0s autopkgtest [16:37:58]: starting date and time: 2024-11-13 16:37:58+0000 0s autopkgtest [16:37:58]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:37:58]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.un69betr/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-3.secgroup --name adt-plucky-s390x-tombo-20241113-163758-juju-7f2275-prod-proposed-migration-environment-20-1daf3800-a763-46e5-a140-eba0899cb53e --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 75s autopkgtest [16:39:13]: testbed dpkg architecture: s390x 76s autopkgtest [16:39:14]: testbed apt version: 2.9.8 76s autopkgtest [16:39:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 76s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 77s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 77s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 77s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [950 kB] 77s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 77s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [110 kB] 77s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [636 kB] 77s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [17.8 kB] 77s Fetched 1916 kB in 1s (2262 kB/s) 77s Reading package lists... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s Calculating upgrade... 80s The following NEW packages will be installed: 80s python3.13-gdbm 80s The following packages will be upgraded: 80s libgnutls30t64 libgpgme11t64 libjson-glib-1.0-0 libjson-glib-1.0-common 80s libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal 80s 9 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 80s Need to get 1285 kB of archives. 80s After this operation, 103 kB of additional disk space will be used. 80s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB] 80s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB] 80s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB] 80s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgnutls30t64 s390x 3.8.8-2ubuntu1 [950 kB] 80s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB] 80s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B] 80s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB] 80s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 80s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libjson-glib-1.0-0 s390x 1.10.0+ds-3 [67.5 kB] 80s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libutempter0 s390x 1.2.1-4 [9708 B] 80s Fetched 1285 kB in 1s (2067 kB/s) 81s (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 ... 55510 files and directories currently installed.) 81s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ... 81s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 81s Setting up python3-minimal (3.12.7-1) ... 81s (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 ... 55510 files and directories currently installed.) 81s Preparing to unpack .../python3_3.12.7-1_s390x.deb ... 81s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 81s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ... 81s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ... 81s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_s390x.deb ... 81s Unpacking libgnutls30t64:s390x (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 81s Setting up libgnutls30t64:s390x (3.8.8-2ubuntu1) ... 81s Selecting previously unselected package python3.13-gdbm. 81s (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 ... 55510 files and directories currently installed.) 81s Preparing to unpack .../0-python3.13-gdbm_3.13.0-2_s390x.deb ... 81s Unpacking python3.13-gdbm (3.13.0-2) ... 81s Preparing to unpack .../1-python3-gdbm_3.12.7-1_s390x.deb ... 81s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ... 81s Preparing to unpack .../2-libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ... 81s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 81s Preparing to unpack .../3-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 81s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 81s Preparing to unpack .../4-libjson-glib-1.0-0_1.10.0+ds-3_s390x.deb ... 81s Unpacking libjson-glib-1.0-0:s390x (1.10.0+ds-3) over (1.10.0+ds-2) ... 81s Preparing to unpack .../5-libutempter0_1.2.1-4_s390x.deb ... 81s Unpacking libutempter0:s390x (1.2.1-4) over (1.2.1-3build1) ... 81s Setting up libutempter0:s390x (1.2.1-4) ... 81s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 81s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ... 81s Setting up python3.13-gdbm (3.13.0-2) ... 81s Setting up libpython3-stdlib:s390x (3.12.7-1) ... 81s Setting up python3 (3.12.7-1) ... 81s Setting up libjson-glib-1.0-0:s390x (1.10.0+ds-3) ... 81s Setting up python3-gdbm:s390x (3.12.7-1) ... 81s Processing triggers for man-db (2.12.1-3) ... 81s Processing triggers for libc-bin (2.40-1ubuntu3) ... 82s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 82s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 82s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 82s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 83s Reading package lists... 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Calculating upgrade... 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s autopkgtest [16:39:24]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 86s autopkgtest [16:39:24]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 90s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (dsc) [2291 B] 90s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (tar) [22.3 MB] 90s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (diff) [7100 B] 90s gpgv: Signature made Wed Apr 10 17:15:32 2024 UTC 90s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 90s gpgv: Can't check signature: No public key 90s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6build1.dsc: no acceptable signature found 90s autopkgtest [16:39:28]: testing package tombo version 1.5.1-6build1 90s autopkgtest [16:39:28]: build not needed 92s autopkgtest [16:39:30]: test run-unit-test: preparing testbed 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s Starting pkgProblemResolver with broken count: 0 93s Starting 2 pkgProblemResolver with broken count: 0 93s Done 93s The following additional packages will be installed: 93s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 93s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 93s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 93s python3-decorator python3-h5py python3-h5py-serial python3-mappy 93s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 93s tombo-doc 93s Suggested packages: 93s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 93s gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 93s Recommended packages: 93s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 93s python3-rpy2 93s The following NEW packages will be installed: 93s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 93s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 93s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 93s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 93s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 93s tombo-doc 93s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 93s Need to get 63.4 MB/63.4 MB of archives. 93s After this operation, 200 MB of additional disk space will be used. 93s Get:1 /tmp/autopkgtest.JrLH7T/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [712 B] 94s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-lato all 2.015-1 [2781 kB] 94s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 94s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 94s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 94s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 94s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB] 94s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 94s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-103-1t64 s390x 1.10.10+repack-4ubuntu3 [1426 kB] 94s Get:10 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-100t64 s390x 1.10.10+repack-4ubuntu3 [58.0 kB] 94s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 94s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 94s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-sphinxdoc all 7.4.7-4 [158 kB] 94s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 94s Get:15 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 94s Get:16 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B] 94s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 94s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11build1 [4113 kB] 95s Get:19 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py-serial s390x 3.11.0-5ubuntu1 [1151 kB] 95s Get:20 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py all 3.11.0-5ubuntu1 [7974 B] 95s Get:21 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mappy s390x 2.27+dfsg-1 [208 kB] 95s Get:22 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-tqdm all 4.67.0-1 [91.6 kB] 95s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 95s Get:24 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.13.1-5 [17.5 MB] 95s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x tombo s390x 1.5.1-6build1 [465 kB] 95s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 95s Get:27 http://ftpmaster.internal/ubuntu plucky/universe s390x tombo-doc all 1.5.1-6build1 [21.7 MB] 96s Fetched 63.4 MB in 3s (24.8 MB/s) 96s Selecting previously unselected package fonts-lato. 96s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 55517 files and directories currently installed.) 96s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 96s Unpacking fonts-lato (2.015-1) ... 96s Selecting previously unselected package fonts-font-awesome. 96s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 97s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 97s Selecting previously unselected package fonts-mathjax. 97s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 97s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 97s Selecting previously unselected package libaec0:s390x. 97s Preparing to unpack .../03-libaec0_1.1.3-1_s390x.deb ... 97s Unpacking libaec0:s390x (1.1.3-1) ... 97s Selecting previously unselected package libblas3:s390x. 97s Preparing to unpack .../04-libblas3_3.12.0-3build2_s390x.deb ... 97s Unpacking libblas3:s390x (3.12.0-3build2) ... 97s Selecting previously unselected package libgfortran5:s390x. 97s Preparing to unpack .../05-libgfortran5_14.2.0-8ubuntu1_s390x.deb ... 97s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ... 97s Selecting previously unselected package libsz2:s390x. 97s Preparing to unpack .../06-libsz2_1.1.3-1_s390x.deb ... 97s Unpacking libsz2:s390x (1.1.3-1) ... 97s Selecting previously unselected package libhdf5-103-1t64:s390x. 97s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_s390x.deb ... 97s Unpacking libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 97s Selecting previously unselected package libhdf5-hl-100t64:s390x. 97s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_s390x.deb ... 97s Unpacking libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ... 97s Selecting previously unselected package libjs-jquery. 97s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 97s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 97s Selecting previously unselected package libjs-underscore. 