1s autopkgtest [09:11:25]: starting date and time: 2024-11-13 09:11:25+0000 1s autopkgtest [09:11:25]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 1s autopkgtest [09:11:25]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6z0v3psq/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-31.secgroup --name adt-plucky-amd64-tombo-20241113-091124-juju-7f2275-prod-proposed-migration-environment-2-6e74b294-308d-4f2e-b67a-be72d4a69cb7 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,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/ 66s autopkgtest [09:12:30]: testbed dpkg architecture: amd64 66s autopkgtest [09:12:30]: testbed apt version: 2.9.8 66s autopkgtest [09:12:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 66s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 66s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 66s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 66s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 66s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 67s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 67s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 67s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 67s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 67s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 67s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 67s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 67s Fetched 2173 kB in 1s (3937 kB/s) 67s Reading package lists... 68s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Calculating upgrade... 69s The following NEW packages will be installed: 69s python3.13-gdbm 69s The following packages will be upgraded: 69s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 69s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 69s Need to get 253 kB of archives. 69s After this operation, 147 kB of additional disk space will be used. 69s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 69s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 69s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 69s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 69s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 69s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 70s Fetched 253 kB in 0s (2145 kB/s) 70s (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 ... 75541 files and directories currently installed.) 70s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 70s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 70s Setting up python3-minimal (3.12.7-1) ... 70s (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 ... 75541 files and directories currently installed.) 70s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 70s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 70s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 70s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 70s Selecting previously unselected package python3.13-gdbm. 70s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 70s Unpacking python3.13-gdbm (3.13.0-2) ... 70s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 70s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 70s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 70s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 70s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 70s Setting up python3.13-gdbm (3.13.0-2) ... 70s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 70s Setting up python3 (3.12.7-1) ... 71s Setting up python3-gdbm:amd64 (3.12.7-1) ... 71s Processing triggers for man-db (2.12.1-3) ... 71s Processing triggers for libc-bin (2.40-1ubuntu3) ... 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 73s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 73s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 73s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 73s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 74s Reading package lists... 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Calculating upgrade... 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s autopkgtest [09:12:40]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 76s autopkgtest [09:12:40]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 79s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (dsc) [2291 B] 79s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (tar) [22.3 MB] 79s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (diff) [7100 B] 80s gpgv: Signature made Wed Apr 10 17:15:32 2024 UTC 80s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 80s gpgv: Can't check signature: No public key 80s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6build1.dsc: no acceptable signature found 80s autopkgtest [09:12:44]: testing package tombo version 1.5.1-6build1 80s autopkgtest [09:12:44]: build not needed 80s autopkgtest [09:12:44]: test run-unit-test: preparing testbed 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s Starting pkgProblemResolver with broken count: 0 81s Starting 2 