0s autopkgtest [10:47:23]: starting date and time: 2025-11-01 10:47:23+0000 0s autopkgtest [10:47:23]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [10:47:23]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.l3k9zlss/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:scipy --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scipy/1.16.3-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-11.secgroup --name adt-resolute-s390x-tombo-20251101-104723-juju-7f2275-prod-proposed-migration-environment-2-09a332b0-7ebe-42cc-8221-3773215b0ef8 --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-s390x-tombo-20251101-104723-juju-7f2275-prod-proposed-migration-environment-2-09a332b0-7ebe-42cc-8221-3773215b0ef8 from image adt/ubuntu-resolute-s390x-server-20251031.img (UUID 0c045c9f-9f12-44be-973b-1d1fecbe207a)... 59s autopkgtest [10:48:22]: testbed dpkg architecture: s390x 59s autopkgtest [10:48:22]: testbed apt version: 3.1.11 60s autopkgtest [10:48:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 60s autopkgtest [10:48:23]: testbed release detected to be: None 61s autopkgtest [10:48:24]: updating testbed package index (apt update) 61s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 61s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 61s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 61s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 61s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [2408 kB] 62s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 62s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [138 kB] 62s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [50.0 kB] 62s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [198 kB] 62s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 62s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [1727 kB] 62s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [28.9 kB] 62s Fetched 4647 kB in 2s (3014 kB/s) 63s Reading package lists... 64s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 64s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 64s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 64s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 65s Reading package lists... 65s Reading package lists... 65s Building dependency tree... 65s Reading state information... 65s Calculating upgrade... 65s The following packages will be upgraded: 65s gcc-15-base libatomic1 libfribidi0 libgcc-s1 libstdc++6 publicsuffix 65s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s Need to get 1174 kB of archives. 65s After this operation, 14.3 kB of additional disk space will be used. 65s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libatomic1 s390x 15.2.0-7ubuntu1 [9488 B] 65s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libstdc++6 s390x 15.2.0-7ubuntu1 [907 kB] 66s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15-base s390x 15.2.0-7ubuntu1 [58.4 kB] 66s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libgcc-s1 s390x 15.2.0-7ubuntu1 [35.7 kB] 66s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libfribidi0 s390x 1.0.16-3 [27.6 kB] 66s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x publicsuffix all 20251016.1743-0.1 [136 kB] 66s dpkg-preconfigure: unable to re-open stdin: No such file or directory 66s Fetched 1174 kB in 1s (1518 kB/s) 66s (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 ... 56953 files and directories currently installed.) 66s Preparing to unpack .../libatomic1_15.2.0-7ubuntu1_s390x.deb ... 66s Unpacking libatomic1:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 66s Preparing to unpack .../libstdc++6_15.2.0-7ubuntu1_s390x.deb ... 66s Unpacking libstdc++6:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 66s Preparing to unpack .../gcc-15-base_15.2.0-7ubuntu1_s390x.deb ... 66s Unpacking gcc-15-base:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 66s Setting up gcc-15-base:s390x (15.2.0-7ubuntu1) ... 66s (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 ... 56953 files and directories currently installed.) 66s Preparing to unpack .../libgcc-s1_15.2.0-7ubuntu1_s390x.deb ... 66s Unpacking libgcc-s1:s390x (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 66s Setting up libgcc-s1:s390x (15.2.0-7ubuntu1) ... 66s (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 ... 56953 files and directories currently installed.) 66s Preparing to unpack .../libfribidi0_1.0.16-3_s390x.deb ... 66s Unpacking libfribidi0:s390x (1.0.16-3) over (1.0.16-1) ... 67s Preparing to unpack .../publicsuffix_20251016.1743-0.1_all.deb ... 67s Unpacking publicsuffix (20251016.1743-0.1) over (20250328.1952-0.1) ... 67s Setting up libfribidi0:s390x (1.0.16-3) ... 67s Setting up libatomic1:s390x (15.2.0-7ubuntu1) ... 67s Setting up publicsuffix (20251016.1743-0.1) ... 67s Setting up libstdc++6:s390x (15.2.0-7ubuntu1) ... 67s Processing triggers for libc-bin (2.42-0ubuntu3) ... 67s autopkgtest [10:48:30]: upgrading testbed (apt dist-upgrade and autopurge) 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Calculating upgrade... 67s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Solving dependencies... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s autopkgtest [10:48:33]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 71s autopkgtest [10:48:34]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 74s Get:1 http://ftpmaster.internal/ubuntu resolute/universe tombo 1.5.1-7build3 (dsc) [2291 B] 74s Get:2 http://ftpmaster.internal/ubuntu resolute/universe tombo 1.5.1-7build3 (tar) [22.3 MB] 74s Get:3 http://ftpmaster.internal/ubuntu resolute/universe tombo 1.5.1-7build3 (diff) [9656 B] 74s gpgv: Signature made Tue Oct 21 17:53:35 2025 UTC 74s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 74s gpgv: Can't check signature: No public key 74s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7build3.dsc: no acceptable signature found 74s autopkgtest [10:48:37]: testing package tombo version 1.5.1-7build3 75s autopkgtest [10:48:38]: build not needed 88s autopkgtest [10:48:51]: test run-unit-test: preparing testbed 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s Solving dependencies... 88s The following NEW packages will be installed: 88s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 88s libhdf5-310 libhdf5-hl-310 libjs-jquery libjs-mathjax libjs-sphinxdoc 88s libjs-underscore liblapack3 liblzf1 libqhull-r8.0 libsz2 python3-decorator 88s python3-h5py python3-h5py-serial python3-mappy python3-numpy 88s python3-numpy-dev python3-packaging python3-scipy python3-tqdm 88s sphinx-rtd-theme-common tombo tombo-doc 88s 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded. 88s Need to get 66.2 MB of archives. 88s After this operation, 241 MB of additional disk space will be used. 88s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-lato all 2.015-1 [2781 kB] 89s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.2.4+ds-1ubuntu1 [147 kB] 89s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-6build1 [245 kB] 89s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-7ubuntu1 [629 kB] 89s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-6build1 [2910 kB] 90s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.2.4+ds-1ubuntu1 [4399 kB] 90s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 90s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 91s Get:9 http://ftpmaster.internal/ubuntu resolute/universe s390x libaec0 s390x 1.1.4-2 [26.1 kB] 91s Get:10 http://ftpmaster.internal/ubuntu resolute/universe s390x libsz2 s390x 1.1.4-2 [5628 B] 91s Get:11 http://ftpmaster.internal/ubuntu resolute/universe s390x libhdf5-310 s390x 1.14.5+repack-3build1 [1477 kB] 91s Get:12 http://ftpmaster.internal/ubuntu resolute/universe s390x libhdf5-hl-310 s390x 1.14.5+repack-3build1 [61.1 kB] 91s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 91s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 91s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 91s Get:16 http://ftpmaster.internal/ubuntu resolute/universe s390x liblzf1 s390x 3.6-4 [7020 B] 91s Get:17 http://ftpmaster.internal/ubuntu resolute/universe s390x libqhull-r8.0 s390x 2020.2-6build1 [199 kB] 91s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x python3-decorator all 5.2.1-2 [28.1 kB] 91s Get:19 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-h5py-serial s390x 3.13.0-1ubuntu1 [1182 kB] 91s Get:20 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-h5py all 3.13.0-1ubuntu1 [8230 B] 91s Get:21 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mappy s390x 2.27+dfsg-1build3 [258 kB] 91s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x python3-packaging all 25.0-1 [52.8 kB] 91s Get:23 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-tqdm all 4.67.1-5 [92.1 kB] 91s Get:24 http://ftpmaster.internal/ubuntu resolute/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 91s Get:25 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x python3-scipy s390x 1.16.3-1 [19.6 MB] 93s Get:26 http://ftpmaster.internal/ubuntu resolute/universe s390x tombo s390x 1.5.1-7build3 [528 kB] 93s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 94s Get:28 http://ftpmaster.internal/ubuntu resolute/universe s390x tombo-doc all 1.5.1-7build3 [21.7 MB] 95s Fetched 66.2 MB in 7s (10.2 MB/s) 95s Selecting previously unselected package fonts-lato. 95s (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 ... 56953 files and directories currently installed.) 95s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 95s Unpacking fonts-lato (2.015-1) ... 95s Selecting previously unselected package python3-numpy-dev:s390x. 95s Preparing to unpack .../01-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 95s Unpacking python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 95s Selecting previously unselected package libblas3:s390x. 95s Preparing to unpack .../02-libblas3_3.12.1-6build1_s390x.deb ... 95s Unpacking libblas3:s390x (3.12.1-6build1) ... 95s Selecting previously unselected package libgfortran5:s390x. 95s Preparing to unpack .../03-libgfortran5_15.2.0-7ubuntu1_s390x.deb ... 95s Unpacking libgfortran5:s390x (15.2.0-7ubuntu1) ... 95s Selecting previously unselected package liblapack3:s390x. 95s Preparing to unpack .../04-liblapack3_3.12.1-6build1_s390x.deb ... 95s Unpacking liblapack3:s390x (3.12.1-6build1) ... 95s Selecting previously unselected package python3-numpy. 95s Preparing to unpack .../05-python3-numpy_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 95s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 95s Selecting previously unselected package fonts-font-awesome. 95s Preparing to unpack .../06-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 95s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 95s Selecting previously unselected package fonts-mathjax. 95s Preparing to unpack .../07-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 95s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 96s Selecting previously unselected package libaec0:s390x. 96s Preparing to unpack .../08-libaec0_1.1.4-2_s390x.deb ... 