97s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 97s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 97s Selecting previously unselected package libjs-sphinxdoc. 97s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-4_all.deb ... 97s Unpacking libjs-sphinxdoc (7.4.7-4) ... 97s Selecting previously unselected package liblapack3:s390x. 97s Preparing to unpack .../12-liblapack3_3.12.0-3build2_s390x.deb ... 97s Unpacking liblapack3:s390x (3.12.0-3build2) ... 97s Selecting previously unselected package liblbfgsb0:s390x. 97s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 97s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 97s Selecting previously unselected package liblzf1:s390x. 97s Preparing to unpack .../14-liblzf1_3.6-4_s390x.deb ... 97s Unpacking liblzf1:s390x (3.6-4) ... 97s Selecting previously unselected package python3-decorator. 97s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 97s Unpacking python3-decorator (5.1.1-5) ... 97s Selecting previously unselected package python3-numpy. 97s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-11build1_s390x.deb ... 97s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 97s Selecting previously unselected package python3-h5py-serial. 97s Preparing to unpack .../17-python3-h5py-serial_3.11.0-5ubuntu1_s390x.deb ... 97s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 97s Selecting previously unselected package python3-h5py. 97s Preparing to unpack .../18-python3-h5py_3.11.0-5ubuntu1_all.deb ... 97s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 97s Selecting previously unselected package python3-mappy. 97s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1_s390x.deb ... 97s Unpacking python3-mappy (2.27+dfsg-1) ... 97s Selecting previously unselected package python3-tqdm. 97s Preparing to unpack .../20-python3-tqdm_4.67.0-1_all.deb ... 97s Unpacking python3-tqdm (4.67.0-1) ... 97s Selecting previously unselected package sphinx-rtd-theme-common. 97s Preparing to unpack .../21-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 97s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 97s Selecting previously unselected package python3-scipy. 97s Preparing to unpack .../22-python3-scipy_1.13.1-5_s390x.deb ... 97s Unpacking python3-scipy (1.13.1-5) ... 97s Selecting previously unselected package tombo. 97s Preparing to unpack .../23-tombo_1.5.1-6build1_s390x.deb ... 97s Unpacking tombo (1.5.1-6build1) ... 97s Selecting previously unselected package libjs-mathjax. 97s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 97s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 98s Selecting previously unselected package tombo-doc. 98s Preparing to unpack .../25-tombo-doc_1.5.1-6build1_all.deb ... 98s Unpacking tombo-doc (1.5.1-6build1) ... 98s Selecting previously unselected package autopkgtest-satdep. 98s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 98s Unpacking autopkgtest-satdep (0) ... 98s Setting up fonts-lato (2.015-1) ... 98s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 98s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 98s Setting up python3-tqdm (4.67.0-1) ... 98s Setting up python3-mappy (2.27+dfsg-1) ... 98s Setting up libaec0:s390x (1.1.3-1) ... 98s Setting up python3-decorator (5.1.1-5) ... 98s Setting up libblas3:s390x (3.12.0-3build2) ... 98s 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 98s Setting up liblzf1:s390x (3.6-4) ... 98s Setting up libgfortran5:s390x (14.2.0-8ubuntu1) ... 98s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 98s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 98s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 98s Setting up libsz2:s390x (1.1.3-1) ... 98s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 98s Setting up liblapack3:s390x (3.12.0-3build2) ... 98s 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 98s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 100s Setting up libjs-sphinxdoc (7.4.7-4) ... 100s Setting up tombo-doc (1.5.1-6build1) ... 100s Setting up libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 100s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 100s Setting up libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ... 100s Setting up python3-scipy (1.13.1-5) ... 104s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 104s Setting up python3-h5py (3.11.0-5ubuntu1) ... 104s Setting up tombo (1.5.1-6build1) ... 104s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 104s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 104s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 104s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 104s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 104s re.match('\+', fastq_rec[2]) is None): 104s Setting up autopkgtest-satdep (0) ... 104s Processing triggers for man-db (2.12.1-3) ... 104s Processing triggers for libc-bin (2.40-1ubuntu3) ... 106s (Reading database ... 62719 files and directories currently installed.) 106s Removing autopkgtest-satdep (0) ... 107s autopkgtest [16:39:45]: test run-unit-test: [----------------------- 107s ********* Testing help commands ********** 107s usage: tombo [-h] [-v] 107s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 107s ... 107s 107s ********** Tombo ********* 107s 107s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 107s 107s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 107s 107s Tombo command groups (additional help available within each command group): 107s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 107s preprocess Pre-process nanopore reads for Tombo processing. 107s filter Apply filter to Tombo index file for specified criterion. 107s detect_modifications Perform statistical testing to detect non-standard nucleotides. 107s text_output Output Tombo results in text files. 107s build_model Create canonical and alternative base Tombo models. 107s plot Save plots to visualize raw nanopore signal or testing results. 107s 107s options: 107s -h, --help show this help message and exit 107s -v, --version show Tombo version and exit. 107s usage: tombo resquiggle [--dna] [--rna] 107s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 107s [--q-score Q_SCORE] 107s [--signal-matching-score SIGNAL_MATCHING_SCORE] 107s [--processes PROCESSES] 107s [--corrected-group CORRECTED_GROUP] 107s [--basecall-group BASECALL_GROUP] 107s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 107s [--overwrite] 107s [--failed-reads-filename FAILED_READS_FILENAME] 107s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 107s [--print-advanced-arguments] [--quiet] [--help] 107s fast5s_basedir reference 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 Reference genome/transcriptome FASTA file or minimap2 107s index (with "map-ont" preset) for mapping. 107s 107s Model Parameters: 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 107s Read Filtering Argument: 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 --q-score Q_SCORE Q-score threshold for filtering low quality reads. 107s Default: 0.000000 107s --signal-matching-score SIGNAL_MATCHING_SCORE 107s Observed to expected signal matching score (higher 107s score indicates poor matching). Sample type defaults: 107s RNA : 2 || DNA : 1.1 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-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 --overwrite Overwrite previous corrected group in FAST5 files. 107s Note: only effects --corrected-group or --new- 107s corrected-group. 107s 107s Input/Output Arguments: 107s --failed-reads-filename FAILED_READS_FILENAME 107s Output failed read filenames with assoicated error. 107s Default: Do not store failed reads. 107s --num-most-common-errors NUM_MOST_COMMON_ERRORS 107s Dynamically show this many most common errors so far 107s through run. Default: 0; Just show progress 107s 107s Advanced Arguments: 107s --print-advanced-arguments 107s Print advanced re-squiggle arguments and exit. 107s 107s Miscellaneous Arguments: 107s --quiet, -q Don't print status information. 107s --help, -h Print this help message and exit 107s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 107s --fastq-filenames 107s FASTQ_FILENAMES 107s [FASTQ_FILENAMES ...] 107s [--basecall-group BASECALL_GROUP] 107s [--basecall-subgroup BASECALL_SUBGROUP] 107s [--overwrite] 107s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 107s [--processes PROCESSES] 107s [--quiet] [--help] 107s 107s Required Arguments: 107s --fast5-basedir FAST5_BASEDIR 107s Directory containing fast5 files. 107s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 107s FASTQ filenames containing basecalls to be added to 107s raw FAST5 files. 107s 107s FAST5 Data Arguments: 107s --basecall-group BASECALL_GROUP 107s FAST5 group obtain original basecalls (under Analyses 107s group). Default: Basecall_1D_000 107s --basecall-subgroup BASECALL_SUBGROUP 107s FAST5 subgroup (under /Analyses/[--basecall-group]/) 107s under which to store basecalls from FASTQs. Default: 107s BaseCalled_template 107s --overwrite Overwrite previous corrected group in FAST5 files. 107s Note: only effects --corrected-group or --new- 107s corrected-group. 107s 107s Sequencing Summary Argument: 107s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 107s Sequencing summary filenames produced by albacore. 107s These can make annotation of raw FAST5 files with 107s FASTQ sequence much faster. 107s 107s Multiprocessing Argument: 107s --processes PROCESSES 107s Number of processes. Default: 1 107s 107s Miscellaneous Arguments: 107s --quiet, -q Don't print status information. 107s --help, -h Print this help message and exit 107s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 107s [FAST5_BASEDIRS ...] 107s [--corrected-group CORRECTED_GROUP] 107s [--quiet] [--help] 107s 107s Required Argument: 107s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 107s Directories containing fast5 files. 107s 107s FAST5 Data Argument: 107s --corrected-group CORRECTED_GROUP 107s FAST5 group created by resquiggle command. Default: 107s RawGenomeCorrected_000 107s 107s Miscellaneous Arguments: 107s --quiet, -q Don't print status information. 107s --help, -h Print this help message and exit 107s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 107s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 107s [--corrected-group CORRECTED_GROUP] [--quiet] 107s [--help] 107s 107s Required Argument: 107s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 107s Directories containing fast5 files. 107s 107s Read Filtering Argument: 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 107s FAST5 Data Argument: 107s --corrected-group CORRECTED_GROUP 107s FAST5 group created by resquiggle command. Default: 107s RawGenomeCorrected_000 107s 107s Miscellaneous Arguments: 107s --quiet, -q Don't print status information. 107s --help, -h Print this help message and exit 108s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 108s [FAST5_BASEDIRS ...] 108s [--percent-to-filter PERCENT_TO_FILTER] 108s [--corrected-group CORRECTED_GROUP] 108s [--quiet] [--help] 108s 108s Required Arguments: 108s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 108s Directories containing fast5 files. 