pkgProblemResolver with broken count: 0 81s Done 82s The following additional packages will be installed: 82s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 82s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 82s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 82s python3-decorator python3-h5py python3-h5py-serial python3-mappy 82s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 82s tombo-doc 82s Suggested packages: 82s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 82s gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 82s Recommended packages: 82s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 82s python3-rpy2 82s The following NEW packages will be installed: 82s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 82s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 82s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 82s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 82s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 82s tombo-doc 82s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 82s Need to get 64.2 MB/64.2 MB of archives. 82s After this operation, 207 MB of additional disk space will be used. 82s Get:1 /tmp/autopkgtest.35pQ6O/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [708 B] 82s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-lato all 2.015-1 [2781 kB] 82s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 82s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 82s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 82s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 82s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 83s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 83s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 83s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB] 83s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 83s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 83s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 83s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 83s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 83s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 83s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 83s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 83s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.11.0-5ubuntu1 [1107 kB] 83s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 83s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mappy amd64 2.27+dfsg-1 [150 kB] 83s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tqdm all 4.67.0-1 [91.6 kB] 83s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 83s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 85s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 tombo amd64 1.5.1-6build1 [450 kB] 85s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 85s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 tombo-doc all 1.5.1-6build1 [21.7 MB] 87s Fetched 64.2 MB in 5s (12.4 MB/s) 87s Selecting previously unselected package fonts-lato. 87s (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 ... 75548 files and directories currently installed.) 87s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 87s Unpacking fonts-lato (2.015-1) ... 88s Selecting previously unselected package fonts-font-awesome. 88s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 88s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 88s Selecting previously unselected package fonts-mathjax. 88s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 88s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 88s Selecting previously unselected package libaec0:amd64. 88s Preparing to unpack .../03-libaec0_1.1.3-1_amd64.deb ... 88s Unpacking libaec0:amd64 (1.1.3-1) ... 88s Selecting previously unselected package libblas3:amd64. 88s Preparing to unpack .../04-libblas3_3.12.0-3build2_amd64.deb ... 88s Unpacking libblas3:amd64 (3.12.0-3build2) ... 88s Selecting previously unselected package libgfortran5:amd64. 88s Preparing to unpack .../05-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 88s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 88s Selecting previously unselected package libsz2:amd64. 88s Preparing to unpack .../06-libsz2_1.1.3-1_amd64.deb ... 88s Unpacking libsz2:amd64 (1.1.3-1) ... 88s Selecting previously unselected package libhdf5-103-1t64:amd64. 88s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ... 88s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 88s Selecting previously unselected package libhdf5-hl-100t64:amd64. 88s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_amd64.deb ... 88s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 88s Selecting previously unselected package libjs-jquery. 88s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 88s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 88s Selecting previously unselected package libjs-underscore. 88s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 88s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 88s Selecting previously unselected package libjs-sphinxdoc. 