96s Unpacking libaec0:s390x (1.1.4-2) ... 96s Selecting previously unselected package libsz2:s390x. 96s Preparing to unpack .../09-libsz2_1.1.4-2_s390x.deb ... 96s Unpacking libsz2:s390x (1.1.4-2) ... 96s Selecting previously unselected package libhdf5-310:s390x. 96s Preparing to unpack .../10-libhdf5-310_1.14.5+repack-3build1_s390x.deb ... 96s Unpacking libhdf5-310:s390x (1.14.5+repack-3build1) ... 96s Selecting previously unselected package libhdf5-hl-310:s390x. 96s Preparing to unpack .../11-libhdf5-hl-310_1.14.5+repack-3build1_s390x.deb ... 96s Unpacking libhdf5-hl-310:s390x (1.14.5+repack-3build1) ... 96s Selecting previously unselected package libjs-jquery. 96s Preparing to unpack .../12-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 96s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 96s Selecting previously unselected package libjs-underscore. 96s Preparing to unpack .../13-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 96s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 96s Selecting previously unselected package libjs-sphinxdoc. 96s Preparing to unpack .../14-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 96s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 96s Selecting previously unselected package liblzf1:s390x. 96s Preparing to unpack .../15-liblzf1_3.6-4_s390x.deb ... 96s Unpacking liblzf1:s390x (3.6-4) ... 96s Selecting previously unselected package libqhull-r8.0:s390x. 96s Preparing to unpack .../16-libqhull-r8.0_2020.2-6build1_s390x.deb ... 96s Unpacking libqhull-r8.0:s390x (2020.2-6build1) ... 96s Selecting previously unselected package python3-decorator. 96s Preparing to unpack .../17-python3-decorator_5.2.1-2_all.deb ... 96s Unpacking python3-decorator (5.2.1-2) ... 96s Selecting previously unselected package python3-h5py-serial. 96s Preparing to unpack .../18-python3-h5py-serial_3.13.0-1ubuntu1_s390x.deb ... 96s Unpacking python3-h5py-serial (3.13.0-1ubuntu1) ... 96s Selecting previously unselected package python3-h5py. 96s Preparing to unpack .../19-python3-h5py_3.13.0-1ubuntu1_all.deb ... 96s Unpacking python3-h5py (3.13.0-1ubuntu1) ... 96s Selecting previously unselected package python3-mappy. 96s Preparing to unpack .../20-python3-mappy_2.27+dfsg-1build3_s390x.deb ... 96s Unpacking python3-mappy (2.27+dfsg-1build3) ... 96s Selecting previously unselected package python3-packaging. 96s Preparing to unpack .../21-python3-packaging_25.0-1_all.deb ... 96s Unpacking python3-packaging (25.0-1) ... 96s Selecting previously unselected package python3-tqdm. 96s Preparing to unpack .../22-python3-tqdm_4.67.1-5_all.deb ... 96s Unpacking python3-tqdm (4.67.1-5) ... 96s Selecting previously unselected package sphinx-rtd-theme-common. 96s Preparing to unpack .../23-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 96s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 96s Selecting previously unselected package python3-scipy. 96s Preparing to unpack .../24-python3-scipy_1.16.3-1_s390x.deb ... 96s Unpacking python3-scipy (1.16.3-1) ... 96s Selecting previously unselected package tombo. 96s Preparing to unpack .../25-tombo_1.5.1-7build3_s390x.deb ... 96s Unpacking tombo (1.5.1-7build3) ... 96s Selecting previously unselected package libjs-mathjax. 96s Preparing to unpack .../26-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 96s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 97s Selecting previously unselected package tombo-doc. 97s Preparing to unpack .../27-tombo-doc_1.5.1-7build3_all.deb ... 97s Unpacking tombo-doc (1.5.1-7build3) ... 97s Setting up fonts-lato (2.015-1) ... 97s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 97s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 97s Setting up python3-tqdm (4.67.1-5) ... 97s Setting up libqhull-r8.0:s390x (2020.2-6build1) ... 97s Setting up python3-mappy (2.27+dfsg-1build3) ... 97s Setting up libaec0:s390x (1.1.4-2) ... 97s Setting up python3-decorator (5.2.1-2) ... 97s Setting up libblas3:s390x (3.12.1-6build1) ... 97s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 97s Setting up python3-packaging (25.0-1) ... 97s Setting up liblzf1:s390x (3.6-4) ... 97s Setting up python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 97s Setting up libgfortran5:s390x (15.2.0-7ubuntu1) ... 97s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 97s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 97s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 97s Setting up libsz2:s390x (1.1.4-2) ... 97s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 97s Setting up liblapack3:s390x (3.12.1-6build1) ... 97s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 97s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 99s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 99s Setting up tombo-doc (1.5.1-7build3) ... 99s Setting up libhdf5-310:s390x (1.14.5+repack-3build1) ... 99s Setting up libhdf5-hl-310:s390x (1.14.5+repack-3build1) ... 99s Setting up python3-scipy (1.16.3-1) ... 103s Setting up python3-h5py-serial (3.13.0-1ubuntu1) ... 103s Setting up python3-h5py (3.13.0-1ubuntu1) ... 103s Setting up tombo (1.5.1-7build3) ... 103s Processing triggers for man-db (2.13.1-1) ... 104s Processing triggers for libc-bin (2.42-0ubuntu3) ... 105s autopkgtest [10:49:08]: test run-unit-test: [----------------------- 105s ********* Testing help commands ********** 105s usage: tombo [-h] [-v] 105s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} ... 105s 105s ********** Tombo ********* 105s 105s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 105s 105s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 105s 105s Tombo command groups (additional help available within each command group): 105s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 105s preprocess Pre-process nanopore reads for Tombo processing. 105s filter Apply filter to Tombo index file for specified criterion. 105s detect_modifications Perform statistical testing to detect non-standard nucleotides. 105s text_output Output Tombo results in text files. 105s build_model Create canonical and alternative base Tombo models. 105s plot Save plots to visualize raw nanopore signal or testing results. 105s 105s options: 105s -h, --help show this help message and exit 105s -v, --version show Tombo version and exit. 105s usage: tombo resquiggle [--dna] [--rna] 105s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 105s [--q-score Q_SCORE] 105s [--signal-matching-score SIGNAL_MATCHING_SCORE] 105s [--processes PROCESSES] 105s [--corrected-group CORRECTED_GROUP] 105s [--basecall-group BASECALL_GROUP] 105s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 105s [--overwrite] 105s [--failed-reads-filename FAILED_READS_FILENAME] 105s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 105s [--print-advanced-arguments] [--quiet] [--help] 105s fast5s_basedir reference 105s 105s Required Arguments: 105s fast5s_basedir Directory containing fast5 files. All files ending in 105s "fast5" found recursively within this base directory 105s will be processed. 105s reference Reference genome/transcriptome FASTA file or minimap2 105s index (with "map-ont" preset) for mapping. 105s 105s Model Parameters: 105s --dna Explicitly select canonical DNA model. Default: 105s Automatically determine from FAST5s 105s --rna Explicitly select canonical RNA model. Default: 105s Automatically determine from FAST5s 105s 105s Read Filtering Argument: 105s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 105s Filter reads based on observations per base percentile 105s thresholds. Format thresholds as "percentile:thresh 105s [pctl2:thresh2 ...]". For example to filter reads with 105s 99th pctl > 200 obs/base or max > 5k obs/base use 105s "99:200 100:5000". 105s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 105s Default: 0.000000 105s --signal-matching-score SIGNAL_MATCHING_SCORE 105s Observed to expected signal matching score (higher 105s score indicates poor matching). Sample type defaults: 105s RNA : 2 || DNA : 1.1 105s 105s Multiprocessing Arguments: 105s --processes PROCESSES 105s Number of processes. Default: 1 105s 105s FAST5 Data Arguments: 105s --corrected-group CORRECTED_GROUP 105s FAST5 group created by resquiggle command. Default: 105s RawGenomeCorrected_000 105s --basecall-group BASECALL_GROUP 105s FAST5 group obtain original basecalls (under Analyses 105s group). Default: Basecall_1D_000 105s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 105s FAST5 subgroup(s) (under /Analyses/[--basecall- 105s group]/) containing basecalls and created within 105s [--corrected-group] containing re-squiggle results. 105s Default: ['BaseCalled_template'] 105s --overwrite Overwrite previous corrected group in FAST5 files. 105s Note: only effects --corrected-group or --new- 105s corrected-group. 105s 105s Input/Output Arguments: 105s --failed-reads-filename FAILED_READS_FILENAME 105s Output failed read filenames with assoicated error. 105s Default: Do not store failed reads. 105s --num-most-common-errors NUM_MOST_COMMON_ERRORS 105s Dynamically show this many most common errors so far 105s through run. Default: 0; Just show progress 105s 105s Advanced Arguments: 105s --print-advanced-arguments 105s Print advanced re-squiggle arguments and exit. 105s 105s Miscellaneous Arguments: 105s --quiet, -q Don't print status information. 105s --help, -h Print this help message and exit 105s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 105s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 105s [--basecall-group BASECALL_GROUP] 105s [--basecall-subgroup BASECALL_SUBGROUP] 105s [--overwrite] 105s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 105s [--processes PROCESSES] 105s [--quiet] [--help] 105s 105s Required Arguments: 105s --fast5-basedir FAST5_BASEDIR 105s Directory containing fast5 files. 105s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 105s FASTQ filenames containing basecalls to be added to 105s raw FAST5 files. 105s 105s FAST5 Data Arguments: 105s --basecall-group BASECALL_GROUP 105s FAST5 group obtain original basecalls (under Analyses 105s group). Default: Basecall_1D_000 105s --basecall-subgroup BASECALL_SUBGROUP 105s FAST5 subgroup (under /Analyses/[--basecall-group]/) 105s under which to store basecalls from FASTQs. Default: 105s BaseCalled_template 105s --overwrite Overwrite previous corrected group in FAST5 files. 105s Note: only effects --corrected-group or --new- 105s corrected-group. 105s 105s Sequencing Summary Argument: 105s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 105s Sequencing summary filenames produced by albacore. 105s These can make annotation of raw FAST5 files with 105s FASTQ sequence much faster. 105s 105s Multiprocessing Argument: 105s --processes PROCESSES 105s Number of processes. Default: 1 105s 105s Miscellaneous Arguments: 105s --quiet, -q Don't print status information. 