108s 108s Read Filtering Argument: 108s --percent-to-filter PERCENT_TO_FILTER 108s Percentage of all reads to filter. Reads are randomly 108s selected weighted according to the approximate 108s coverage at the mapped genomic location. This can be 108s useful in modeling and testing. Default: 10.000000 108s 108s FAST5 Data Arguments: 108s --corrected-group CORRECTED_GROUP 108s FAST5 group created by resquiggle command. Default: 108s RawGenomeCorrected_000 108s 108s Miscellaneous Arguments: 108s --quiet, -q Don't print status information. 108s --help, -h Print this help message and exit 108s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 108s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 108s [--corrected-group CORRECTED_GROUP] 108s [--basecall-group BASECALL_GROUP] [--quiet] 108s [--help] 108s 108s Required Arguments: 108s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 108s Directories containing fast5 files. 108s 108s Read Filtering Argument: 108s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 108s Default: 7.000000 108s 108s FAST5 Data Arguments: 108s --corrected-group CORRECTED_GROUP 108s FAST5 group created by resquiggle command. Default: 108s RawGenomeCorrected_000 108s --basecall-group BASECALL_GROUP 108s FAST5 group obtain original basecalls (under Analyses 108s group). Default: Basecall_1D_000 108s 108s Miscellaneous Arguments: 108s --quiet, -q Don't print status information. 108s --help, -h Print this help message and exit 108s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 108s [FAST5_BASEDIRS ...] 108s --signal-matching-score 108s SIGNAL_MATCHING_SCORE 108s [--corrected-group CORRECTED_GROUP] 108s [--quiet] [--help] 108s 108s Required Arguments: 108s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 108s Directories containing fast5 files. 108s --signal-matching-score SIGNAL_MATCHING_SCORE 108s Observed to expected signal matching score (higher 108s score indicates poor matching). Sample type defaults: 108s RNA : 2 || DNA : 1.1 108s 108s FAST5 Data Arguments: 108s --corrected-group CORRECTED_GROUP 108s FAST5 group created by resquiggle command. Default: 108s RawGenomeCorrected_000 108s 108s Miscellaneous Arguments: 108s --quiet, -q Don't print status information. 108s --help, -h Print this help message and exit 108s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 108s [FAST5_BASEDIRS ...] 108s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 108s [--include-partial-overlap] 108s [--corrected-group CORRECTED_GROUP] 108s [--quiet] [--help] 108s 108s Required Arguments: 108s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 108s Directories containing fast5 files. 108s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 108s Filter out reads not falling completely within include 108s regions. Omit start and end coordinates to include an 108s entire chromosome/sequence record. Format regions as 108s "chrm[:start-end] [chrm2[:start2-end2] ...]". 108s 108s Filter Argument: 108s --include-partial-overlap 108s Include reads that partially overlap the specified 108s region. Default: Only include reads completely 108s contained in a specified region 108s 108s FAST5 Data Argument: 108s --corrected-group CORRECTED_GROUP 108s FAST5 group created by resquiggle command. Default: 108s RawGenomeCorrected_000 108s 108s Miscellaneous Arguments: 108s --quiet, -q Don't print status information. 108s --help, -h Print this help message and exit 108s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 108s [FAST5_BASEDIRS ...] 108s --statistics-file-basename 108s STATISTICS_FILE_BASENAME [--dna] 108s [--rna] 108s [--fishers-method-context FISHERS_METHOD_CONTEXT] 108s [--minimum-test-reads MINIMUM_TEST_READS] 108s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 108s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 108s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 108s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 108s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 108s [--processes PROCESSES] 108s [--corrected-group CORRECTED_GROUP] 108s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 108s [--quiet] [--help] 108s 108s Required Argument: 108s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 108s Directories containing fast5 files. 108s --statistics-file-basename STATISTICS_FILE_BASENAME 108s File base name to save base by base statistics from 108s testing. Filenames will be [--statistics-file- 108s basename].[--alternate-bases]?.tombo.stats 108s 108s Comparison Model Arguments: 108s --dna Explicitly select canonical DNA model. Default: 108s Automatically determine from FAST5s 108s --rna Explicitly select canonical RNA model. Default: 108s Automatically determine from FAST5s 108s 108s Significance Test Arguments: 108s --fishers-method-context FISHERS_METHOD_CONTEXT 108s Number of context bases up and downstream over which 108s to compute Fisher's method combined p-values. Note: 108s Not applicable for alternative model likelihood ratio 108s tests. Default: 1. 108s --minimum-test-reads MINIMUM_TEST_READS 108s Number of reads required at a position to perform 108s significance testing or contribute to model 108s estimation. Default: 1 108s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 108s P-value threshold when computing fraction of 108s significant reads at each genomic position. If two 108s values are provided, statistics between these values 108s are not considered. Default thresholds: DNA:0.15-0.5 , 108s RNA:0.05-0.4 108s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 108s Dampen fraction modified estimates for low coverage 108s sites. Two parameters are unmodified and modified 108s pseudo read counts. This is equivalent to a beta prior 108s on the fraction estimate. Set to "0 0" to disable 108s dampened fraction estimation. Default: [2, 0] 108s 108s Output Argument: 108s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 108s Base for binary files containing per-read statistics 108s from statistical testing. Filenames will be [--per- 108s read-statistics-basename].[--alternate- 108s bases]?.tombo.per_read_stats 108s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 108s Number of the most significant sites to store for 108s faster access. If a longer list of most significant 108s sites is required the list must be re-computed from 108s all batches. Very large values can increase RAM usage. 108s Default: 100000 108s 108s Multiprocessing Arguments: 108s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 108s Size of regions over which to multiprocesses statistic 108s computation. For very deep samples a smaller value is 108s recommmended in order to control memory consumption. 108s Default: 10000 108s --processes PROCESSES 108s Number of processes. Default: 1 108s 108s FAST5 Data Arguments: 108s --corrected-group CORRECTED_GROUP 108s FAST5 group created by resquiggle command. Default: 108s RawGenomeCorrected_000 108s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 108s FAST5 subgroup(s) (under /Analyses/[--basecall- 108s group]/) containing basecalls and created within 108s [--corrected-group] containing re-squiggle results. 108s Default: ['BaseCalled_template'] 108s 108s Miscellaneous Arguments: 108s --quiet, -q Don't print status information. 108s --help, -h Print this help message and exit 108s usage: tombo detect_modifications alternative_model 108s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 108s [--statistics-file-basename STATISTICS_FILE_BASENAME] 108s [--alternate-bases {dam,5mC,6mA,dcm,CpG} [{dam,5mC,6mA,dcm,CpG} ...]] 108s [--print-available-models] 108s [--dna] [--rna] 108s [--minimum-test-reads MINIMUM_TEST_READS] 108s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 108s [--standard-log-likelihood-ratio] 108s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 108s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 108s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 108s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 108s [--processes PROCESSES] 108s [--corrected-group CORRECTED_GROUP] 108s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 108s [--quiet] [--help] 108s 108s Required Argument: 108s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 108s Directories containing fast5 files. 108s --statistics-file-basename STATISTICS_FILE_BASENAME 108s File base name to save base by base statistics from 108s testing. Filenames will be [--statistics-file- 108s basename].[--alternate-bases]?.tombo.stats 108s --alternate-bases {dam,5mC,6mA,dcm,CpG} [{dam,5mC,6mA,dcm,CpG} ...] 108s Default non-standard base model for testing (not 108s required if user created --alternate-model-filenames 108s is provided). 108s 108s Comparison Arguments: 108s --print-available-models 108s Print available alternative models and exit. 108s --dna Explicitly select canonical DNA model. Default: 108s Automatically determine from FAST5s 108s --rna Explicitly select canonical RNA model. Default: 108s Automatically determine from FAST5s 108s 108s Significance Test Arguments: 108s --minimum-test-reads MINIMUM_TEST_READS 108s Number of reads required at a position to perform 108s significance testing or contribute to model 108s estimation. Default: 1 108s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 108s Log likelihood ratio threshold when computing fraction 108s of significant reads at each genomic position. If two 108s values are provided, statistics between these values 108s are not considered. Default thresholds: DNA:-1.5-2.5 , 108s RNA:-2.5-2.5 108s --standard-log-likelihood-ratio 108s Use a standard log likelihood ratio (LLR) statistic. 108s Default is to use an outlier-robust LLR-like 108s statistic. Detail in full online documentation. 108s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 108s Dampen fraction modified estimates for low coverage 108s sites. Two parameters are unmodified and modified 108s pseudo read counts. This is equivalent to a beta prior 108s on the fraction estimate. Set to "0 0" to disable 108s dampened fraction estimation. Default: [2, 0] 108s 108s Output Argument: 108s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 108s Base for binary files containing per-read statistics 108s from statistical testing. Filenames will be [--per- 108s read-statistics-basename].[--alternate- 108s bases]?.tombo.per_read_stats 108s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 108s Number of the most significant sites to store for 108s faster access. If a longer list of most significant 108s sites is required the list must be re-computed from 108s all batches. Very large values can increase RAM usage. 108s Default: 100000 108s 108s Multiprocessing Arguments: 108s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 108s Size of regions over which to multiprocesses statistic 108s computation. For very deep samples a smaller value is 108s recommmended in order to control memory consumption. 108s Default: 10000 108s --processes PROCESSES 108s Number of processes. Default: 1 108s 108s FAST5 Data Arguments: 108s --corrected-group CORRECTED_GROUP 108s FAST5 group created by resquiggle command. Default: 108s RawGenomeCorrected_000 108s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 108s FAST5 subgroup(s) (under /Analyses/[--basecall- 108s group]/) containing basecalls and created within 108s [--corrected-group] containing re-squiggle results. 