 480s Size of regions over which to multiprocesses statistic 480s computation. For very deep samples a smaller value is 480s recommmended in order to control memory consumption. 480s Default: 10000 480s --processes PROCESSES 480s Number of processes. Default: 1 480s 480s FAST5 Data Arguments: 480s --corrected-group CORRECTED_GROUP 480s FAST5 group created by resquiggle command. Default: 480s RawGenomeCorrected_000 480s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 480s FAST5 subgroup(s) (under /Analyses/[--basecall- 480s group]/) containing basecalls and created within 480s [--corrected-group] containing re-squiggle results. 480s Default: ['BaseCalled_template'] 480s 480s Miscellaneous Arguments: 480s --quiet, -q Don't print status information. 480s --help, -h Print this help message and exit 480s usage: tombo build_model estimate_alt_reference --alternate-model-filename 480s ALTERNATE_MODEL_FILENAME 480s --alternate-model-name 480s ALTERNATE_MODEL_NAME 480s --alternate-model-base 480s {A,C,G,T} 480s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 480s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 480s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 480s [--control-density-filename CONTROL_DENSITY_FILENAME] 480s [--dna] [--rna] 480s [--tombo-model-filename TOMBO_MODEL_FILENAME] 480s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 480s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 480s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 480s [--save-density-basename SAVE_DENSITY_BASENAME] 480s [--processes PROCESSES] 480s [--corrected-group CORRECTED_GROUP] 480s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 480s [--quiet] [--help] 480s 480s Required Arguments: 480s --alternate-model-filename ALTERNATE_MODEL_FILENAME 480s Tombo model for alternative likelihood ratio 480s significance testing. 480s --alternate-model-name ALTERNATE_MODEL_NAME 480s A short name to associate with this alternate model 480s (e.g. 5mC, 6mA, etc.). This text will be included in 480s output filenames when this model is used for testing. 480s --alternate-model-base {A,C,G,T} 480s Non-standard base is an alternative to this base. 480s 480s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 480s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 480s Directories containing fast5 files. 480s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 480s Set of directories containing fast5 files for control 480s reads, containing only canonical nucleotides. 480s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 480s File containing k-mer level kernel density estimates 480s for the alternative sample saved using --save-density- 480s basename. 480s --control-density-filename CONTROL_DENSITY_FILENAME 480s File containing k-mer level kernel density estimates 480s for the control sample saved using --save-density- 480s basename. 480s 480s Standard Model Arguments: 480s --dna Explicitly select canonical DNA model. Default: 480s Automatically determine from FAST5s 480s --rna Explicitly select canonical RNA model. Default: 480s Automatically determine from FAST5s 480s --tombo-model-filename TOMBO_MODEL_FILENAME 480s Tombo model filename. If no file is provided, the 480s default DNA or RNA Tombo model will be used. 480s 480s Model Fitting Arguments: 480s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 480s When esitmating the alternative base incorporation 480s rate, this percent of k-mers are assumed to have 480s significantly shifted signal so the alternative 480s distribution minimally overlaps the standard base 480s distribution. Default: 5.000000 480s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 480s Bandwidth applied when performing Gaussian kernal 480s density esitmation on standard and alternative base 480s signal distributions. Default: 0.050000 480s 480s Filtering Argument: 480s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 480s Number of each k-mer observations required in order to 480s produce a reference (genomic locations for standard 480s reference and per-read for alternative reference). 480s Default: 1000 480s 480s Output Argument: 480s --save-density-basename SAVE_DENSITY_BASENAME 480s Basename to save alternative model estimation density 480s estimation information. See scripts/debug_est_alt.R 480s for info use example. Default: Don't save. 480s 480s Multiprocessing Arguments: 480s --processes PROCESSES 480s Number of processes. Default: 1 480s 480s FAST5 Data Arguments: 480s --corrected-group CORRECTED_GROUP 480s FAST5 group created by resquiggle command. Default: 480s RawGenomeCorrected_000 480s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 480s FAST5 subgroup(s) (under /Analyses/[--basecall- 480s group]/) containing basecalls and created within 480s [--corrected-group] containing re-squiggle results. 480s Default: ['BaseCalled_template'] 480s 480s Miscellaneous Arguments: 480s --quiet, -q Don't print status information. 480s --help, -h Print this help message and exit 480s This test only tests the help system 480s There is an extensive test in 480s 480s tombo/tests/shell_tests.sh 480s 480s but this requires to download larger data 480s sets which is not done for the moment. 480s autopkgtest [10:16:10]: test run-unit-test: -----------------------] 481s run-unit-test PASS 481s autopkgtest [10:16:11]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 481s autopkgtest [10:16:11]: @@@@@@@@@@@@@@@@@@@@ summary 481s run-unit-test PASS 494s Creating nova instance adt-noble-ppc64el-tombo-20240323-100810-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240322.img (UUID 8499323f-6fcd-4f77-8a53-77410adea6d3)...