105s --help, -h Print this help message and exit 105s usage: tombo filter clear_filters 105s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 105s [--corrected-group CORRECTED_GROUP] 105s [--quiet] [--help] 105s 105s Required Argument: 105s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 105s Directories containing fast5 files. 105s 105s FAST5 Data Argument: 105s --corrected-group CORRECTED_GROUP 105s FAST5 group created by resquiggle command. Default: 105s RawGenomeCorrected_000 105s 105s Miscellaneous Arguments: 105s --quiet, -q Don't print status information. 105s --help, -h Print this help message and exit 105s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 105s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 105s [--corrected-group CORRECTED_GROUP] [--quiet] 105s [--help] 105s 105s Required Argument: 105s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 105s Directories containing fast5 files. 105s 105s Read Filtering Argument: 105s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 105s Filter reads based on observations per base percentile 105s thresholds. Format thresholds as "percentile:thresh 105s [pctl2:thresh2 ...]". For example to filter reads with 105s 99th pctl > 200 obs/base or max > 5k obs/base use 105s "99:200 100:5000". 105s 105s FAST5 Data Argument: 105s --corrected-group CORRECTED_GROUP 105s FAST5 group created by resquiggle command. Default: 105s RawGenomeCorrected_000 105s 105s Miscellaneous Arguments: 105s --quiet, -q Don't print status information. 105s --help, -h Print this help message and exit 105s usage: tombo filter level_coverage 105s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 105s [--percent-to-filter PERCENT_TO_FILTER] 105s [--corrected-group CORRECTED_GROUP] 105s [--quiet] [--help] 105s 105s Required Arguments: 105s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 105s Directories containing fast5 files. 105s 105s Read Filtering Argument: 105s --percent-to-filter PERCENT_TO_FILTER 105s Percentage of all reads to filter. Reads are randomly 105s selected weighted according to the approximate 105s coverage at the mapped genomic location. This can be 105s useful in modeling and testing. Default: 10.000000 105s 105s FAST5 Data Arguments: 105s --corrected-group CORRECTED_GROUP 105s FAST5 group created by resquiggle command. Default: 105s RawGenomeCorrected_000 105s 105s Miscellaneous Arguments: 105s --quiet, -q Don't print status information. 105s --help, -h Print this help message and exit 105s usage: tombo filter q_score 105s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 105s [--q-score Q_SCORE] 105s [--corrected-group CORRECTED_GROUP] 105s [--basecall-group BASECALL_GROUP] [--quiet] 105s [--help] 105s 105s Required Arguments: 105s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 105s Directories containing fast5 files. 105s 105s Read Filtering Argument: 105s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 105s Default: 7.000000 105s 105s FAST5 Data Arguments: 105s --corrected-group CORRECTED_GROUP 105s FAST5 group created by resquiggle command. Default: 105s RawGenomeCorrected_000 105s --basecall-group BASECALL_GROUP 105s FAST5 group obtain original basecalls (under Analyses 105s group). Default: Basecall_1D_000 105s 105s Miscellaneous Arguments: 105s --quiet, -q Don't print status information. 105s --help, -h Print this help message and exit 105s usage: tombo filter raw_signal_matching 105s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 105s --signal-matching-score SIGNAL_MATCHING_SCORE 105s [--corrected-group CORRECTED_GROUP] 105s [--quiet] [--help] 105s 105s Required Arguments: 105s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 105s Directories containing fast5 files. 105s --signal-matching-score SIGNAL_MATCHING_SCORE 105s Observed to expected signal matching score (higher 105s score indicates poor matching). Sample type defaults: 105s RNA : 2 || DNA : 1.1 105s 105s FAST5 Data Arguments: 105s --corrected-group CORRECTED_GROUP 105s FAST5 group created by resquiggle command. Default: 105s RawGenomeCorrected_000 105s 105s Miscellaneous Arguments: 105s --quiet, -q Don't print status information. 105s --help, -h Print this help message and exit 106s usage: tombo filter genome_locations 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 106s [--include-partial-overlap] 106s [--corrected-group CORRECTED_GROUP] 106s [--quiet] [--help] 106s 106s Required Arguments: 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s Directories containing fast5 files. 106s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 106s Filter out reads not falling completely within include 106s regions. Omit start and end coordinates to include an 106s entire chromosome/sequence record. Format regions as 106s "chrm[:start-end] [chrm2[:start2-end2] ...]". 106s 106s Filter Argument: 106s --include-partial-overlap 106s Include reads that partially overlap the specified 106s region. Default: Only include reads completely 106s contained in a specified region 106s 106s FAST5 Data Argument: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 106s usage: tombo detect_modifications de_novo 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s --statistics-file-basename STATISTICS_FILE_BASENAME 106s [--dna] [--rna] 106s [--fishers-method-context FISHERS_METHOD_CONTEXT] 106s [--minimum-test-reads MINIMUM_TEST_READS] 106s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 106s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 106s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 106s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 106s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 106s [--processes PROCESSES] 106s [--corrected-group CORRECTED_GROUP] 106s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 106s [--quiet] [--help] 106s 106s Required Argument: 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s Directories containing fast5 files. 106s --statistics-file-basename STATISTICS_FILE_BASENAME 106s File base name to save base by base statistics from 106s testing. Filenames will be [--statistics-file- 106s basename].[--alternate-bases]?.tombo.stats 106s 106s Comparison Model Arguments: 106s --dna Explicitly select canonical DNA model. Default: 106s Automatically determine from FAST5s 106s --rna Explicitly select canonical RNA model. Default: 106s Automatically determine from FAST5s 106s 106s Significance Test Arguments: 106s --fishers-method-context FISHERS_METHOD_CONTEXT 106s Number of context bases up and downstream over which 106s to compute Fisher's method combined p-values. Note: 106s Not applicable for alternative model likelihood ratio 106s tests. Default: 1. 106s --minimum-test-reads MINIMUM_TEST_READS 106s Number of reads required at a position to perform 106s significance testing or contribute to model 106s estimation. Default: 1 106s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 106s P-value threshold when computing fraction of 106s significant reads at each genomic position. If two 106s values are provided, statistics between these values 106s are not considered. Default thresholds: DNA:0.15-0.5 , 106s RNA:0.05-0.4 106s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 106s Dampen fraction modified estimates for low coverage 106s sites. Two parameters are unmodified and modified 106s pseudo read counts. This is equivalent to a beta prior 106s on the fraction estimate. Set to "0 0" to disable 106s dampened fraction estimation. Default: [2, 0] 106s 106s Output Argument: 106s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 106s Base for binary files containing per-read statistics 106s from statistical testing. Filenames will be [--per- 106s read-statistics-basename].[--alternate- 106s bases]?.tombo.per_read_stats 106s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 106s Number of the most significant sites to store for 106s faster access. If a longer list of most significant 106s sites is required the list must be re-computed from 106s all batches. Very large values can increase RAM usage. 106s Default: 100000 106s 106s Multiprocessing Arguments: 106s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 106s Size of regions over which to multiprocesses statistic 106s computation. For very deep samples a smaller value is 106s recommmended in order to control memory consumption. 106s Default: 10000 106s --processes PROCESSES 106s Number of processes. Default: 1 106s 106s FAST5 Data Arguments: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 106s FAST5 subgroup(s) (under /Analyses/[--basecall- 106s group]/) containing basecalls and created within 106s [--corrected-group] containing re-squiggle results. 106s Default: ['BaseCalled_template'] 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 106s usage: tombo detect_modifications alternative_model 106s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 106s [--statistics-file-basename STATISTICS_FILE_BASENAME] 106s [--alternate-bases {dam,dcm,6mA,5mC,CpG} [{dam,dcm,6mA,5mC,CpG} ...]] 106s [--print-available-models] 106s [--dna] [--rna] 106s [--minimum-test-reads MINIMUM_TEST_READS] 106s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 106s [--standard-log-likelihood-ratio] 106s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 106s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 106s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 106s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 106s [--processes PROCESSES] 106s [--corrected-group CORRECTED_GROUP] 106s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 106s [--quiet] [--help] 106s 106s Required Argument: 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s Directories containing fast5 files. 106s --statistics-file-basename STATISTICS_FILE_BASENAME 106s File base name to save base by base statistics from 106s testing. Filenames will be [--statistics-file- 106s basename].[--alternate-bases]?.tombo.stats 106s --alternate-bases {dam,dcm,6mA,5mC,CpG} [{dam,dcm,6mA,5mC,CpG} ...] 106s Default non-standard base model for testing (not 106s required if user created --alternate-model-filenames 106s is provided). 106s 106s Comparison Arguments: 106s --print-available-models 106s Print available alternative models and exit. 106s --dna Explicitly select canonical DNA model. Default: 106s Automatically determine from FAST5s 106s --rna Explicitly select canonical RNA model. Default: 106s Automatically determine from FAST5s 106s 106s Significance Test Arguments: 106s --minimum-test-reads MINIMUM_TEST_READS 106s Number of reads required at a position to perform 106s significance testing or contribute to model 106s estimation. Default: 1 106s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 106s Log likelihood ratio threshold when computing fraction 106s of significant reads at each genomic position. If two 106s values are provided, statistics between these values 106s are not considered. Default thresholds: DNA:-1.5-2.5 , 106s RNA:-2.5-2.5 106s --standard-log-likelihood-ratio 106s Use a standard log likelihood ratio (LLR) statistic. 