108s Default: ['BaseCalled_template'] 108s 108s Miscellaneous Arguments: 108s --quiet, -q Don't print status information. 108s --help, -h Print this help message and exit 108s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 108s FAST5_BASEDIRS 108s [FAST5_BASEDIRS ...] 108s --statistics-file-basename 108s STATISTICS_FILE_BASENAME 108s --control-fast5-basedirs 108s CONTROL_FAST5_BASEDIRS 108s [CONTROL_FAST5_BASEDIRS ...] 108s [--sample-only-estimates] 108s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 108s [--dna] [--rna] 108s [--fishers-method-context FISHERS_METHOD_CONTEXT] 108s [--minimum-test-reads MINIMUM_TEST_READS] 108s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 108s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 108s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 108s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 108s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 108s [--processes PROCESSES] 108s [--corrected-group CORRECTED_GROUP] 108s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 108s [--quiet] [--help] 108s 108s Required Argument: 108s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 108s Directories containing fast5 files. 108s --statistics-file-basename STATISTICS_FILE_BASENAME 108s File base name to save base by base statistics from 108s testing. Filenames will be [--statistics-file- 108s basename].[--alternate-bases]?.tombo.stats 108s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 108s Set of directories containing fast5 files for control 108s reads, containing only canonical nucleotides. 108s 108s Model Prior Arguments: 108s --sample-only-estimates 108s Only use canonical sample to estimate expected signal 108s level and spread. Default: Use canonical model to 108s improve estimtates (esp. for low coverage regions) 108s using baysian posterior estimates. 108s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 108s Prior weights (one each for mean and spread) applied 108s to canonical base model for estimating posterior model 108s parameters for sample comparison. Default: [5, 40] 108s --dna Explicitly select canonical DNA model. Default: 108s Automatically determine from FAST5s 108s --rna Explicitly select canonical RNA model. Default: 108s Automatically determine from FAST5s 108s 108s Significance Test Arguments: 108s --fishers-method-context FISHERS_METHOD_CONTEXT 108s Number of context bases up and downstream over which 108s to compute Fisher's method combined p-values. Note: 108s Not applicable for alternative model likelihood ratio 108s tests. Default: 1. 108s --minimum-test-reads MINIMUM_TEST_READS 108s Number of reads required at a position to perform 108s significance testing or contribute to model 108s estimation. Default: 1 108s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 108s P-value threshold when computing fraction of 108s significant reads at each genomic position. If two 108s values are provided, statistics between these values 108s are not considered. Default thresholds: DNA:0.15-0.5 , 108s RNA:0.05-0.4 108s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 108s Dampen fraction modified estimates for low coverage 108s sites. Two parameters are unmodified and modified 108s pseudo read counts. This is equivalent to a beta prior 108s on the fraction estimate. Set to "0 0" to disable 108s dampened fraction estimation. Default: [2, 0] 108s 108s Output Argument: 108s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 108s Base for binary files containing per-read statistics 108s from statistical testing. Filenames will be [--per- 108s read-statistics-basename].[--alternate- 108s bases]?.tombo.per_read_stats 108s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 108s Number of the most significant sites to store for 108s faster access. If a longer list of most significant 108s sites is required the list must be re-computed from 108s all batches. Very large values can increase RAM usage. 108s Default: 100000 108s 108s Multiprocessing Arguments: 108s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 108s Size of regions over which to multiprocesses statistic 108s computation. For very deep samples a smaller value is 108s recommmended in order to control memory consumption. 108s Default: 10000 108s --processes PROCESSES 108s Number of processes. Default: 1 108s 108s FAST5 Data Arguments: 108s --corrected-group CORRECTED_GROUP 108s FAST5 group created by resquiggle command. Default: 108s RawGenomeCorrected_000 108s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 108s FAST5 subgroup(s) (under /Analyses/[--basecall- 108s group]/) containing basecalls and created within 108s [--corrected-group] containing re-squiggle results. 108s Default: ['BaseCalled_template'] 108s 108s Miscellaneous Arguments: 108s --quiet, -q Don't print status information. 108s --help, -h Print this help message and exit 108s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 108s FAST5_BASEDIRS 108s [FAST5_BASEDIRS ...] 108s --statistics-file-basename 108s STATISTICS_FILE_BASENAME 108s --alternate-fast5-basedirs 108s ALTERNATE_FAST5_BASEDIRS 108s [ALTERNATE_FAST5_BASEDIRS ...] 108s [--fishers-method-context FISHERS_METHOD_CONTEXT] 108s [--minimum-test-reads MINIMUM_TEST_READS] 108s [--statistic-type {ks,u,t}] 108s [--store-p-value] 108s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 108s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 108s [--processes PROCESSES] 108s [--corrected-group CORRECTED_GROUP] 108s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 108s [--quiet] [--help] 108s 108s Required Argument: 108s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 108s Directories containing fast5 files. 108s --statistics-file-basename STATISTICS_FILE_BASENAME 108s File base name to save base by base statistics from 108s testing. Filenames will be [--statistics-file- 108s basename].[--alternate-bases]?.tombo.stats 108s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 108s Set of directories containing fast5 files for 108s alternate set of reads. 108s 108s Significance Test Arguments: 108s --fishers-method-context FISHERS_METHOD_CONTEXT 108s Number of context bases up and downstream over which 108s to compute Fisher's method combined p-values. Note: 108s Not applicable for alternative model likelihood ratio 108s tests. Default: 1. 108s --minimum-test-reads MINIMUM_TEST_READS 108s Number of reads required at a position to perform 108s significance testing or contribute to model 108s estimation. Default: 50 108s --statistic-type {ks,u,t} 108s Type of statistical test to apply. Default: "ks" 108s --store-p-value Store p-value instead of effect-size statistic. 108s Statistics are D-statistic (KS-test), deviation from 108s even common language effect size (u-test), and Cohen's 108s D (t-test). 108s 108s Output Argument: 108s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 108s Number of the most significant sites to store for 108s faster access. If a longer list of most significant 108s sites is required the list must be re-computed from 108s all batches. Very large values can increase RAM usage. 108s Default: 100000 108s 108s Multiprocessing Arguments: 108s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 108s Size of regions over which to multiprocesses statistic 108s computation. For very deep samples a smaller value is 108s recommmended in order to control memory consumption. 108s Default: 10000 108s --processes PROCESSES 108s Number of processes. Default: 1 108s 108s FAST5 Data Arguments: 108s --corrected-group CORRECTED_GROUP 108s FAST5 group created by resquiggle command. Default: 108s RawGenomeCorrected_000 108s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 108s FAST5 subgroup(s) (under /Analyses/[--basecall- 108s group]/) containing basecalls and created within 108s [--corrected-group] containing re-squiggle results. 108s Default: ['BaseCalled_template'] 108s 108s Miscellaneous Arguments: 108s --quiet, -q Don't print status information. 108s --help, -h Print this help message and exit 108s usage: tombo detect_modifications aggregate_per_read_stats 108s --per-read-statistics-filename 108s PER_READ_STATISTICS_FILENAME 108s --statistics-filename 108s STATISTICS_FILENAME 108s --single-read-threshold 108s SINGLE_READ_THRESHOLD 108s [SINGLE_READ_THRESHOLD ...] 108s [--minimum-test-reads MINIMUM_TEST_READS] 108s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 108s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 108s [--processes PROCESSES] 108s [--corrected-group CORRECTED_GROUP] 108s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 108s [--quiet] [--help] 108s 108s Required Argument: 108s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 108s Binary file containing per-read statistics from 108s statistical testing. 108s --statistics-filename STATISTICS_FILENAME 108s File to save/load genomic base anchored statistics. 108s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 108s P-value or log likelihood ratio threshold when 108s computing fraction of significant reads at each 108s genomic position. If two values are provided, 108s statistics between these values are not considered. 108s 108s Significance Test Arguments: 108s --minimum-test-reads MINIMUM_TEST_READS 108s Number of reads required at a position to perform 108s significance testing or contribute to model 108s estimation. Default: 1 108s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 108s Dampen fraction modified estimates for low coverage 108s sites. Two parameters are unmodified and modified 108s pseudo read counts. This is equivalent to a beta prior 108s on the fraction estimate. Set to "0 0" to disable 108s dampened fraction estimation. Default: [2, 0] 108s 108s Output Argument: 108s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 108s Number of the most significant sites to store for 108s faster access. If a longer list of most significant 108s sites is required the list must be re-computed from 108s all batches. Very large values can increase RAM usage. 108s Default: 100000 108s 108s Multiprocessing Arguments: 108s --processes PROCESSES 108s Number of processes. Default: 1 108s 108s FAST5 Data Arguments: 108s --corrected-group CORRECTED_GROUP 108s FAST5 group created by resquiggle command. Default: 108s RawGenomeCorrected_000 108s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 108s FAST5 subgroup(s) (under /Analyses/[--basecall- 108s group]/) containing basecalls and created within 108s [--corrected-group] containing re-squiggle results. 108s Default: ['BaseCalled_template'] 108s 108s Miscellaneous Arguments: 108s --quiet, -q Don't print status information. 108s --help, -h Print this help message and exit 108s usage: tombo text_output browser_files 108s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 108s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 108s [--statistics-filename STATISTICS_FILENAME] 108s [--genome-fasta GENOME_FASTA] 108s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 108s [--browser-file-basename BROWSER_FILE_BASENAME] 108s [--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} ...]] 