88s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-4_all.deb ... 88s Unpacking libjs-sphinxdoc (7.4.7-4) ... 88s Selecting previously unselected package liblapack3:amd64. 88s Preparing to unpack .../12-liblapack3_3.12.0-3build2_amd64.deb ... 88s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 88s Selecting previously unselected package liblbfgsb0:amd64. 88s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 88s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 88s Selecting previously unselected package liblzf1:amd64. 88s Preparing to unpack .../14-liblzf1_3.6-4_amd64.deb ... 88s Unpacking liblzf1:amd64 (3.6-4) ... 88s Selecting previously unselected package python3-decorator. 88s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 88s Unpacking python3-decorator (5.1.1-5) ... 88s Selecting previously unselected package python3-numpy. 88s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 88s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 88s Selecting previously unselected package python3-h5py-serial. 88s Preparing to unpack .../17-python3-h5py-serial_3.11.0-5ubuntu1_amd64.deb ... 88s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 89s Selecting previously unselected package python3-h5py. 89s Preparing to unpack .../18-python3-h5py_3.11.0-5ubuntu1_all.deb ... 89s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 89s Selecting previously unselected package python3-mappy. 89s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1_amd64.deb ... 89s Unpacking python3-mappy (2.27+dfsg-1) ... 89s Selecting previously unselected package python3-tqdm. 89s Preparing to unpack .../20-python3-tqdm_4.67.0-1_all.deb ... 89s Unpacking python3-tqdm (4.67.0-1) ... 89s Selecting previously unselected package sphinx-rtd-theme-common. 89s Preparing to unpack .../21-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 89s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 89s Selecting previously unselected package python3-scipy. 89s Preparing to unpack .../22-python3-scipy_1.13.1-5_amd64.deb ... 89s Unpacking python3-scipy (1.13.1-5) ... 89s Selecting previously unselected package tombo. 89s Preparing to unpack .../23-tombo_1.5.1-6build1_amd64.deb ... 89s Unpacking tombo (1.5.1-6build1) ... 89s Selecting previously unselected package libjs-mathjax. 89s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 89s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 90s Selecting previously unselected package tombo-doc. 90s Preparing to unpack .../25-tombo-doc_1.5.1-6build1_all.deb ... 90s Unpacking tombo-doc (1.5.1-6build1) ... 90s Selecting previously unselected package autopkgtest-satdep. 90s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 90s Unpacking autopkgtest-satdep (0) ... 90s Setting up fonts-lato (2.015-1) ... 90s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 90s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 90s Setting up python3-tqdm (4.67.0-1) ... 90s Setting up python3-mappy (2.27+dfsg-1) ... 91s Setting up libaec0:amd64 (1.1.3-1) ... 91s Setting up python3-decorator (5.1.1-5) ... 91s Setting up libblas3:amd64 (3.12.0-3build2) ... 91s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 91s Setting up liblzf1:amd64 (3.6-4) ... 91s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 91s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 91s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 91s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 91s Setting up libsz2:amd64 (1.1.3-1) ... 91s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 91s Setting up liblapack3:amd64 (3.12.0-3build2) ... 91s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 91s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 92s Setting up libjs-sphinxdoc (7.4.7-4) ... 92s Setting up tombo-doc (1.5.1-6build1) ... 92s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 92s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 92s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 92s Setting up python3-scipy (1.13.1-5) ... 95s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 96s Setting up python3-h5py (3.11.0-5ubuntu1) ... 96s Setting up tombo (1.5.1-6build1) ... 96s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 96s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 96s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 96s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 96s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 96s re.match('\+', fastq_rec[2]) is None): 96s Setting up autopkgtest-satdep (0) ... 96s Processing triggers for man-db (2.12.1-3) ... 96s Processing triggers for libc-bin (2.40-1ubuntu3) ... 100s (Reading database ... 82750 files and directories currently installed.) 100s Removing autopkgtest-satdep (0) ... 100s autopkgtest [09:13:04]: test run-unit-test: [----------------------- 100s ********* Testing help commands ********** 100s usage: tombo [-h] [-v] 100s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 100s ... 