106s Default is to use an outlier-robust LLR-like 106s statistic. Detail in full online documentation. 106s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 106s Dampen fraction modified estimates for low coverage 106s sites. Two parameters are unmodified and modified 106s pseudo read counts. This is equivalent to a beta prior 106s on the fraction estimate. Set to "0 0" to disable 106s dampened fraction estimation. Default: [2, 0] 106s 106s Output Argument: 106s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 106s Base for binary files containing per-read statistics 106s from statistical testing. Filenames will be [--per- 106s read-statistics-basename].[--alternate- 106s bases]?.tombo.per_read_stats 106s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 106s Number of the most significant sites to store for 106s faster access. If a longer list of most significant 106s sites is required the list must be re-computed from 106s all batches. Very large values can increase RAM usage. 106s Default: 100000 106s 106s Multiprocessing Arguments: 106s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 106s Size of regions over which to multiprocesses statistic 106s computation. For very deep samples a smaller value is 106s recommmended in order to control memory consumption. 106s Default: 10000 106s --processes PROCESSES 106s Number of processes. Default: 1 106s 106s FAST5 Data Arguments: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 106s FAST5 subgroup(s) (under /Analyses/[--basecall- 106s group]/) containing basecalls and created within 106s [--corrected-group] containing re-squiggle results. 106s Default: ['BaseCalled_template'] 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 106s usage: tombo detect_modifications model_sample_compare 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s --statistics-file-basename STATISTICS_FILE_BASENAME 106s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 106s [--sample-only-estimates] 106s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 106s [--dna] [--rna] 106s [--fishers-method-context FISHERS_METHOD_CONTEXT] 106s [--minimum-test-reads MINIMUM_TEST_READS] 106s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 106s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 106s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 106s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 106s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 106s [--processes PROCESSES] 106s [--corrected-group CORRECTED_GROUP] 106s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 106s [--quiet] [--help] 106s 106s Required Argument: 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s Directories containing fast5 files. 106s --statistics-file-basename STATISTICS_FILE_BASENAME 106s File base name to save base by base statistics from 106s testing. Filenames will be [--statistics-file- 106s basename].[--alternate-bases]?.tombo.stats 106s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 106s Set of directories containing fast5 files for control 106s reads, containing only canonical nucleotides. 106s 106s Model Prior Arguments: 106s --sample-only-estimates 106s Only use canonical sample to estimate expected signal 106s level and spread. Default: Use canonical model to 106s improve estimtates (esp. for low coverage regions) 106s using baysian posterior estimates. 106s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 106s Prior weights (one each for mean and spread) applied 106s to canonical base model for estimating posterior model 106s parameters for sample comparison. Default: [5, 40] 106s --dna Explicitly select canonical DNA model. Default: 106s Automatically determine from FAST5s 106s --rna Explicitly select canonical RNA model. Default: 106s Automatically determine from FAST5s 106s 106s Significance Test Arguments: 106s --fishers-method-context FISHERS_METHOD_CONTEXT 106s Number of context bases up and downstream over which 106s to compute Fisher's method combined p-values. Note: 106s Not applicable for alternative model likelihood ratio 106s tests. Default: 1. 106s --minimum-test-reads MINIMUM_TEST_READS 106s Number of reads required at a position to perform 106s significance testing or contribute to model 106s estimation. Default: 1 106s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 106s P-value threshold when computing fraction of 106s significant reads at each genomic position. If two 106s values are provided, statistics between these values 106s are not considered. Default thresholds: DNA:0.15-0.5 , 106s RNA:0.05-0.4 106s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 106s Dampen fraction modified estimates for low coverage 106s sites. Two parameters are unmodified and modified 106s pseudo read counts. This is equivalent to a beta prior 106s on the fraction estimate. Set to "0 0" to disable 106s dampened fraction estimation. Default: [2, 0] 106s 106s Output Argument: 106s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 106s Base for binary files containing per-read statistics 106s from statistical testing. Filenames will be [--per- 106s read-statistics-basename].[--alternate- 106s bases]?.tombo.per_read_stats 106s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 106s Number of the most significant sites to store for 106s faster access. If a longer list of most significant 106s sites is required the list must be re-computed from 106s all batches. Very large values can increase RAM usage. 106s Default: 100000 106s 106s Multiprocessing Arguments: 106s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 106s Size of regions over which to multiprocesses statistic 106s computation. For very deep samples a smaller value is 106s recommmended in order to control memory consumption. 106s Default: 10000 106s --processes PROCESSES 106s Number of processes. Default: 1 106s 106s FAST5 Data Arguments: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 106s FAST5 subgroup(s) (under /Analyses/[--basecall- 106s group]/) containing basecalls and created within 106s [--corrected-group] containing re-squiggle results. 106s Default: ['BaseCalled_template'] 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 106s usage: tombo detect_modifications level_sample_compare 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s --statistics-file-basename STATISTICS_FILE_BASENAME 106s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 106s [--fishers-method-context FISHERS_METHOD_CONTEXT] 106s [--minimum-test-reads MINIMUM_TEST_READS] 106s [--statistic-type {ks,u,t}] 106s [--store-p-value] 106s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 106s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 106s [--processes PROCESSES] 106s [--corrected-group CORRECTED_GROUP] 106s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 106s [--quiet] [--help] 106s 106s Required Argument: 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s Directories containing fast5 files. 106s --statistics-file-basename STATISTICS_FILE_BASENAME 106s File base name to save base by base statistics from 106s testing. Filenames will be [--statistics-file- 106s basename].[--alternate-bases]?.tombo.stats 106s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 106s Set of directories containing fast5 files for 106s alternate set of reads. 106s 106s Significance Test Arguments: 106s --fishers-method-context FISHERS_METHOD_CONTEXT 106s Number of context bases up and downstream over which 106s to compute Fisher's method combined p-values. Note: 106s Not applicable for alternative model likelihood ratio 106s tests. Default: 1. 106s --minimum-test-reads MINIMUM_TEST_READS 106s Number of reads required at a position to perform 106s significance testing or contribute to model 106s estimation. Default: 50 106s --statistic-type {ks,u,t} 106s Type of statistical test to apply. Default: "ks" 106s --store-p-value Store p-value instead of effect-size statistic. 106s Statistics are D-statistic (KS-test), deviation from 106s even common language effect size (u-test), and Cohen's 106s D (t-test). 106s 106s Output Argument: 106s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 106s Number of the most significant sites to store for 106s faster access. If a longer list of most significant 106s sites is required the list must be re-computed from 106s all batches. Very large values can increase RAM usage. 106s Default: 100000 106s 106s Multiprocessing Arguments: 106s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 106s Size of regions over which to multiprocesses statistic 106s computation. For very deep samples a smaller value is 106s recommmended in order to control memory consumption. 106s Default: 10000 106s --processes PROCESSES 106s Number of processes. Default: 1 106s 106s FAST5 Data Arguments: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 106s FAST5 subgroup(s) (under /Analyses/[--basecall- 106s group]/) containing basecalls and created within 106s [--corrected-group] containing re-squiggle results. 106s Default: ['BaseCalled_template'] 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 106s usage: tombo detect_modifications aggregate_per_read_stats 106s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 106s --statistics-filename STATISTICS_FILENAME 106s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 106s [--minimum-test-reads MINIMUM_TEST_READS] 106s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 106s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 106s [--processes PROCESSES] 106s [--corrected-group CORRECTED_GROUP] 106s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 106s [--quiet] [--help] 106s 106s Required Argument: 106s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 106s Binary file containing per-read statistics from 106s statistical testing. 106s --statistics-filename STATISTICS_FILENAME 106s File to save/load genomic base anchored statistics. 106s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 106s P-value or log likelihood ratio threshold when 106s computing fraction of significant reads at each 106s genomic position. If two values are provided, 106s statistics between these values are not considered. 106s 106s Significance Test Arguments: 106s --minimum-test-reads MINIMUM_TEST_READS 106s Number of reads required at a position to perform 106s significance testing or contribute to model 106s estimation. Default: 1 106s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 106s Dampen fraction modified estimates for low coverage 106s sites. Two parameters are unmodified and modified 106s pseudo read counts. This is equivalent to a beta prior 106s on the fraction estimate. Set to "0 0" to disable 106s dampened fraction estimation. Default: [2, 0] 106s 106s Output Argument: 106s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 106s Number of the most significant sites to store for 106s faster access. If a longer list of most significant 106s sites is required the list must be re-computed from 106s all batches. Very large values can increase RAM usage. 