108s [--corrected-group CORRECTED_GROUP] 108s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 108s [--quiet] [--help] 108s 108s Data Arguments: 108s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 108s Directories containing fast5 files. 108s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 108s Set of directories containing fast5 files for control 108s reads, containing only canonical nucleotides. 108s --statistics-filename STATISTICS_FILENAME 108s File to save/load genomic base anchored statistics. 108s 108s Statistic Motif Filter Arguments: 108s --genome-fasta GENOME_FASTA 108s FASTA file used to re-squiggle. For faster sequence 108s access. 108s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 108s Ground truth, motif centered, modified base 108s descriptions for output filtering. Format descriptions 108s as: "motif:mod_pos:name". The mod_pos indicates the 108s modified base within the motif (1-based index). 108s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 108s output for identification of E. coli dam and dcm 108s methylation. 108s 108s Output Arguments: 108s --browser-file-basename BROWSER_FILE_BASENAME 108s Basename for output browser files. Two files (plus and 108s minus strand) will be produced for each --file-types 108s supplied. Filenames formatted as "[browser-file- 108s basename].[file- 108s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 108s Default: tombo_results 108s --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} ...] 108s Data types of genome browser files to produce. 108s Produced coverage files are in bedGraph format, while 108s all other file types will be in wiggle format 108s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 108s Default: "coverage" 108s 108s FAST5 Data Arguments: 108s --corrected-group CORRECTED_GROUP 108s FAST5 group created by resquiggle command. Default: 108s RawGenomeCorrected_000 108s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 108s FAST5 subgroup(s) (under /Analyses/[--basecall- 108s group]/) containing basecalls and created within 108s [--corrected-group] containing re-squiggle results. 108s Default: ['BaseCalled_template'] 108s 108s Miscellaneous Arguments: 108s --quiet, -q Don't print status information. 108s --help, -h Print this help message and exit 108s usage: tombo text_output signif_sequence_context --statistics-filename 108s STATISTICS_FILENAME 108s [--genome-fasta GENOME_FASTA] 108s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 108s [--num-regions NUM_REGIONS] 108s [--num-bases NUM_BASES] 108s [--sequences-filename SEQUENCES_FILENAME] 108s [--corrected-group CORRECTED_GROUP] 108s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 108s [--quiet] [--help] 108s 108s Required Argument: 108s --statistics-filename STATISTICS_FILENAME 108s File to save/load genomic base anchored statistics. 108s 108s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 108s --genome-fasta GENOME_FASTA 108s FASTA file used to re-squiggle. For faster sequence 108s access. 108s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 108s Directories containing fast5 files. 108s 108s Region Selection Arguments: 108s --num-regions NUM_REGIONS 108s Number of regions to plot. Default: 100 108s --num-bases NUM_BASES 108s Number of bases to plot/output. Default: 15 108s 108s Output Arguments: 108s --sequences-filename SEQUENCES_FILENAME 108s File for sequences from selected regions. Sequences 108s will be stored in FASTA format. Default: 108s tombo_results.significant_regions.fasta. 108s 108s FAST5 Data Arguments: 108s --corrected-group CORRECTED_GROUP 108s FAST5 group created by resquiggle command. Default: 108s RawGenomeCorrected_000 108s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 108s FAST5 subgroup(s) (under /Analyses/[--basecall- 108s group]/) containing basecalls and created within 108s [--corrected-group] containing re-squiggle results. 108s Default: ['BaseCalled_template'] 108s 108s Miscellaneous Arguments: 108s --quiet, -q Don't print status information. 108s --help, -h Print this help message and exit 108s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 108s [FAST5_BASEDIRS ...] 108s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 108s [--plot-standard-model] 108s [--plot-alternate-model {6mA,dam,dcm,CpG,5mC}] 108s [--overplot-threshold OVERPLOT_THRESHOLD] 108s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 108s [--num-regions NUM_REGIONS] 108s [--num-bases NUM_BASES] 108s [--pdf-filename PDF_FILENAME] 108s [--corrected-group CORRECTED_GROUP] 108s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 108s [--quiet] [--help] 108s 108s Required Argument: 108s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 108s Directories containing fast5 files. 108s 108s Comparison Arguments: 108s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 108s Set of directories containing fast5 files for control 108s reads, containing only canonical nucleotides. 108s --plot-standard-model 108s Add default standard model distribution to the plot. 108s --plot-alternate-model {6mA,dam,dcm,CpG,5mC} 108s Add alternative model distribution to the plot. 108s 108s Overplotting Arguments: 108s --overplot-threshold OVERPLOT_THRESHOLD 108s Coverage level to trigger alternative plot type 108s instead of raw signal. Default: 50 108s --overplot-type {Downsample,Boxplot,Quantile,Density} 108s Plot type for regions with higher coverage. Default: 108s Downsample 108s 108s Plotting Region Arguments: 108s --num-regions NUM_REGIONS 108s Number of regions to plot. Default: 10 108s --num-bases NUM_BASES 108s Number of bases to plot/output. Default: 21 108s 108s Output Argument: 108s --pdf-filename PDF_FILENAME 108s PDF filename to store plot(s). Default: 108s tombo_results.max_coverage.pdf 108s 108s FAST5 Data Arguments: 108s --corrected-group CORRECTED_GROUP 108s FAST5 group created by resquiggle command. Default: 108s RawGenomeCorrected_000 108s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 108s FAST5 subgroup(s) (under /Analyses/[--basecall- 108s group]/) containing basecalls and created within 108s [--corrected-group] containing re-squiggle results. 108s Default: ['BaseCalled_template'] 108s 108s Miscellaneous Arguments: 108s --quiet, -q Don't print status information. 108s --help, -h Print this help message and exit 108s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 108s [FAST5_BASEDIRS ...] --genome-locations 108s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 108s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 108s [--plot-standard-model] 108s [--plot-alternate-model {dcm,dam,5mC,6mA,CpG}] 108s [--overplot-threshold OVERPLOT_THRESHOLD] 108s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 108s [--num-bases NUM_BASES] 108s [--pdf-filename PDF_FILENAME] 108s [--corrected-group CORRECTED_GROUP] 108s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 108s [--quiet] [--help] 108s 108s Required Arguments: 108s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 108s Directories containing fast5 files. 108s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 108s Genomic locations at which to plot signal. Format 108s locations as "chrm:position[:strand] 108s [chrm2:position2[:strand2] ...]" (strand not 108s applicable for all applications) 108s 108s Comparison Arguments: 108s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 108s Set of directories containing fast5 files for control 108s reads, containing only canonical nucleotides. 108s --plot-standard-model 108s Add default standard model distribution to the plot. 108s --plot-alternate-model {dcm,dam,5mC,6mA,CpG} 108s Add alternative model distribution to the plot. 108s 108s Overplotting Arguments: 108s --overplot-threshold OVERPLOT_THRESHOLD 108s Coverage level to trigger alternative plot type 108s instead of raw signal. Default: 50 108s --overplot-type {Downsample,Boxplot,Quantile,Density} 108s Plot type for regions with higher coverage. Default: 108s Downsample 108s 108s Plotting Region Argument: 108s --num-bases NUM_BASES 108s Number of bases to plot/output. Default: 21 108s 108s Output Argument: 108s --pdf-filename PDF_FILENAME 108s PDF filename to store plot(s). Default: 108s tombo_results.genome_locations.pdf 108s 108s FAST5 Data Arguments: 108s --corrected-group CORRECTED_GROUP 108s FAST5 group created by resquiggle command. Default: 108s RawGenomeCorrected_000 108s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 108s FAST5 subgroup(s) (under /Analyses/[--basecall- 108s group]/) containing basecalls and created within 108s [--corrected-group] containing re-squiggle results. 108s Default: ['BaseCalled_template'] 108s 108s Miscellaneous Arguments: 108s --quiet, -q Don't print status information. 108s --help, -h Print this help message and exit 108s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 108s [FAST5_BASEDIRS ...] --motif MOTIF 108s --genome-fasta GENOME_FASTA 108s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 108s [--plot-standard-model] 108s [--plot-alternate-model {CpG,6mA,dam,dcm,5mC}] 108s [--overplot-threshold OVERPLOT_THRESHOLD] 108s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 108s [--num-regions NUM_REGIONS] 108s [--num-bases NUM_BASES] [--deepest-coverage] 108s [--pdf-filename PDF_FILENAME] 108s [--corrected-group CORRECTED_GROUP] 108s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 108s [--quiet] [--help] 108s 108s Required Arguments: 108s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 108s Directories containing fast5 files. 108s --motif MOTIF Motif of interest at which to plot signal and 108s statsitics. Supports IUPAC single letter codes (use T 108s for RNA). 108s --genome-fasta GENOME_FASTA 108s FASTA file used to re-squiggle. For faster sequence 108s access. 108s 108s Comparison Arguments: 108s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 108s Set of directories containing fast5 files for control 108s reads, containing only canonical nucleotides. 108s --plot-standard-model 108s Add default standard model distribution to the plot. 108s --plot-alternate-model {CpG,6mA,dam,dcm,5mC} 108s Add alternative model distribution to the plot. 108s 108s Overplotting Arguments: 108s --overplot-threshold OVERPLOT_THRESHOLD 108s Coverage level to trigger alternative plot type 108s instead of raw signal. Default: 50 108s --overplot-type {Downsample,Boxplot,Quantile,Density} 108s Plot type for regions with higher coverage. Default: 108s Downsample 108s 108s Plotting Region Arguments: 108s --num-regions NUM_REGIONS 108s Number of regions to plot. Default: 10 108s --num-bases NUM_BASES 108s Number of bases to plot/output. Default: 21 108s --deepest-coverage Plot the deepest coverage regions. 108s 108s Output Argument: 108s --pdf-filename PDF_FILENAME 108s PDF filename to store plot(s). Default: 108s tombo_results.motif_centered.pdf 108s 108s FAST5 Data Arguments: 108s --corrected-group CORRECTED_GROUP 108s FAST5 group created by resquiggle command. Default: 108s RawGenomeCorrected_000 108s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 108s FAST5 subgroup(s) (under /Analyses/[--basecall- 108s group]/) containing basecalls and created within 108s [--corrected-group] containing re-squiggle results. 108s Default: ['BaseCalled_template'] 108s 108s Miscellaneous Arguments: 108s --quiet, -q Don't print status information. 