100s 100s ********** Tombo ********* 100s 100s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 100s 100s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 100s 100s Tombo command groups (additional help available within each command group): 100s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 100s preprocess Pre-process nanopore reads for Tombo processing. 100s filter Apply filter to Tombo index file for specified criterion. 100s detect_modifications Perform statistical testing to detect non-standard nucleotides. 100s text_output Output Tombo results in text files. 100s build_model Create canonical and alternative base Tombo models. 100s plot Save plots to visualize raw nanopore signal or testing results. 100s 100s options: 100s -h, --help show this help message and exit 100s -v, --version show Tombo version and exit. 100s usage: tombo resquiggle [--dna] [--rna] 100s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 100s [--q-score Q_SCORE] 100s [--signal-matching-score SIGNAL_MATCHING_SCORE] 100s [--processes PROCESSES] 100s [--corrected-group CORRECTED_GROUP] 100s [--basecall-group BASECALL_GROUP] 100s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 100s [--overwrite] 100s [--failed-reads-filename FAILED_READS_FILENAME] 100s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 100s [--print-advanced-arguments] [--quiet] [--help] 100s fast5s_basedir reference 100s 100s Required Arguments: 100s fast5s_basedir Directory containing fast5 files. All files ending in 100s "fast5" found recursively within this base directory 100s will be processed. 100s reference Reference genome/transcriptome FASTA file or minimap2 100s index (with "map-ont" preset) for mapping. 100s 100s Model Parameters: 100s --dna Explicitly select canonical DNA model. Default: 100s Automatically determine from FAST5s 100s --rna Explicitly select canonical RNA model. Default: 100s Automatically determine from FAST5s 100s 100s Read Filtering Argument: 100s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 100s Filter reads based on observations per base percentile 100s thresholds. Format thresholds as "percentile:thresh 100s [pctl2:thresh2 ...]". For example to filter reads with 100s 99th pctl > 200 obs/base or max > 5k obs/base use 100s "99:200 100:5000". 100s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 100s Default: 0.000000 100s --signal-matching-score SIGNAL_MATCHING_SCORE 100s Observed to expected signal matching score (higher 100s score indicates poor matching). Sample type defaults: 100s RNA : 2 || DNA : 1.1 100s 100s Multiprocessing Arguments: 100s --processes PROCESSES 100s Number of processes. Default: 1 100s 100s FAST5 Data Arguments: 100s --corrected-group CORRECTED_GROUP 100s FAST5 group created by resquiggle command. Default: 100s RawGenomeCorrected_000 100s --basecall-group BASECALL_GROUP 100s FAST5 group obtain original basecalls (under Analyses 100s group). Default: Basecall_1D_000 100s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 100s FAST5 subgroup(s) (under /Analyses/[--basecall- 100s group]/) containing basecalls and created within 100s [--corrected-group] containing re-squiggle results. 100s Default: ['BaseCalled_template'] 100s --overwrite Overwrite previous corrected group in FAST5 files. 100s Note: only effects --corrected-group or --new- 100s corrected-group. 100s 100s Input/Output Arguments: 100s --failed-reads-filename FAILED_READS_FILENAME 100s Output failed read filenames with assoicated error. 100s Default: Do not store failed reads. 100s --num-most-common-errors NUM_MOST_COMMON_ERRORS 100s Dynamically show this many most common errors so far 100s through run. Default: 0; Just show progress 100s 100s Advanced Arguments: 100s --print-advanced-arguments 100s Print advanced re-squiggle arguments and exit. 100s 100s Miscellaneous Arguments: 100s --quiet, -q Don't print status information. 100s --help, -h Print this help message and exit 100s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 100s --fastq-filenames 100s FASTQ_FILENAMES 100s [FASTQ_FILENAMES ...] 100s [--basecall-group BASECALL_GROUP] 100s [--basecall-subgroup BASECALL_SUBGROUP] 100s [--overwrite] 100s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 100s [--processes PROCESSES] 100s [--quiet] [--help] 100s 100s Required Arguments: 100s --fast5-basedir FAST5_BASEDIR 100s Directory containing fast5 files. 100s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 100s FASTQ filenames containing basecalls to be added to 100s raw FAST5 files. 100s 100s FAST5 Data Arguments: 100s --basecall-group BASECALL_GROUP 100s FAST5 group obtain original basecalls (under Analyses 100s group). Default: Basecall_1D_000 100s --basecall-subgroup BASECALL_SUBGROUP 100s FAST5 subgroup (under /Analyses/[--basecall-group]/) 100s under which to store basecalls from FASTQs. Default: 100s BaseCalled_template 100s --overwrite Overwrite previous corrected group in FAST5 files. 