106s Default: 100000 106s 106s Multiprocessing Arguments: 106s --processes PROCESSES 106s Number of processes. Default: 1 106s 106s FAST5 Data Arguments: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 106s FAST5 subgroup(s) (under /Analyses/[--basecall- 106s group]/) containing basecalls and created within 106s [--corrected-group] containing re-squiggle results. 106s Default: ['BaseCalled_template'] 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 106s usage: tombo text_output browser_files 106s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 106s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 106s [--statistics-filename STATISTICS_FILENAME] 106s [--genome-fasta GENOME_FASTA] 106s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 106s [--browser-file-basename BROWSER_FILE_BASENAME] 106s [--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} ...]] 106s [--corrected-group CORRECTED_GROUP] 106s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 106s [--quiet] [--help] 106s 106s Data Arguments: 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s Directories containing fast5 files. 106s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 106s Set of directories containing fast5 files for control 106s reads, containing only canonical nucleotides. 106s --statistics-filename STATISTICS_FILENAME 106s File to save/load genomic base anchored statistics. 106s 106s Statistic Motif Filter Arguments: 106s --genome-fasta GENOME_FASTA 106s FASTA file used to re-squiggle. For faster sequence 106s access. 106s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 106s Ground truth, motif centered, modified base 106s descriptions for output filtering. Format descriptions 106s as: "motif:mod_pos:name". The mod_pos indicates the 106s modified base within the motif (1-based index). 106s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 106s output for identification of E. coli dam and dcm 106s methylation. 106s 106s Output Arguments: 106s --browser-file-basename BROWSER_FILE_BASENAME 106s Basename for output browser files. Two files (plus and 106s minus strand) will be produced for each --file-types 106s supplied. Filenames formatted as "[browser-file- 106s basename].[file- 106s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 106s Default: tombo_results 106s --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} ...] 106s Data types of genome browser files to produce. 106s Produced coverage files are in bedGraph format, while 106s all other file types will be in wiggle format 106s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 106s Default: "coverage" 106s 106s FAST5 Data Arguments: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 106s FAST5 subgroup(s) (under /Analyses/[--basecall- 106s group]/) containing basecalls and created within 106s [--corrected-group] containing re-squiggle results. 106s Default: ['BaseCalled_template'] 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 106s usage: tombo text_output signif_sequence_context 106s --statistics-filename STATISTICS_FILENAME 106s [--genome-fasta GENOME_FASTA] 106s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 106s [--num-regions NUM_REGIONS] 106s [--num-bases NUM_BASES] 106s [--sequences-filename SEQUENCES_FILENAME] 106s [--corrected-group CORRECTED_GROUP] 106s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 106s [--quiet] [--help] 106s 106s Required Argument: 106s --statistics-filename STATISTICS_FILENAME 106s File to save/load genomic base anchored statistics. 106s 106s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 106s --genome-fasta GENOME_FASTA 106s FASTA file used to re-squiggle. For faster sequence 106s access. 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s Directories containing fast5 files. 106s 106s Region Selection Arguments: 106s --num-regions NUM_REGIONS 106s Number of regions to plot. Default: 100 106s --num-bases NUM_BASES 106s Number of bases to plot/output. Default: 15 106s 106s Output Arguments: 106s --sequences-filename SEQUENCES_FILENAME 106s File for sequences from selected regions. Sequences 106s will be stored in FASTA format. Default: 106s tombo_results.significant_regions.fasta. 106s 106s FAST5 Data Arguments: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 106s FAST5 subgroup(s) (under /Analyses/[--basecall- 106s group]/) containing basecalls and created within 106s [--corrected-group] containing re-squiggle results. 106s Default: ['BaseCalled_template'] 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 106s usage: tombo plot max_coverage 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 106s [--plot-standard-model] 106s [--plot-alternate-model {dcm,6mA,dam,CpG,5mC}] 106s [--overplot-threshold OVERPLOT_THRESHOLD] 106s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 106s [--num-regions NUM_REGIONS] 106s [--num-bases NUM_BASES] 106s [--pdf-filename PDF_FILENAME] 106s [--corrected-group CORRECTED_GROUP] 106s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 106s [--quiet] [--help] 106s 106s Required Argument: 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s Directories containing fast5 files. 106s 106s Comparison Arguments: 106s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 106s Set of directories containing fast5 files for control 106s reads, containing only canonical nucleotides. 106s --plot-standard-model 106s Add default standard model distribution to the plot. 106s --plot-alternate-model {dcm,6mA,dam,CpG,5mC} 106s Add alternative model distribution to the plot. 106s 106s Overplotting Arguments: 106s --overplot-threshold OVERPLOT_THRESHOLD 106s Coverage level to trigger alternative plot type 106s instead of raw signal. Default: 50 106s --overplot-type {Downsample,Boxplot,Quantile,Density} 106s Plot type for regions with higher coverage. Default: 106s Downsample 106s 106s Plotting Region Arguments: 106s --num-regions NUM_REGIONS 106s Number of regions to plot. Default: 10 106s --num-bases NUM_BASES 106s Number of bases to plot/output. Default: 21 106s 106s Output Argument: 106s --pdf-filename PDF_FILENAME 106s PDF filename to store plot(s). Default: 106s tombo_results.max_coverage.pdf 106s 106s FAST5 Data Arguments: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 106s FAST5 subgroup(s) (under /Analyses/[--basecall- 106s group]/) containing basecalls and created within 106s [--corrected-group] containing re-squiggle results. 106s Default: ['BaseCalled_template'] 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 106s usage: tombo plot genome_locations 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 106s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 106s [--plot-standard-model] 106s [--plot-alternate-model {dam,5mC,6mA,dcm,CpG}] 106s [--overplot-threshold OVERPLOT_THRESHOLD] 106s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 106s [--num-bases NUM_BASES] 106s [--pdf-filename PDF_FILENAME] 106s [--corrected-group CORRECTED_GROUP] 106s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 106s [--quiet] [--help] 106s 106s Required Arguments: 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s Directories containing fast5 files. 106s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 106s Genomic locations at which to plot signal. Format 106s locations as "chrm:position[:strand] 106s [chrm2:position2[:strand2] ...]" (strand not 106s applicable for all applications) 106s 106s Comparison Arguments: 106s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 106s Set of directories containing fast5 files for control 106s reads, containing only canonical nucleotides. 106s --plot-standard-model 106s Add default standard model distribution to the plot. 106s --plot-alternate-model {dam,5mC,6mA,dcm,CpG} 106s Add alternative model distribution to the plot. 106s 106s Overplotting Arguments: 106s --overplot-threshold OVERPLOT_THRESHOLD 106s Coverage level to trigger alternative plot type 106s instead of raw signal. Default: 50 106s --overplot-type {Downsample,Boxplot,Quantile,Density} 106s Plot type for regions with higher coverage. Default: 106s Downsample 106s 106s Plotting Region Argument: 106s --num-bases NUM_BASES 106s Number of bases to plot/output. Default: 21 106s 106s Output Argument: 106s --pdf-filename PDF_FILENAME 106s PDF filename to store plot(s). Default: 106s tombo_results.genome_locations.pdf 106s 106s FAST5 Data Arguments: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 106s FAST5 subgroup(s) (under /Analyses/[--basecall- 106s group]/) containing basecalls and created within 106s [--corrected-group] containing re-squiggle results. 106s Default: ['BaseCalled_template'] 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 106s usage: tombo plot motif_centered 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s --motif MOTIF --genome-fasta GENOME_FASTA 106s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 106s [--plot-standard-model] 106s [--plot-alternate-model {dcm,dam,5mC,CpG,6mA}] 106s [--overplot-threshold OVERPLOT_THRESHOLD] 106s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 106s [--num-regions NUM_REGIONS] 106s [--num-bases NUM_BASES] [--deepest-coverage] 106s [--pdf-filename PDF_FILENAME] 106s [--corrected-group CORRECTED_GROUP] 106s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 106s [--quiet] [--help] 106s 106s Required Arguments: 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s Directories containing fast5 files. 106s --motif MOTIF Motif of interest at which to plot signal and 106s statsitics. Supports IUPAC single letter codes (use T 106s for RNA). 106s --genome-fasta GENOME_FASTA 106s FASTA file used to re-squiggle. For faster sequence 106s access. 106s 106s Comparison Arguments: 106s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 106s Set of directories containing fast5 files for control 106s reads, containing only canonical nucleotides. 106s --plot-standard-model 106s Add default standard model distribution to the plot. 106s --plot-alternate-model {dcm,dam,5mC,CpG,6mA} 106s Add alternative model distribution to the plot. 106s 106s Overplotting Arguments: 106s --overplot-threshold OVERPLOT_THRESHOLD 106s Coverage level to trigger alternative plot type 106s instead of raw signal. Default: 50 106s --overplot-type {Downsample,Boxplot,Quantile,Density} 106s Plot type for regions with higher coverage. Default: 106s Downsample 106s 106s Plotting Region Arguments: 106s --num-regions NUM_REGIONS 106s Number of regions to plot. Default: 10 106s --num-bases NUM_BASES 106s Number of bases to plot/output. Default: 21 106s --deepest-coverage Plot the deepest coverage regions. 106s 106s Output Argument: 106s --pdf-filename PDF_FILENAME 106s PDF filename to store plot(s). Default: 106s tombo_results.motif_centered.pdf 106s 106s FAST5 Data Arguments: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 106s FAST5 subgroup(s) (under /Analyses/[--basecall- 106s group]/) containing basecalls and created within 106s [--corrected-group] containing re-squiggle results. 