108s --help, -h Print this help message and exit 109s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 109s [FAST5_BASEDIRS ...] --control-fast5-basedirs 109s CONTROL_FAST5_BASEDIRS 109s [CONTROL_FAST5_BASEDIRS ...] 109s [--overplot-threshold OVERPLOT_THRESHOLD] 109s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 109s [--num-regions NUM_REGIONS] 109s [--num-bases NUM_BASES] 109s [--pdf-filename PDF_FILENAME] 109s [--sequences-filename SEQUENCES_FILENAME] 109s [--corrected-group CORRECTED_GROUP] 109s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 109s [--quiet] [--help] 109s 109s Required Arguments: 109s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 109s Directories containing fast5 files. 109s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 109s Set of directories containing fast5 files for control 109s reads, containing only canonical nucleotides. 109s 109s Overplotting Arguments: 109s --overplot-threshold OVERPLOT_THRESHOLD 109s Coverage level to trigger alternative plot type 109s instead of raw signal. Default: 50 109s --overplot-type {Downsample,Boxplot,Quantile,Density} 109s Plot type for regions with higher coverage. Default: 109s Downsample 109s 109s Plotting Region Arguments: 109s --num-regions NUM_REGIONS 109s Number of regions to plot. Default: 10 109s --num-bases NUM_BASES 109s Number of bases to plot/output. Default: 21 109s 109s Output Arguments: 109s --pdf-filename PDF_FILENAME 109s PDF filename to store plot(s). Default: 109s tombo_results.max_difference.pdf 109s --sequences-filename SEQUENCES_FILENAME 109s File for sequences from selected regions. Sequences 109s will be stored in FASTA format. Default: None. 109s 109s FAST5 Data Arguments: 109s --corrected-group CORRECTED_GROUP 109s FAST5 group created by resquiggle command. Default: 109s RawGenomeCorrected_000 109s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 109s FAST5 subgroup(s) (under /Analyses/[--basecall- 109s group]/) containing basecalls and created within 109s [--corrected-group] containing re-squiggle results. 109s Default: ['BaseCalled_template'] 109s 109s Miscellaneous Arguments: 109s --quiet, -q Don't print status information. 109s --help, -h Print this help message and exit 109s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 109s [FAST5_BASEDIRS ...] --statistics-filename 109s STATISTICS_FILENAME 109s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 109s [--plot-standard-model] 109s [--plot-alternate-model {5mC,6mA,CpG,dam,dcm}] 109s [--overplot-threshold OVERPLOT_THRESHOLD] 109s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 109s [--num-regions NUM_REGIONS] 109s [--num-bases NUM_BASES] 109s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 109s [--pdf-filename PDF_FILENAME] 109s [--sequences-filename SEQUENCES_FILENAME] 109s [--corrected-group CORRECTED_GROUP] 109s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 109s [--quiet] [--help] 109s 109s Required Arguments: 109s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 109s Directories containing fast5 files. 109s --statistics-filename STATISTICS_FILENAME 109s File to save/load genomic base anchored statistics. 109s 109s Comparison Arguments: 109s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 109s Set of directories containing fast5 files for control 109s reads, containing only canonical nucleotides. 109s --plot-standard-model 109s Add default standard model distribution to the plot. 109s --plot-alternate-model {5mC,6mA,CpG,dam,dcm} 109s Add alternative model distribution to the plot. 109s 109s Overplotting Arguments: 109s --overplot-threshold OVERPLOT_THRESHOLD 109s Coverage level to trigger alternative plot type 109s instead of raw signal. Default: 50 109s --overplot-type {Downsample,Boxplot,Quantile,Density} 109s Plot type for regions with higher coverage. Default: 109s Downsample 109s 109s Plotting Region Arguments: 109s --num-regions NUM_REGIONS 109s Number of regions to plot. Default: 10 109s --num-bases NUM_BASES 109s Number of bases to plot/output. Default: 21 109s 109s Statistical Argument: 109s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 109s Dampen fraction modified estimates for low coverage 109s sites. Two parameters are unmodified and modified 109s pseudo read counts. This is equivalent to a beta prior 109s on the fraction estimate. Set to "0 0" to disable 109s dampened fraction estimation. Default: [2, 0] 109s 109s Output Arguments: 109s --pdf-filename PDF_FILENAME 109s PDF filename to store plot(s). Default: 109s tombo_results.significant_difference.pdf 109s --sequences-filename SEQUENCES_FILENAME 109s File for sequences from selected regions. Sequences 109s will be stored in FASTA format. Default: None. 109s 109s FAST5 Data Arguments: 109s --corrected-group CORRECTED_GROUP 109s FAST5 group created by resquiggle command. Default: 109s RawGenomeCorrected_000 109s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 109s FAST5 subgroup(s) (under /Analyses/[--basecall- 109s group]/) containing basecalls and created within 109s [--corrected-group] containing re-squiggle results. 109s Default: ['BaseCalled_template'] 109s 109s Miscellaneous Arguments: 109s --quiet, -q Don't print status information. 109s --help, -h Print this help message and exit 109s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 109s [FAST5_BASEDIRS ...] --motif MOTIF 109s --statistics-filename STATISTICS_FILENAME 109s --genome-fasta GENOME_FASTA 109s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 109s [--plot-standard-model] 109s [--plot-alternate-model {dam,CpG,dcm,6mA,5mC}] 109s [--overplot-threshold OVERPLOT_THRESHOLD] 109s [--num-regions NUM_REGIONS] 109s [--num-context NUM_CONTEXT] 109s [--num-statistics NUM_STATISTICS] 109s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 109s [--pdf-filename PDF_FILENAME] 109s [--corrected-group CORRECTED_GROUP] 109s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 109s [--quiet] [--help] 109s 109s Required Arguments: 109s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 109s Directories containing fast5 files. 109s --motif MOTIF Motif of interest at which to plot signal and 109s statsitics. Supports IUPAC single letter codes (use T 109s for RNA). 109s --statistics-filename STATISTICS_FILENAME 109s File to save/load genomic base anchored statistics. 109s --genome-fasta GENOME_FASTA 109s FASTA file used to re-squiggle. For faster sequence 109s access. 109s 109s Comparison Arguments: 109s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 109s Set of directories containing fast5 files for control 109s reads, containing only canonical nucleotides. 109s --plot-standard-model 109s Add default standard model distribution to the plot. 109s --plot-alternate-model {dam,CpG,dcm,6mA,5mC} 109s Add alternative model distribution to the plot. 109s 109s Overplotting Argument: 109s --overplot-threshold OVERPLOT_THRESHOLD 109s Coverage level to trigger alternative plot type 109s instead of raw signal. Default: 50 109s 109s Plotting Region Arguments: 109s --num-regions NUM_REGIONS 109s Number of regions to plot. Default: 3 109s --num-context NUM_CONTEXT 109s Number of context bases around motif. Default: 5 109s --num-statistics NUM_STATISTICS 109s Number of motif centered regions to include in 109s statistic distributions. Default: 200 109s 109s Statistical Argument: 109s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 109s Dampen fraction modified estimates for low coverage 109s sites. Two parameters are unmodified and modified 109s pseudo read counts. This is equivalent to a beta prior 109s on the fraction estimate. Set to "0 0" to disable 109s dampened fraction estimation. Default: [2, 0] 109s 109s Output Argument: 109s --pdf-filename PDF_FILENAME 109s PDF filename to store plot(s). Default: 109s tombo_results.motif_statistics.pdf 109s 109s FAST5 Data Arguments: 109s --corrected-group CORRECTED_GROUP 109s FAST5 group created by resquiggle command. Default: 109s RawGenomeCorrected_000 109s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 109s FAST5 subgroup(s) (under /Analyses/[--basecall- 109s group]/) containing basecalls and created within 109s [--corrected-group] containing re-squiggle results. 109s Default: ['BaseCalled_template'] 109s 109s Miscellaneous Arguments: 109s --quiet, -q Don't print status information. 109s --help, -h Print this help message and exit 109s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 109s [GENOME_LOCATIONS ...] 109s --per-read-statistics-filename 109s PER_READ_STATISTICS_FILENAME 109s [--genome-fasta GENOME_FASTA] 109s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 109s [--num-reads NUM_READS] [--num-bases NUM_BASES] 109s [--box-center] [--pdf-filename PDF_FILENAME] 109s [--corrected-group CORRECTED_GROUP] 109s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 109s [--quiet] [--help] 109s 109s Required Arguments: 109s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 109s Genomic locations at which to plot signal. Format 109s locations as "chrm:position[:strand] 109s [chrm2:position2[:strand2] ...]" (strand not 109s applicable for all applications) 109s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 109s Binary file containing per-read statistics from 109s statistical testing. 109s 109s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 109s --genome-fasta GENOME_FASTA 109s FASTA file used to re-squiggle. For faster sequence 109s access. 109s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 109s Directories containing fast5 files. 109s 109s Plotting Region Arguments: 109s --num-reads NUM_READS 109s Number of reads to plot. Default: 100 109s --num-bases NUM_BASES 109s Number of bases to plot/output. Default: 51 109s --box-center Plot a box around the central base. 109s 109s Output Argument: 109s --pdf-filename PDF_FILENAME 109s PDF filename to store plot(s). Default: 109s tombo_results.per_read_stats.pdf 109s 109s FAST5 Data Arguments: 109s --corrected-group CORRECTED_GROUP 109s FAST5 group created by resquiggle command. Default: 109s RawGenomeCorrected_000 109s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 109s FAST5 subgroup(s) (under /Analyses/[--basecall- 109s group]/) containing basecalls and created within 109s [--corrected-group] containing re-squiggle results. 109s Default: ['BaseCalled_template'] 109s 109s Miscellaneous Arguments: 109s --quiet, -q Don't print status information. 109s --help, -h Print this help message and exit 109s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 109s [STATISTICS_FILENAMES ...] 109s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 109s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 109s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 109s [--genome-fasta GENOME_FASTA] 109s [--pdf-filename PDF_FILENAME] 109s [--statistics-per-block STATISTICS_PER_BLOCK] 109s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 109s [--quiet] [--help] 109s 109s Required Argument: 109s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 109s Files to load genomic base anchored statistics. 