100s Note: only effects --corrected-group or --new- 100s corrected-group. 100s 100s Sequencing Summary Argument: 100s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 100s Sequencing summary filenames produced by albacore. 100s These can make annotation of raw FAST5 files with 100s FASTQ sequence much faster. 100s 100s Multiprocessing Argument: 100s --processes PROCESSES 100s Number of processes. Default: 1 100s 100s Miscellaneous Arguments: 100s --quiet, -q Don't print status information. 100s --help, -h Print this help message and exit 100s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 100s [FAST5_BASEDIRS ...] 100s [--corrected-group CORRECTED_GROUP] 100s [--quiet] [--help] 100s 100s Required Argument: 100s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 100s Directories containing fast5 files. 100s 100s FAST5 Data Argument: 100s --corrected-group CORRECTED_GROUP 100s FAST5 group created by resquiggle command. Default: 100s RawGenomeCorrected_000 100s 100s Miscellaneous Arguments: 100s --quiet, -q Don't print status information. 100s --help, -h Print this help message and exit 100s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 100s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 100s [--corrected-group CORRECTED_GROUP] [--quiet] 100s [--help] 100s 100s Required Argument: 100s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 100s Directories containing fast5 files. 100s 100s Read Filtering Argument: 100s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 100s Filter reads based on observations per base percentile 100s thresholds. Format thresholds as "percentile:thresh 100s [pctl2:thresh2 ...]". For example to filter reads with 100s 99th pctl > 200 obs/base or max > 5k obs/base use 100s "99:200 100:5000". 100s 100s FAST5 Data Argument: 100s --corrected-group CORRECTED_GROUP 100s FAST5 group created by resquiggle command. Default: 100s RawGenomeCorrected_000 100s 100s Miscellaneous Arguments: 100s --quiet, -q Don't print status information. 100s --help, -h Print this help message and exit 101s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 101s [FAST5_BASEDIRS ...] 101s [--percent-to-filter PERCENT_TO_FILTER] 101s [--corrected-group CORRECTED_GROUP] 101s [--quiet] [--help] 101s 101s Required Arguments: 101s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 101s Directories containing fast5 files. 101s 101s Read Filtering Argument: 101s --percent-to-filter PERCENT_TO_FILTER 101s Percentage of all reads to filter. Reads are randomly 101s selected weighted according to the approximate 101s coverage at the mapped genomic location. This can be 101s useful in modeling and testing. Default: 10.000000 101s 101s FAST5 Data Arguments: 101s --corrected-group CORRECTED_GROUP 101s FAST5 group created by resquiggle command. Default: 101s RawGenomeCorrected_000 101s 101s Miscellaneous Arguments: 101s --quiet, -q Don't print status information. 101s --help, -h Print this help message and exit 101s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 101s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 101s [--corrected-group CORRECTED_GROUP] 101s [--basecall-group BASECALL_GROUP] [--quiet] 101s [--help] 101s 101s Required Arguments: 101s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 101s Directories containing fast5 files. 101s 101s Read Filtering Argument: 101s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 101s Default: 7.000000 101s 101s FAST5 Data Arguments: 101s --corrected-group CORRECTED_GROUP 101s FAST5 group created by resquiggle command. Default: 101s RawGenomeCorrected_000 101s --basecall-group BASECALL_GROUP 101s FAST5 group obtain original basecalls (under Analyses 101s group). Default: Basecall_1D_000 101s 101s Miscellaneous Arguments: 101s --quiet, -q Don't print status information. 101s --help, -h Print this help message and exit 101s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 101s [FAST5_BASEDIRS ...] 101s --signal-matching-score 101s SIGNAL_MATCHING_SCORE 101s [--corrected-group CORRECTED_GROUP] 101s [--quiet] [--help] 101s 101s Required Arguments: 101s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 101s Directories containing fast5 files. 101s --signal-matching-score SIGNAL_MATCHING_SCORE 101s Observed to expected signal matching score (higher 101s score indicates poor matching). Sample type defaults: 101s RNA : 2 || DNA : 1.1 101s 101s FAST5 Data Arguments: 101s --corrected-group CORRECTED_GROUP 101s FAST5 group created by resquiggle command. Default: 101s RawGenomeCorrected_000 101s 101s Miscellaneous Arguments: 101s --quiet, -q Don't print status information. 101s --help, -h Print this help message and exit 101s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 101s [FAST5_BASEDIRS ...] 101s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 101s [--include-partial-overlap] 101s [--corrected-group CORRECTED_GROUP] 101s [--quiet] [--help] 101s 101s Required Arguments: 101s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 101s Directories containing fast5 files. 