106s Default: ['BaseCalled_template'] 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 106s usage: tombo plot max_difference 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 106s [--overplot-threshold OVERPLOT_THRESHOLD] 106s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 106s [--num-regions NUM_REGIONS] 106s [--num-bases NUM_BASES] 106s [--pdf-filename PDF_FILENAME] 106s [--sequences-filename SEQUENCES_FILENAME] 106s [--corrected-group CORRECTED_GROUP] 106s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 106s [--quiet] [--help] 106s 106s Required Arguments: 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s Directories containing fast5 files. 106s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 106s Set of directories containing fast5 files for control 106s reads, containing only canonical nucleotides. 106s 106s Overplotting Arguments: 106s --overplot-threshold OVERPLOT_THRESHOLD 106s Coverage level to trigger alternative plot type 106s instead of raw signal. Default: 50 106s --overplot-type {Downsample,Boxplot,Quantile,Density} 106s Plot type for regions with higher coverage. Default: 106s Downsample 106s 106s Plotting Region Arguments: 106s --num-regions NUM_REGIONS 106s Number of regions to plot. Default: 10 106s --num-bases NUM_BASES 106s Number of bases to plot/output. Default: 21 106s 106s Output Arguments: 106s --pdf-filename PDF_FILENAME 106s PDF filename to store plot(s). Default: 106s tombo_results.max_difference.pdf 106s --sequences-filename SEQUENCES_FILENAME 106s File for sequences from selected regions. Sequences 106s will be stored in FASTA format. Default: None. 106s 106s FAST5 Data Arguments: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 106s FAST5 subgroup(s) (under /Analyses/[--basecall- 106s group]/) containing basecalls and created within 106s [--corrected-group] containing re-squiggle results. 106s Default: ['BaseCalled_template'] 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 106s usage: tombo plot most_significant 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s --statistics-filename STATISTICS_FILENAME 106s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 106s [--plot-standard-model] 106s [--plot-alternate-model {6mA,CpG,dcm,5mC,dam}] 106s [--overplot-threshold OVERPLOT_THRESHOLD] 106s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 106s [--num-regions NUM_REGIONS] 106s [--num-bases NUM_BASES] 106s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 106s [--pdf-filename PDF_FILENAME] 106s [--sequences-filename SEQUENCES_FILENAME] 106s [--corrected-group CORRECTED_GROUP] 106s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 106s [--quiet] [--help] 106s 106s Required Arguments: 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s Directories containing fast5 files. 106s --statistics-filename STATISTICS_FILENAME 106s File to save/load genomic base anchored statistics. 106s 106s Comparison Arguments: 106s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 106s Set of directories containing fast5 files for control 106s reads, containing only canonical nucleotides. 106s --plot-standard-model 106s Add default standard model distribution to the plot. 106s --plot-alternate-model {6mA,CpG,dcm,5mC,dam} 106s Add alternative model distribution to the plot. 106s 106s Overplotting Arguments: 106s --overplot-threshold OVERPLOT_THRESHOLD 106s Coverage level to trigger alternative plot type 106s instead of raw signal. Default: 50 106s --overplot-type {Downsample,Boxplot,Quantile,Density} 106s Plot type for regions with higher coverage. Default: 106s Downsample 106s 106s Plotting Region Arguments: 106s --num-regions NUM_REGIONS 106s Number of regions to plot. Default: 10 106s --num-bases NUM_BASES 106s Number of bases to plot/output. Default: 21 106s 106s Statistical Argument: 106s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 106s Dampen fraction modified estimates for low coverage 106s sites. Two parameters are unmodified and modified 106s pseudo read counts. This is equivalent to a beta prior 106s on the fraction estimate. Set to "0 0" to disable 106s dampened fraction estimation. Default: [2, 0] 106s 106s Output Arguments: 106s --pdf-filename PDF_FILENAME 106s PDF filename to store plot(s). Default: 106s tombo_results.significant_difference.pdf 106s --sequences-filename SEQUENCES_FILENAME 106s File for sequences from selected regions. Sequences 106s will be stored in FASTA format. Default: None. 106s 106s FAST5 Data Arguments: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 106s FAST5 subgroup(s) (under /Analyses/[--basecall- 106s group]/) containing basecalls and created within 106s [--corrected-group] containing re-squiggle results. 106s Default: ['BaseCalled_template'] 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 106s usage: tombo plot motif_with_stats 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s --motif MOTIF 106s --statistics-filename STATISTICS_FILENAME 106s --genome-fasta GENOME_FASTA 106s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 106s [--plot-standard-model] 106s [--plot-alternate-model {dcm,CpG,6mA,5mC,dam}] 106s [--overplot-threshold OVERPLOT_THRESHOLD] 106s [--num-regions NUM_REGIONS] 106s [--num-context NUM_CONTEXT] 106s [--num-statistics NUM_STATISTICS] 106s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 106s [--pdf-filename PDF_FILENAME] 106s [--corrected-group CORRECTED_GROUP] 106s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 106s [--quiet] [--help] 106s 106s Required Arguments: 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s Directories containing fast5 files. 106s --motif MOTIF Motif of interest at which to plot signal and 106s statsitics. Supports IUPAC single letter codes (use T 106s for RNA). 106s --statistics-filename STATISTICS_FILENAME 106s File to save/load genomic base anchored statistics. 106s --genome-fasta GENOME_FASTA 106s FASTA file used to re-squiggle. For faster sequence 106s access. 106s 106s Comparison Arguments: 106s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 106s Set of directories containing fast5 files for control 106s reads, containing only canonical nucleotides. 106s --plot-standard-model 106s Add default standard model distribution to the plot. 106s --plot-alternate-model {dcm,CpG,6mA,5mC,dam} 106s Add alternative model distribution to the plot. 106s 106s Overplotting Argument: 106s --overplot-threshold OVERPLOT_THRESHOLD 106s Coverage level to trigger alternative plot type 106s instead of raw signal. Default: 50 106s 106s Plotting Region Arguments: 106s --num-regions NUM_REGIONS 106s Number of regions to plot. Default: 3 106s --num-context NUM_CONTEXT 106s Number of context bases around motif. Default: 5 106s --num-statistics NUM_STATISTICS 106s Number of motif centered regions to include in 106s statistic distributions. Default: 200 106s 106s Statistical Argument: 106s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 106s Dampen fraction modified estimates for low coverage 106s sites. Two parameters are unmodified and modified 106s pseudo read counts. This is equivalent to a beta prior 106s on the fraction estimate. Set to "0 0" to disable 106s dampened fraction estimation. Default: [2, 0] 106s 106s Output Argument: 106s --pdf-filename PDF_FILENAME 106s PDF filename to store plot(s). Default: 106s tombo_results.motif_statistics.pdf 106s 106s FAST5 Data Arguments: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 106s FAST5 subgroup(s) (under /Analyses/[--basecall- 106s group]/) containing basecalls and created within 106s [--corrected-group] containing re-squiggle results. 106s Default: ['BaseCalled_template'] 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 106s usage: tombo plot per_read 106s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 106s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 106s [--genome-fasta GENOME_FASTA] 106s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 106s [--num-reads NUM_READS] [--num-bases NUM_BASES] 106s [--box-center] [--pdf-filename PDF_FILENAME] 106s [--corrected-group CORRECTED_GROUP] 106s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 106s [--quiet] [--help] 106s 106s Required Arguments: 106s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 106s Genomic locations at which to plot signal. Format 106s locations as "chrm:position[:strand] 106s [chrm2:position2[:strand2] ...]" (strand not 106s applicable for all applications) 106s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 106s Binary file containing per-read statistics from 106s statistical testing. 106s 106s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 106s --genome-fasta GENOME_FASTA 106s FASTA file used to re-squiggle. For faster sequence 106s access. 106s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 106s Directories containing fast5 files. 106s 106s Plotting Region Arguments: 106s --num-reads NUM_READS 106s Number of reads to plot. Default: 100 106s --num-bases NUM_BASES 106s Number of bases to plot/output. Default: 51 106s --box-center Plot a box around the central base. 106s 106s Output Argument: 106s --pdf-filename PDF_FILENAME 106s PDF filename to store plot(s). Default: 106s tombo_results.per_read_stats.pdf 106s 106s FAST5 Data Arguments: 106s --corrected-group CORRECTED_GROUP 106s FAST5 group created by resquiggle command. Default: 106s RawGenomeCorrected_000 106s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 106s FAST5 subgroup(s) (under /Analyses/[--basecall- 106s group]/) containing basecalls and created within 106s [--corrected-group] containing re-squiggle results. 106s Default: ['BaseCalled_template'] 106s 106s Miscellaneous Arguments: 106s --quiet, -q Don't print status information. 106s --help, -h Print this help message and exit 107s usage: tombo plot roc 107s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 107s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 107s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 107s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 107s [--genome-fasta GENOME_FASTA] 107s [--pdf-filename PDF_FILENAME] 107s [--statistics-per-block STATISTICS_PER_BLOCK] 107s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 107s [--quiet] [--help] 107s 107s Required Argument: 107s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 107s Files to load genomic base anchored statistics. 107s 107s Ground Truth Arguments (provide bed files or motifs): 107s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 107s Modification description and bed format files 107s containing single base locations of ground truth 107s modified sites. Bed files should contain 6 fields 107s including strand. Format descriptions as 107s "mod_name:locs.bed". Example: "CpG 107s bisulfite":bisulfite_locs.bed 107s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 107s Bed format files containing single base locations of 107s ground truth unmodified sites. Bed files should 107s contain 6 fields including strand. 