109s 109s Ground Truth Arguments (provide bed files or motifs): 109s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 109s Modification description and bed format files 109s containing single base locations of ground truth 109s modified sites. Bed files should contain 6 fields 109s including strand. Format descriptions as 109s "mod_name:locs.bed". Example: "CpG 109s bisulfite":bisulfite_locs.bed 109s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 109s Bed format files containing single base locations of 109s ground truth unmodified sites. Bed files should 109s contain 6 fields including strand. 109s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 109s Ground truth, motif centered, modified base 109s descriptions for computing ROC and PR curves. Each 109s statistics file is associated with a set of motif 109s descriptions. Format descriptions as: 109s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 109s mod_pos indicates the alternate-base within the motif 109s (1-based index). Example: CCWGG:2:"dcm 109s 5mC"::GATC:2:"dam 6mA" would assess the performance of 109s a single Tombo statistics file for identification of 109s E. coli dam and dcm methylation. 109s --genome-fasta GENOME_FASTA 109s FASTA file used to re-squiggle. For faster sequence 109s access. 109s 109s Output Arguments: 109s --pdf-filename PDF_FILENAME 109s PDF filename to store plot(s). Default: 109s tombo_results.roc.pdf 109s 109s Down-sampling Arguments: 109s --statistics-per-block STATISTICS_PER_BLOCK 109s Number of randomly selected per-read, per-base 109s statistics to extract from each genomic block for 109s plotting. Default: Include all stats 109s --total-statistics-limit TOTAL_STATISTICS_LIMIT 109s Total per-read statistics to be extracted for 109s plotting. Avoids memory overflow for large runs. 109s Default: 5000000 109s 109s Miscellaneous Arguments: 109s --quiet, -q Don't print status information. 109s --help, -h Print this help message and exit 109s usage: tombo plot per_read_roc --per-read-statistics-filenames 109s PER_READ_STATISTICS_FILENAMES 109s [PER_READ_STATISTICS_FILENAMES ...] 109s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 109s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 109s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 109s [--genome-fasta GENOME_FASTA] 109s [--statistics-per-block STATISTICS_PER_BLOCK] 109s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 109s [--pdf-filename PDF_FILENAME] [--quiet] 109s [--help] 109s 109s Required Argument: 109s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 109s Binary files containing per-read statistics from 109s statistical testing. 109s 109s Ground Truth Arguments (provide bed files or motifs): 109s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 109s Modification description and bed format files 109s containing single base locations of ground truth 109s modified sites. Bed files should contain 6 fields 109s including strand. Format descriptions as 109s "mod_name:locs.bed". Example: "CpG 109s bisulfite":bisulfite_locs.bed 109s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 109s Bed format files containing single base locations of 109s ground truth unmodified sites. Bed files should 109s contain 6 fields including strand. 109s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 109s Ground truth, motif centered, modified base 109s descriptions for computing ROC and PR curves. Each 109s statistics file is associated with a set of motif 109s descriptions. Format descriptions as: 109s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 109s mod_pos indicates the alternate-base within the motif 109s (1-based index). Example: CCWGG:2:"dcm 109s 5mC"::GATC:2:"dam 6mA" would assess the performance of 109s a single Tombo statistics file for identification of 109s E. coli dam and dcm methylation. 109s --genome-fasta GENOME_FASTA 109s FASTA file used to re-squiggle. For faster sequence 109s access. 109s 109s Down-sampling Arguments: 109s --statistics-per-block STATISTICS_PER_BLOCK 109s Number of randomly selected per-read, per-base 109s statistics to extract from each genomic block for 109s plotting. Default: 100000 109s --total-statistics-limit TOTAL_STATISTICS_LIMIT 109s Total per-read statistics to be extracted for 109s plotting. Avoids memory overflow for large runs. 109s Default: 5000000 109s 109s Output Arguments: 109s --pdf-filename PDF_FILENAME 109s PDF filename to store plot(s). Default: 109s tombo_results.per_reads_roc.pdf 109s 109s Miscellaneous Arguments: 109s --quiet, -q Don't print status information. 109s --help, -h Print this help message and exit 109s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 109s [--upstream-bases {0,1,2,3,4}] 109s [--downstream-bases {0,1,2,3,4}] [--read-mean] 109s [--num-kmer-threshold NUM_KMER_THRESHOLD] 109s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 109s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 109s [--corrected-group CORRECTED_GROUP] 109s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 109s [--quiet] [--help] 109s 109s Required Argument: 109s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 109s Directories containing fast5 files. 109s 109s Data Processing Arguments: 109s --upstream-bases {0,1,2,3,4} 109s Upstream bases in k-mer. Default: 1 109s --downstream-bases {0,1,2,3,4} 109s Downstream bases in k-mer. Default: 2 109s --read-mean Plot k-mer means across whole reads as opposed to 109s individual k-mer event levels. 109s --num-kmer-threshold NUM_KMER_THRESHOLD 109s Observations of each k-mer required to include a read 109s in read level averages. Default: 1 109s 109s Plotting Region Arguments: 109s --num-reads NUM_READS 109s Number of reads to plot. Default: 100 109s 109s Output Arguments: 109s --pdf-filename PDF_FILENAME 109s PDF filename to store plot(s). Default: 109s tombo_results.kmer_distribution.pdf 109s --r-data-filename R_DATA_FILENAME 109s Filename to save R data structure. Default: Don't save 109s --dont-plot Don't plot result. Useful to produce only R data file. 109s 109s FAST5 Data Arguments: 109s --corrected-group CORRECTED_GROUP 109s FAST5 group created by resquiggle command. Default: 109s RawGenomeCorrected_000 109s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 109s FAST5 subgroup(s) (under /Analyses/[--basecall- 109s group]/) containing basecalls and created within 109s [--corrected-group] containing re-squiggle results. 109s Default: ['BaseCalled_template'] 109s 109s Miscellaneous Arguments: 109s --quiet, -q Don't print status information. 109s --help, -h Print this help message and exit 109s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 109s [FAST5_BASEDIRS ...] 109s --control-fast5-basedirs 109s CONTROL_FAST5_BASEDIRS 109s [CONTROL_FAST5_BASEDIRS ...] 109s --statistics-filename 109s STATISTICS_FILENAME 109s [--genome-fasta GENOME_FASTA] 109s [--processes PROCESSES] 109s [--num-regions NUM_REGIONS] 109s [--num-bases NUM_BASES] 109s [--slide-span SLIDE_SPAN] 109s [--pdf-filename PDF_FILENAME] 109s [--r-data-filename R_DATA_FILENAME] 109s [--corrected-group CORRECTED_GROUP] 109s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 109s [--quiet] [--help] 109s 109s Required Arguments: 109s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 109s Directories containing fast5 files. 109s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 109s Set of directories containing fast5 files for control 109s reads, containing only canonical nucleotides. 109s --statistics-filename STATISTICS_FILENAME 109s File to save/load genomic base anchored statistics. 109s 109s FASTA Sequence Argument: 109s --genome-fasta GENOME_FASTA 109s FASTA file used to re-squiggle. For faster sequence 109s access. 109s 109s Multiprocessing Argument: 109s --processes PROCESSES 109s Number of processes. Default: 1 109s 109s Plotting Region Arguments: 109s --num-regions NUM_REGIONS 109s Number of regions to plot. Default: 10 109s --num-bases NUM_BASES 109s Number of bases to plot/output. Default: 21 109s --slide-span SLIDE_SPAN 109s Number of bases offset over which to search when 109s computing distances for signal cluster plotting. 109s Default: 0 (exact position) 109s 109s Output Arguments: 109s --pdf-filename PDF_FILENAME 109s PDF filename to store plot(s). Default: 109s tombo_results.signal_clusters.pdf 109s --r-data-filename R_DATA_FILENAME 109s Filename to save R data structure. Default: Don't save 109s 109s FAST5 Data Arguments: 109s --corrected-group CORRECTED_GROUP 109s FAST5 group created by resquiggle command. Default: 109s RawGenomeCorrected_000 109s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 109s FAST5 subgroup(s) (under /Analyses/[--basecall- 109s group]/) containing basecalls and created within 109s [--corrected-group] containing re-squiggle results. 109s Default: ['BaseCalled_template'] 109s 109s Miscellaneous Arguments: 109s --quiet, -q Don't print status information. 109s --help, -h Print this help message and exit 109s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 109s 109s Required Arguments: 109s fast5s_basedir Directory containing fast5 files. All files ending in 109s "fast5" found recursively within this base directory will be 109s processed. 109s 109s Miscellaneous Arguments: 109s --quiet, -q Don't print status information. 109s --help, -h Print this help message and exit 109s usage: tombo build_model event_resquiggle 109s [--minimap2-executable MINIMAP2_EXECUTABLE] 109s [--minimap2-index MINIMAP2_INDEX] 109s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 109s [--graphmap-executable GRAPHMAP_EXECUTABLE] 109s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 109s [--normalization-type {median,pA,pA_raw,none}] 109s [--pore-model-filename PORE_MODEL_FILENAME] 109s [--outlier-threshold OUTLIER_THRESHOLD] 109s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 109s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 109s [--timeout TIMEOUT] 109s [--cpts-limit CPTS_LIMIT] 109s [--skip-index] [--overwrite] 109s [--failed-reads-filename FAILED_READS_FILENAME] 109s [--include-event-stdev] 109s [--corrected-group CORRECTED_GROUP] 109s [--basecall-group BASECALL_GROUP] 109s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 109s [--processes PROCESSES] 109s [--align-processes ALIGN_PROCESSES] 109s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 109s [--resquiggle-processes RESQUIGGLE_PROCESSES] 109s [--quiet] [--help] 109s fast5s_basedir reference_fasta 109s 109s Required Arguments: 109s fast5s_basedir Directory containing fast5 files. All files ending in 109s "fast5" found recursively within this base directory 109s will be processed. 109s reference_fasta Reference genome/transcriptome FASTA file for mapping. 109s 109s Mapper Arguments (One mapper is required): 109s --minimap2-executable MINIMAP2_EXECUTABLE 109s Path to minimap2 executable. 109s --minimap2-index MINIMAP2_INDEX 109s Path to minimap2 index (with map-ont preset) file 109s corresponding to the [genome_fasta] provided. 109s --bwa-mem-executable BWA_MEM_EXECUTABLE 109s Path to bwa-mem executable. 109s --graphmap-executable GRAPHMAP_EXECUTABLE 109s Path to graphmap executable. 109s --alignment-batch-size ALIGNMENT_BATCH_SIZE 109s Number of reads included in each alignment call. Note: 109s A new system mapping call is made for each batch 109s (including loading of the genome), so it is advised to 109s use larger values for larger genomes. Default: 1000 109s 109s Signal Processing Arguments: 109s --normalization-type {median,pA,pA_raw,none} 109s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 109s as in the ONT events (using offset, range and 109s digitization), "pA": k-mer-based correction for pA 109s drift as in nanopolish (requires [--pore-model- 109s filename]), "median": median and MAD from raw signal. 