101s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 101s Filter out reads not falling completely within include 101s regions. Omit start and end coordinates to include an 101s entire chromosome/sequence record. Format regions as 101s "chrm[:start-end] [chrm2[:start2-end2] ...]". 101s 101s Filter Argument: 101s --include-partial-overlap 101s Include reads that partially overlap the specified 101s region. Default: Only include reads completely 101s contained in a specified region 101s 101s FAST5 Data Argument: 101s --corrected-group CORRECTED_GROUP 101s FAST5 group created by resquiggle command. Default: 101s RawGenomeCorrected_000 101s 101s Miscellaneous Arguments: 101s --quiet, -q Don't print status information. 101s --help, -h Print this help message and exit 101s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 101s [FAST5_BASEDIRS ...] 101s --statistics-file-basename 101s STATISTICS_FILE_BASENAME [--dna] 101s [--rna] 101s [--fishers-method-context FISHERS_METHOD_CONTEXT] 101s [--minimum-test-reads MINIMUM_TEST_READS] 101s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 101s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 101s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 101s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 101s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 101s [--processes PROCESSES] 101s [--corrected-group CORRECTED_GROUP] 101s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 101s [--quiet] [--help] 101s 101s Required Argument: 101s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 101s Directories containing fast5 files. 101s --statistics-file-basename STATISTICS_FILE_BASENAME 101s File base name to save base by base statistics from 101s testing. Filenames will be [--statistics-file- 101s basename].[--alternate-bases]?.tombo.stats 101s 101s Comparison Model Arguments: 101s --dna Explicitly select canonical DNA model. Default: 101s Automatically determine from FAST5s 101s --rna Explicitly select canonical RNA model. Default: 101s Automatically determine from FAST5s 101s 101s Significance Test Arguments: 101s --fishers-method-context FISHERS_METHOD_CONTEXT 101s Number of context bases up and downstream over which 101s to compute Fisher's method combined p-values. Note: 101s Not applicable for alternative model likelihood ratio 101s tests. Default: 1. 101s --minimum-test-reads MINIMUM_TEST_READS 101s Number of reads required at a position to perform 101s significance testing or contribute to model 101s estimation. Default: 1 101s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 101s P-value threshold when computing fraction of 101s significant reads at each genomic position. If two 101s values are provided, statistics between these values 101s are not considered. Default thresholds: DNA:0.15-0.5 , 101s RNA:0.05-0.4 101s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 101s Dampen fraction modified estimates for low coverage 101s sites. Two parameters are unmodified and modified 101s pseudo read counts. This is equivalent to a beta prior 101s on the fraction estimate. Set to "0 0" to disable 101s dampened fraction estimation. Default: [2, 0] 101s 101s Output Argument: 101s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 101s Base for binary files containing per-read statistics 101s from statistical testing. Filenames will be [--per- 101s read-statistics-basename].[--alternate- 101s bases]?.tombo.per_read_stats 101s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 101s Number of the most significant sites to store for 101s faster access. If a longer list of most significant 101s sites is required the list must be re-computed from 101s all batches. Very large values can increase RAM usage. 101s Default: 100000 101s 101s Multiprocessing Arguments: 101s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 101s Size of regions over which to multiprocesses statistic 101s computation. For very deep samples a smaller value is 101s recommmended in order to control memory consumption. 101s Default: 10000 101s --processes PROCESSES 101s Number of processes. Default: 1 101s 101s FAST5 Data Arguments: 101s --corrected-group CORRECTED_GROUP 101s FAST5 group created by resquiggle command. Default: 101s RawGenomeCorrected_000 101s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 101s FAST5 subgroup(s) (under /Analyses/[--basecall- 101s group]/) containing basecalls and created within 101s [--corrected-group] containing re-squiggle results. 101s Default: ['BaseCalled_template'] 101s 101s Miscellaneous Arguments: 101s --quiet, -q Don't print status information. 101s --help, -h Print this help message and exit 101s usage: tombo detect_modifications alternative_model 101s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 101s [--statistics-file-basename STATISTICS_FILE_BASENAME] 101s [--alternate-bases {6mA,dcm,dam,5mC,CpG} [{6mA,dcm,dam,5mC,CpG} ...]] 