107s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 107s Ground truth, motif centered, modified base 107s descriptions for computing ROC and PR curves. Each 107s statistics file is associated with a set of motif 107s descriptions. Format descriptions as: 107s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 107s mod_pos indicates the alternate-base within the motif 107s (1-based index). Example: CCWGG:2:"dcm 107s 5mC"::GATC:2:"dam 6mA" would assess the performance of 107s a single Tombo statistics file for identification of 107s E. coli dam and dcm methylation. 107s --genome-fasta GENOME_FASTA 107s FASTA file used to re-squiggle. For faster sequence 107s access. 107s 107s Output Arguments: 107s --pdf-filename PDF_FILENAME 107s PDF filename to store plot(s). Default: 107s tombo_results.roc.pdf 107s 107s Down-sampling Arguments: 107s --statistics-per-block STATISTICS_PER_BLOCK 107s Number of randomly selected per-read, per-base 107s statistics to extract from each genomic block for 107s plotting. Default: Include all stats 107s --total-statistics-limit TOTAL_STATISTICS_LIMIT 107s Total per-read statistics to be extracted for 107s plotting. Avoids memory overflow for large runs. 107s Default: 5000000 107s 107s Miscellaneous Arguments: 107s --quiet, -q Don't print status information. 107s --help, -h Print this help message and exit 107s usage: tombo plot per_read_roc 107s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 107s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 107s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 107s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 107s [--genome-fasta GENOME_FASTA] 107s [--statistics-per-block STATISTICS_PER_BLOCK] 107s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 107s [--pdf-filename PDF_FILENAME] [--quiet] 107s [--help] 107s 107s Required Argument: 107s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 107s Binary files containing per-read statistics from 107s statistical testing. 107s 107s Ground Truth Arguments (provide bed files or motifs): 107s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 107s Modification description and bed format files 107s containing single base locations of ground truth 107s modified sites. Bed files should contain 6 fields 107s including strand. Format descriptions as 107s "mod_name:locs.bed". Example: "CpG 107s bisulfite":bisulfite_locs.bed 107s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 107s Bed format files containing single base locations of 107s ground truth unmodified sites. Bed files should 107s contain 6 fields including strand. 107s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 107s Ground truth, motif centered, modified base 107s descriptions for computing ROC and PR curves. Each 107s statistics file is associated with a set of motif 107s descriptions. Format descriptions as: 107s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 107s mod_pos indicates the alternate-base within the motif 107s (1-based index). Example: CCWGG:2:"dcm 107s 5mC"::GATC:2:"dam 6mA" would assess the performance of 107s a single Tombo statistics file for identification of 107s E. coli dam and dcm methylation. 107s --genome-fasta GENOME_FASTA 107s FASTA file used to re-squiggle. For faster sequence 107s access. 107s 107s Down-sampling Arguments: 107s --statistics-per-block STATISTICS_PER_BLOCK 107s Number of randomly selected per-read, per-base 107s statistics to extract from each genomic block for 107s plotting. Default: 100000 107s --total-statistics-limit TOTAL_STATISTICS_LIMIT 107s Total per-read statistics to be extracted for 107s plotting. Avoids memory overflow for large runs. 107s Default: 5000000 107s 107s Output Arguments: 107s --pdf-filename PDF_FILENAME 107s PDF filename to store plot(s). Default: 107s tombo_results.per_reads_roc.pdf 107s 107s Miscellaneous Arguments: 107s --quiet, -q Don't print status information. 107s --help, -h Print this help message and exit 107s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 107s [--upstream-bases {0,1,2,3,4}] 107s [--downstream-bases {0,1,2,3,4}] [--read-mean] 107s [--num-kmer-threshold NUM_KMER_THRESHOLD] 107s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 107s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 107s [--corrected-group CORRECTED_GROUP] 107s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 107s [--quiet] [--help] 107s 107s Required Argument: 107s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 107s Directories containing fast5 files. 107s 107s Data Processing Arguments: 107s --upstream-bases {0,1,2,3,4} 107s Upstream bases in k-mer. Default: 1 107s --downstream-bases {0,1,2,3,4} 107s Downstream bases in k-mer. Default: 2 107s --read-mean Plot k-mer means across whole reads as opposed to 107s individual k-mer event levels. 107s --num-kmer-threshold NUM_KMER_THRESHOLD 107s Observations of each k-mer required to include a read 107s in read level averages. Default: 1 107s 107s Plotting Region Arguments: 107s --num-reads NUM_READS 107s Number of reads to plot. Default: 100 107s 107s Output Arguments: 107s --pdf-filename PDF_FILENAME 107s PDF filename to store plot(s). Default: 107s tombo_results.kmer_distribution.pdf 107s --r-data-filename R_DATA_FILENAME 107s Filename to save R data structure. Default: Don't save 107s --dont-plot Don't plot result. Useful to produce only R data file. 107s 107s FAST5 Data Arguments: 107s --corrected-group CORRECTED_GROUP 107s FAST5 group created by resquiggle command. Default: 107s RawGenomeCorrected_000 107s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 107s FAST5 subgroup(s) (under /Analyses/[--basecall- 107s group]/) containing basecalls and created within 107s [--corrected-group] containing re-squiggle results. 107s Default: ['BaseCalled_template'] 107s 107s Miscellaneous Arguments: 107s --quiet, -q Don't print status information. 107s --help, -h Print this help message and exit 107s usage: tombo plot cluster_most_significant 107s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 107s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 107s --statistics-filename STATISTICS_FILENAME 107s [--genome-fasta GENOME_FASTA] 107s [--processes PROCESSES] 107s [--num-regions NUM_REGIONS] 107s [--num-bases NUM_BASES] 107s [--slide-span SLIDE_SPAN] 107s [--pdf-filename PDF_FILENAME] 107s [--r-data-filename R_DATA_FILENAME] 107s [--corrected-group CORRECTED_GROUP] 107s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 107s [--quiet] [--help] 107s 107s Required Arguments: 107s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 107s Directories containing fast5 files. 107s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 107s Set of directories containing fast5 files for control 107s reads, containing only canonical nucleotides. 107s --statistics-filename STATISTICS_FILENAME 107s File to save/load genomic base anchored statistics. 107s 107s FASTA Sequence Argument: 107s --genome-fasta GENOME_FASTA 107s FASTA file used to re-squiggle. For faster sequence 107s access. 107s 107s Multiprocessing Argument: 107s --processes PROCESSES 107s Number of processes. Default: 1 107s 107s Plotting Region Arguments: 107s --num-regions NUM_REGIONS 107s Number of regions to plot. Default: 10 107s --num-bases NUM_BASES 107s Number of bases to plot/output. Default: 21 107s --slide-span SLIDE_SPAN 107s Number of bases offset over which to search when 107s computing distances for signal cluster plotting. 107s Default: 0 (exact position) 107s 107s Output Arguments: 107s --pdf-filename PDF_FILENAME 107s PDF filename to store plot(s). Default: 107s tombo_results.signal_clusters.pdf 107s --r-data-filename R_DATA_FILENAME 107s Filename to save R data structure. Default: Don't save 107s 107s FAST5 Data Arguments: 107s --corrected-group CORRECTED_GROUP 107s FAST5 group created by resquiggle command. Default: 107s RawGenomeCorrected_000 107s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 107s FAST5 subgroup(s) (under /Analyses/[--basecall- 107s group]/) containing basecalls and created within 107s [--corrected-group] containing re-squiggle results. 107s Default: ['BaseCalled_template'] 107s 107s Miscellaneous Arguments: 107s --quiet, -q Don't print status information. 107s --help, -h Print this help message and exit 107s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 107s 107s Required Arguments: 107s fast5s_basedir Directory containing fast5 files. All files ending in 107s "fast5" found recursively within this base directory will be 107s processed. 107s 107s Miscellaneous Arguments: 107s --quiet, -q Don't print status information. 107s --help, -h Print this help message and exit 107s usage: tombo build_model event_resquiggle 107s [--minimap2-executable MINIMAP2_EXECUTABLE] 107s [--minimap2-index MINIMAP2_INDEX] 107s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 107s [--graphmap-executable GRAPHMAP_EXECUTABLE] 107s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 107s [--normalization-type {median,pA,pA_raw,none}] 107s [--pore-model-filename PORE_MODEL_FILENAME] 107s [--outlier-threshold OUTLIER_THRESHOLD] 107s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 107s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 107s [--timeout TIMEOUT] 107s [--cpts-limit CPTS_LIMIT] 107s [--skip-index] [--overwrite] 107s [--failed-reads-filename FAILED_READS_FILENAME] 107s [--include-event-stdev] 107s [--corrected-group CORRECTED_GROUP] 107s [--basecall-group BASECALL_GROUP] 107s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 107s [--processes PROCESSES] 107s [--align-processes ALIGN_PROCESSES] 107s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 107s [--resquiggle-processes RESQUIGGLE_PROCESSES] 107s [--quiet] [--help] 107s fast5s_basedir reference_fasta 107s 107s Required Arguments: 107s fast5s_basedir Directory containing fast5 files. All files ending in 107s "fast5" found recursively within this base directory 107s will be processed. 107s reference_fasta Reference genome/transcriptome FASTA file for mapping. 107s 107s Mapper Arguments (One mapper is required): 107s --minimap2-executable MINIMAP2_EXECUTABLE 107s Path to minimap2 executable. 107s --minimap2-index MINIMAP2_INDEX 107s Path to minimap2 index (with map-ont preset) file 107s corresponding to the [genome_fasta] provided. 107s --bwa-mem-executable BWA_MEM_EXECUTABLE 107s Path to bwa-mem executable. 107s --graphmap-executable GRAPHMAP_EXECUTABLE 107s Path to graphmap executable. 107s --alignment-batch-size ALIGNMENT_BATCH_SIZE 107s Number of reads included in each alignment call. Note: 107s A new system mapping call is made for each batch 107s (including loading of the genome), so it is advised to 107s use larger values for larger genomes. Default: 1000 107s 107s Signal Processing Arguments: 107s --normalization-type {median,pA,pA_raw,none} 107s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 107s as in the ONT events (using offset, range and 107s digitization), "pA": k-mer-based correction for pA 107s drift as in nanopolish (requires [--pore-model- 107s filename]), "median": median and MAD from raw signal. 