109s Default: median 109s --pore-model-filename PORE_MODEL_FILENAME 109s File containing kmer model parameters (level_mean and 109s level_stdv) used in order to compute kmer-based 109s corrected pA values. E.g. https://github.com/jts/nanop 109s olish/blob/master/etc/r9- 109s models/template_median68pA.5mers.model 109s --outlier-threshold OUTLIER_THRESHOLD 109s Windosrize the signal at this number of scale values. 109s Negative value disables outlier clipping. Default: 109s 5.000000 109s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 109s Specify the 2 parameters for segmentation 1) running 109s neighboring windows width 2) minimum raw observations 109s per genomic base. Sample type defaults: RNA : 12 6 || 109s DNA : 5 3 109s 109s Read Filtering Arguments: 109s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 109s Filter reads based on observations per base percentile 109s thresholds. Format thresholds as "percentile:thresh 109s [pctl2:thresh2 ...]". For example to filter reads with 109s 99th pctl > 200 obs/base or max > 5k obs/base use 109s "99:200 100:5000". 109s --timeout TIMEOUT Timeout in seconds for processing a single read. 109s Default: No timeout. 109s --cpts-limit CPTS_LIMIT 109s Maximum number of changepoints to find within a single 109s indel group. Default: No limit. 109s 109s Input/Output Arguments: 109s --skip-index Skip creation of tombo index. This drastically slows 109s downstream tombo commands. Default stores tombo index 109s named ".[--fast5-basedir].[--corrected- 109s group].tombo.index" to be loaded automatically for 109s downstream commands. 109s --overwrite Overwrite previous corrected group in FAST5 files. 109s Note: only effects --corrected-group or --new- 109s corrected-group. 109s --failed-reads-filename FAILED_READS_FILENAME 109s Output failed read filenames with assoicated error. 109s Default: Do not store failed reads. 109s --include-event-stdev 109s Include corrected event standard deviation in output 109s FAST5 data. 109s 109s FAST5 Data Arguments: 109s --corrected-group CORRECTED_GROUP 109s FAST5 group created by resquiggle command. Default: 109s RawGenomeCorrected_000 109s --basecall-group BASECALL_GROUP 109s FAST5 group obtain original basecalls (under Analyses 109s group). Default: Basecall_1D_000 109s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 109s FAST5 subgroup(s) (under /Analyses/[--basecall- 109s group]/) containing basecalls and created within 109s [--corrected-group] containing re-squiggle results. 109s Default: ['BaseCalled_template'] 109s 109s Multiprocessing Arguments: 109s --processes PROCESSES 109s Number of processes. Default: 2 109s --align-processes ALIGN_PROCESSES 109s Number of processes to use for parsing and aligning 109s original basecalls. Each process will independently 109s load the genome into memory, so use caution with 109s larger genomes (e.g. human). Default: 1 109s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 109s Number of threads to use for aligner system call. 109s Default: [--processes] / (2 * [--align-processes)] 109s --resquiggle-processes RESQUIGGLE_PROCESSES 109s Number of processes to use for resquiggle algorithm. 109s Default: [--processes] / 2 109s 109s Miscellaneous Arguments: 109s --quiet, -q Don't print status information. 109s --help, -h Print this help message and exit 109s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 109s [FAST5_BASEDIRS ...] 109s --tombo-model-filename 109s TOMBO_MODEL_FILENAME 109s [--estimate-mean] 109s [--kmer-specific-sd] 109s [--upstream-bases {0,1,2,3,4}] 109s [--downstream-bases {0,1,2,3,4}] 109s [--minimum-test-reads MINIMUM_TEST_READS] 109s [--coverage-threshold COVERAGE_THRESHOLD] 109s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 109s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 109s [--processes PROCESSES] 109s [--corrected-group CORRECTED_GROUP] 109s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 109s [--quiet] [--help] 109s 109s Required Arguments: 109s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 109s Directories containing fast5 files. 109s --tombo-model-filename TOMBO_MODEL_FILENAME 109s Filename to save Tombo model. 109s 109s Modeling Arguments: 109s --estimate-mean Use the mean instead of median for model level 109s estimation. Note: This can cause poor fits due to 109s outliers 109s --kmer-specific-sd Estimate standard deviation for each k-mers 109s individually. 109s --upstream-bases {0,1,2,3,4} 109s Upstream bases in k-mer. Default: 1 109s --downstream-bases {0,1,2,3,4} 109s Downstream bases in k-mer. Default: 2 109s 109s Filtering Arguments: 109s --minimum-test-reads MINIMUM_TEST_READS 109s Number of reads required at a position to perform 109s significance testing or contribute to model 109s estimation. Default: 10 109s --coverage-threshold COVERAGE_THRESHOLD 109s Maximum mean coverage per region when estimating k-mer 109s model (limits compute time for deep samples). Default: 109s 100 109s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 109s Number of each k-mer observations required in order to 109s produce a reference (genomic locations for standard 109s reference and per-read for alternative reference). 109s Default: 5 109s 109s Multiprocessing Arguments: 109s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 109s Size of regions over which to multiprocesses statistic 109s computation. For very deep samples a smaller value is 109s recommmended in order to control memory consumption. 109s Default: 10000 109s --processes PROCESSES 109s Number of processes. Default: 1 109s 109s FAST5 Data Arguments: 109s --corrected-group CORRECTED_GROUP 109s FAST5 group created by resquiggle command. Default: 109s RawGenomeCorrected_000 109s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 109s FAST5 subgroup(s) (under /Analyses/[--basecall- 109s group]/) containing basecalls and created within 109s [--corrected-group] containing re-squiggle results. 109s Default: ['BaseCalled_template'] 109s 109s Miscellaneous Arguments: 109s --quiet, -q Don't print status information. 109s --help, -h Print this help message and exit 109s usage: tombo build_model estimate_alt_reference --alternate-model-filename 109s ALTERNATE_MODEL_FILENAME 109s --alternate-model-name 109s ALTERNATE_MODEL_NAME 109s --alternate-model-base 109s {A,C,G,T} 109s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 109s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 109s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 109s [--control-density-filename CONTROL_DENSITY_FILENAME] 109s [--dna] [--rna] 109s [--tombo-model-filename TOMBO_MODEL_FILENAME] 109s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 109s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 109s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 109s [--save-density-basename SAVE_DENSITY_BASENAME] 109s [--processes PROCESSES] 109s [--corrected-group CORRECTED_GROUP] 109s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 109s [--quiet] [--help] 109s 109s Required Arguments: 109s --alternate-model-filename ALTERNATE_MODEL_FILENAME 109s Tombo model for alternative likelihood ratio 109s significance testing. 109s --alternate-model-name ALTERNATE_MODEL_NAME 109s A short name to associate with this alternate model 109s (e.g. 5mC, 6mA, etc.). This text will be included in 109s output filenames when this model is used for testing. 109s --alternate-model-base {A,C,G,T} 109s Non-standard base is an alternative to this base. 109s 109s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 109s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 109s Directories containing fast5 files. 109s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 109s Set of directories containing fast5 files for control 109s reads, containing only canonical nucleotides. 109s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 109s File containing k-mer level kernel density estimates 109s for the alternative sample saved using --save-density- 109s basename. 109s --control-density-filename CONTROL_DENSITY_FILENAME 109s File containing k-mer level kernel density estimates 109s for the control sample saved using --save-density- 109s basename. 109s 109s Standard Model Arguments: 109s --dna Explicitly select canonical DNA model. Default: 109s Automatically determine from FAST5s 109s --rna Explicitly select canonical RNA model. Default: 109s Automatically determine from FAST5s 109s --tombo-model-filename TOMBO_MODEL_FILENAME 109s Tombo model filename. If no file is provided, the 109s default DNA or RNA Tombo model will be used. 109s 109s Model Fitting Arguments: 109s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 109s When esitmating the alternative base incorporation 109s rate, this percent of k-mers are assumed to have 109s significantly shifted signal so the alternative 109s distribution minimally overlaps the standard base 109s distribution. Default: 5.000000 109s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 109s Bandwidth applied when performing Gaussian kernal 109s density esitmation on standard and alternative base 109s signal distributions. Default: 0.050000 109s 109s Filtering Argument: 109s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 109s Number of each k-mer observations required in order to 109s produce a reference (genomic locations for standard 109s reference and per-read for alternative reference). 109s Default: 1000 109s 109s Output Argument: 109s --save-density-basename SAVE_DENSITY_BASENAME 109s Basename to save alternative model estimation density 109s estimation information. See scripts/debug_est_alt.R 109s for info use example. Default: Don't save. 109s 109s Multiprocessing Arguments: 109s --processes PROCESSES 109s Number of processes. Default: 1 109s 109s FAST5 Data Arguments: 109s --corrected-group CORRECTED_GROUP 109s FAST5 group created by resquiggle command. Default: 109s RawGenomeCorrected_000 109s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 109s FAST5 subgroup(s) (under /Analyses/[--basecall- 109s group]/) containing basecalls and created within 109s [--corrected-group] containing re-squiggle results. 109s Default: ['BaseCalled_template'] 109s 109s Miscellaneous Arguments: 109s --quiet, -q Don't print status information. 109s --help, -h Print this help message and exit 109s This test only tests the help system 109s There is an extensive test in 109s 109s tombo/tests/shell_tests.sh 109s 109s but this requires to download larger data 109s sets which is not done for the moment. 110s autopkgtest [16:39:48]: test run-unit-test: -----------------------] 110s autopkgtest [16:39:48]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 110s run-unit-test PASS 111s autopkgtest [16:39:49]: @@@@@@@@@@@@@@@@@@@@ summary 111s run-unit-test PASS 123s nova [W] Using flock in prodstack6-s390x 123s Creating nova instance adt-plucky-s390x-tombo-20241113-163758-juju-7f2275-prod-proposed-migration-environment-20-1daf3800-a763-46e5-a140-eba0899cb53e from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)...