101s [--print-available-models] 101s [--dna] [--rna] 101s [--minimum-test-reads MINIMUM_TEST_READS] 101s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 101s [--standard-log-likelihood-ratio] 101s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 101s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 101s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 101s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 101s [--processes PROCESSES] 101s [--corrected-group CORRECTED_GROUP] 101s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 101s [--quiet] [--help] 101s 101s Required Argument: 101s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 101s Directories containing fast5 files. 101s --statistics-file-basename STATISTICS_FILE_BASENAME 101s File base name to save base by base statistics from 101s testing. Filenames will be [--statistics-file- 101s basename].[--alternate-bases]?.tombo.stats 101s --alternate-bases {6mA,dcm,dam,5mC,CpG} [{6mA,dcm,dam,5mC,CpG} ...] 101s Default non-standard base model for testing (not 101s required if user created --alternate-model-filenames 101s is provided). 101s 101s Comparison Arguments: 101s --print-available-models 101s Print available alternative models and exit. 101s --dna Explicitly select canonical DNA model. Default: 101s Automatically determine from FAST5s 101s --rna Explicitly select canonical RNA model. Default: 101s Automatically determine from FAST5s 101s 101s Significance Test Arguments: 101s --minimum-test-reads MINIMUM_TEST_READS 101s Number of reads required at a position to perform 101s significance testing or contribute to model 101s estimation. Default: 1 101s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 101s Log likelihood ratio threshold when computing fraction 101s of significant reads at each genomic position. If two 101s values are provided, statistics between these values 101s are not considered. Default thresholds: DNA:-1.5-2.5 , 101s RNA:-2.5-2.5 101s --standard-log-likelihood-ratio 101s Use a standard log likelihood ratio (LLR) statistic. 101s Default is to use an outlier-robust LLR-like 101s statistic. Detail in full online documentation. 101s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 101s Dampen fraction modified estimates for low coverage 101s sites. Two parameters are unmodified and modified 101s pseudo read counts. This is equivalent to a beta prior 101s on the fraction estimate. Set to "0 0" to disable 101s dampened fraction estimation. Default: [2, 0] 101s 101s Output Argument: 101s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 101s Base for binary files containing per-read statistics 101s from statistical testing. Filenames will be [--per- 101s read-statistics-basename].[--alternate- 101s bases]?.tombo.per_read_stats 101s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 101s Number of the most significant sites to store for 101s faster access. If a longer list of most significant 101s sites is required the list must be re-computed from 101s all batches. Very large values can increase RAM usage. 101s Default: 100000 101s 101s Multiprocessing Arguments: 101s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 101s Size of regions over which to multiprocesses statistic 101s computation. For very deep samples a smaller value is 101s recommmended in order to control memory consumption. 101s Default: 10000 101s --processes PROCESSES 101s Number of processes. Default: 1 101s 101s FAST5 Data Arguments: 101s --corrected-group CORRECTED_GROUP 101s FAST5 group created by resquiggle command. Default: 101s RawGenomeCorrected_000 101s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 101s FAST5 subgroup(s) (under /Analyses/[--basecall- 101s group]/) containing basecalls and created within 101s [--corrected-group] containing re-squiggle results. 101s Default: ['BaseCalled_template'] 101s 101s Miscellaneous Arguments: 101s --quiet, -q Don't print status information. 101s --help, -h Print this help message and exit 101s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 101s FAST5_BASEDIRS 101s [FAST5_BASEDIRS ...] 101s --statistics-file-basename 101s STATISTICS_FILE_BASENAME 101s --control-fast5-basedirs 101s CONTROL_FAST5_BASEDIRS 101s [CONTROL_FAST5_BASEDIRS ...] 101s [--sample-only-estimates] 101s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 101s [--dna] [--rna] 101s [--fishers-method-context FISHERS_METHOD_CONTEXT] 101s [--minimum-test-reads MINIMUM_TEST_READS] 101s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 101s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 101s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 101s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 101s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 101s [--processes PROCESSES] 101s [--corrected-group CORRECTED_GROUP] 101s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 101s [--quiet] [--help] 101s 101s Required Argument: 101s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 101s Directories containing fast5 files. 101s --statistics-file-basename STATISTICS_FILE_BASENAME 101s File base name to save base by base statistics from 101s testing. Filenames will be [--statistics-file- 101s basename].