107s Default: median 107s --pore-model-filename PORE_MODEL_FILENAME 107s File containing kmer model parameters (level_mean and 107s level_stdv) used in order to compute kmer-based 107s corrected pA values. E.g. https://github.com/jts/nanop 107s olish/blob/master/etc/r9- 107s models/template_median68pA.5mers.model 107s --outlier-threshold OUTLIER_THRESHOLD 107s Windosrize the signal at this number of scale values. 107s Negative value disables outlier clipping. Default: 107s 5.000000 107s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 107s Specify the 2 parameters for segmentation 1) running 107s neighboring windows width 2) minimum raw observations 107s per genomic base. Sample type defaults: RNA : 12 6 || 107s DNA : 5 3 107s 107s Read Filtering Arguments: 107s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 107s Filter reads based on observations per base percentile 107s thresholds. Format thresholds as "percentile:thresh 107s [pctl2:thresh2 ...]". For example to filter reads with 107s 99th pctl > 200 obs/base or max > 5k obs/base use 107s "99:200 100:5000". 107s --timeout TIMEOUT Timeout in seconds for processing a single read. 107s Default: No timeout. 107s --cpts-limit CPTS_LIMIT 107s Maximum number of changepoints to find within a single 107s indel group. Default: No limit. 107s 107s Input/Output Arguments: 107s --skip-index Skip creation of tombo index. This drastically slows 107s downstream tombo commands. Default stores tombo index 107s named ".[--fast5-basedir].[--corrected- 107s group].tombo.index" to be loaded automatically for 107s downstream commands. 107s --overwrite Overwrite previous corrected group in FAST5 files. 107s Note: only effects --corrected-group or --new- 107s corrected-group. 107s --failed-reads-filename FAILED_READS_FILENAME 107s Output failed read filenames with assoicated error. 107s Default: Do not store failed reads. 107s --include-event-stdev 107s Include corrected event standard deviation in output 107s FAST5 data. 107s 107s FAST5 Data Arguments: 107s --corrected-group CORRECTED_GROUP 107s FAST5 group created by resquiggle command. Default: 107s RawGenomeCorrected_000 107s --basecall-group BASECALL_GROUP 107s FAST5 group obtain original basecalls (under Analyses 107s group). Default: Basecall_1D_000 107s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 107s FAST5 subgroup(s) (under /Analyses/[--basecall- 107s group]/) containing basecalls and created within 107s [--corrected-group] containing re-squiggle results. 107s Default: ['BaseCalled_template'] 107s 107s Multiprocessing Arguments: 107s --processes PROCESSES 107s Number of processes. Default: 2 107s --align-processes ALIGN_PROCESSES 107s Number of processes to use for parsing and aligning 107s original basecalls. Each process will independently 107s load the genome into memory, so use caution with 107s larger genomes (e.g. human). Default: 1 107s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 107s Number of threads to use for aligner system call. 107s Default: [--processes] / (2 * [--align-processes)] 107s --resquiggle-processes RESQUIGGLE_PROCESSES 107s Number of processes to use for resquiggle algorithm. 107s Default: [--processes] / 2 107s 107s Miscellaneous Arguments: 107s --quiet, -q Don't print status information. 107s --help, -h Print this help message and exit 107s usage: tombo build_model estimate_reference 107s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 107s --tombo-model-filename TOMBO_MODEL_FILENAME 107s [--estimate-mean] 107s [--kmer-specific-sd] 107s [--upstream-bases {0,1,2,3,4}] 107s [--downstream-bases {0,1,2,3,4}] 107s [--minimum-test-reads MINIMUM_TEST_READS] 107s [--coverage-threshold COVERAGE_THRESHOLD] 107s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 107s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 107s [--processes PROCESSES] 107s [--corrected-group CORRECTED_GROUP] 107s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 107s [--quiet] [--help] 107s 107s Required Arguments: 107s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 107s Directories containing fast5 files. 107s --tombo-model-filename TOMBO_MODEL_FILENAME 107s Filename to save Tombo model. 107s 107s Modeling Arguments: 107s --estimate-mean Use the mean instead of median for model level 107s estimation. Note: This can cause poor fits due to 107s outliers 107s --kmer-specific-sd Estimate standard deviation for each k-mers 107s individually. 107s --upstream-bases {0,1,2,3,4} 107s Upstream bases in k-mer. Default: 1 107s --downstream-bases {0,1,2,3,4} 107s Downstream bases in k-mer. Default: 2 107s 107s Filtering Arguments: 107s --minimum-test-reads MINIMUM_TEST_READS 107s Number of reads required at a position to perform 107s significance testing or contribute to model 107s estimation. Default: 10 107s --coverage-threshold COVERAGE_THRESHOLD 107s Maximum mean coverage per region when estimating k-mer 107s model (limits compute time for deep samples). Default: 107s 100 107s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 107s Number of each k-mer observations required in order to 107s produce a reference (genomic locations for standard 107s reference and per-read for alternative reference). 107s Default: 5 107s 107s Multiprocessing Arguments: 107s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 107s Size of regions over which to multiprocesses statistic 107s computation. For very deep samples a smaller value is 107s recommmended in order to control memory consumption. 107s Default: 10000 107s --processes PROCESSES 107s Number of processes. Default: 1 107s 107s FAST5 Data Arguments: 107s --corrected-group CORRECTED_GROUP 107s FAST5 group created by resquiggle command. Default: 107s RawGenomeCorrected_000 107s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 107s FAST5 subgroup(s) (under /Analyses/[--basecall- 107s group]/) containing basecalls and created within 107s [--corrected-group] containing re-squiggle results. 107s Default: ['BaseCalled_template'] 107s 107s Miscellaneous Arguments: 107s --quiet, -q Don't print status information. 107s --help, -h Print this help message and exit 107s usage: tombo build_model estimate_alt_reference 107s --alternate-model-filename ALTERNATE_MODEL_FILENAME 107s --alternate-model-name ALTERNATE_MODEL_NAME 107s --alternate-model-base {A,C,G,T} 107s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 107s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 107s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 107s [--control-density-filename CONTROL_DENSITY_FILENAME] 107s [--dna] [--rna] 107s [--tombo-model-filename TOMBO_MODEL_FILENAME] 107s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 107s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 107s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 107s [--save-density-basename SAVE_DENSITY_BASENAME] 107s [--processes PROCESSES] 107s [--corrected-group CORRECTED_GROUP] 107s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 107s [--quiet] [--help] 107s 107s Required Arguments: 107s --alternate-model-filename ALTERNATE_MODEL_FILENAME 107s Tombo model for alternative likelihood ratio 107s significance testing. 107s --alternate-model-name ALTERNATE_MODEL_NAME 107s A short name to associate with this alternate model 107s (e.g. 5mC, 6mA, etc.). This text will be included in 107s output filenames when this model is used for testing. 107s --alternate-model-base {A,C,G,T} 107s Non-standard base is an alternative to this base. 107s 107s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 107s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 107s Directories containing fast5 files. 107s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 107s Set of directories containing fast5 files for control 107s reads, containing only canonical nucleotides. 107s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 107s File containing k-mer level kernel density estimates 107s for the alternative sample saved using --save-density- 107s basename. 107s --control-density-filename CONTROL_DENSITY_FILENAME 107s File containing k-mer level kernel density estimates 107s for the control sample saved using --save-density- 107s basename. 107s 107s Standard Model Arguments: 107s --dna Explicitly select canonical DNA model. Default: 107s Automatically determine from FAST5s 107s --rna Explicitly select canonical RNA model. Default: 107s Automatically determine from FAST5s 107s --tombo-model-filename TOMBO_MODEL_FILENAME 107s Tombo model filename. If no file is provided, the 107s default DNA or RNA Tombo model will be used. 107s 107s Model Fitting Arguments: 107s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 107s When esitmating the alternative base incorporation 107s rate, this percent of k-mers are assumed to have 107s significantly shifted signal so the alternative 107s distribution minimally overlaps the standard base 107s distribution. Default: 5.000000 107s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 107s Bandwidth applied when performing Gaussian kernal 107s density esitmation on standard and alternative base 107s signal distributions. Default: 0.050000 107s 107s Filtering Argument: 107s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 107s Number of each k-mer observations required in order to 107s produce a reference (genomic locations for standard 107s reference and per-read for alternative reference). 107s Default: 1000 107s 107s Output Argument: 107s --save-density-basename SAVE_DENSITY_BASENAME 107s Basename to save alternative model estimation density 107s estimation information. See scripts/debug_est_alt.R 107s for info use example. Default: Don't save. 107s 107s Multiprocessing Arguments: 107s --processes PROCESSES 107s Number of processes. Default: 1 107s 107s FAST5 Data Arguments: 107s --corrected-group CORRECTED_GROUP 107s FAST5 group created by resquiggle command. Default: 107s RawGenomeCorrected_000 107s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 107s FAST5 subgroup(s) (under /Analyses/[--basecall- 107s group]/) containing basecalls and created within 107s [--corrected-group] containing re-squiggle results. 107s Default: ['BaseCalled_template'] 107s 107s Miscellaneous Arguments: 107s --quiet, -q Don't print status information. 107s --help, -h Print this help message and exit 107s This test only tests the help system 107s There is an extensive test in 107s 107s tombo/tests/shell_tests.sh 107s 107s but this requires to download larger data 107s sets which is not done for the moment. 107s autopkgtest [10:49:10]: test run-unit-test: -----------------------] 108s autopkgtest [10:49:11]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 108s run-unit-test PASS 108s autopkgtest [10:49:11]: @@@@@@@@@@@@@@@@@@@@ summary 108s run-unit-test PASS