[--alternate-bases]?.tombo.stats 101s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 101s Set of directories containing fast5 files for control 101s reads, containing only canonical nucleotides. 101s 101s Model Prior Arguments: 101s --sample-only-estimates 101s Only use canonical sample to estimate expected signal 101s level and spread. Default: Use canonical model to 101s improve estimtates (esp. for low coverage regions) 101s using baysian posterior estimates. 101s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 101s Prior weights (one each for mean and spread) applied 101s to canonical base model for estimating posterior model 101s parameters for sample comparison. Default: [5, 40] 101s --dna Explicitly select canonical DNA model. Default: 101s Automatically determine from FAST5s 101s --rna Explicitly select canonical RNA model. Default: 101s Automatically determine from FAST5s 101s 101s Significance Test Arguments: 101s --fishers-method-context FISHERS_METHOD_CONTEXT 101s Number of context bases up and downstream over which 101s to compute Fisher's method combined p-values. Note: 101s Not applicable for alternative model likelihood ratio 101s tests. Default: 1. 101s --minimum-test-reads MINIMUM_TEST_READS 101s Number of reads required at a position to perform 101s significance testing or contribute to model 101s estimation. Default: 1 101s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 101s P-value threshold when computing fraction of 101s significant reads at each genomic position. If two 101s values are provided, statistics between these values 101s are not considered. Default thresholds: DNA:0.15-0.5 , 101s RNA:0.05-0.4 101s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 101s Dampen fraction modified estimates for low coverage 101s sites. Two parameters are unmodified and modified 101s pseudo read counts. This is equivalent to a beta prior 101s on the fraction estimate. Set to "0 0" to disable 101s dampened fraction estimation. Default: [2, 0] 101s 101s Output Argument: 101s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 101s Base for binary files containing per-read statistics 101s from statistical testing. Filenames will be [--per- 101s read-statistics-basename].[--alternate- 101s bases]?.tombo.per_read_stats 101s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 101s Number of the most significant sites to store for 101s faster access. If a longer list of most significant 101s sites is required the list must be re-computed from 101s all batches. Very large values can increase RAM usage. 101s Default: 100000 101s 101s Multiprocessing Arguments: 101s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 101s Size of regions over which to multiprocesses statistic 101s computation. For very deep samples a smaller value is 101s recommmended in order to control memory consumption. 101s Default: 10000 101s --processes PROCESSES 101s Number of processes. Default: 1 101s 101s FAST5 Data Arguments: 101s --corrected-group CORRECTED_GROUP 101s FAST5 group created by resquiggle command. Default: 101s RawGenomeCorrected_000 101s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 101s FAST5 subgroup(s) (under /Analyses/[--basecall- 101s group]/) containing basecalls and created within 101s [--corrected-group] containing re-squiggle results. 101s Default: ['BaseCalled_template'] 101s 101s Miscellaneous Arguments: 101s --quiet, -q Don't print status information. 101s --help, -h Print this help message and exit 101s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 101s FAST5_BASEDIRS 101s [FAST5_BASEDIRS ...] 101s --statistics-file-basename 101s STATISTICS_FILE_BASENAME 101s --alternate-fast5-basedirs 101s ALTERNATE_FAST5_BASEDIRS 101s [ALTERNATE_FAST5_BASEDIRS ...] 101s [--fishers-method-context FISHERS_METHOD_CONTEXT] 101s [--minimum-test-reads MINIMUM_TEST_READS] 101s [--statistic-type {ks,u,t}] 101s [--store-p-value] 101s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 101s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 101s [--processes PROCESSES] 101s [--corrected-group CORRECTED_GROUP] 101s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 101s [--quiet] [--help] 101s 101s Required Argument: 101s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 101s Directories containing fast5 files. 101s --statistics-file-basename STATISTICS_FILE_BASENAME 101s File base name to save base by base statistics from 101s testing. Filenames will be [--statistics-file- 101s basename].[--alternate-bases]?.tombo.stats 101s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 101s Set of directories containing fast5 files for 101s alternate set of reads. 101s 101s Significance Test Arguments: 101s --fishers-method-context FISHERS_METHOD_CONTEXT 101s Number of context bases up and downstream over which 101s to compute Fisher's method combined p-values. Note: 101s Not applicable for alternative model likelihood ratio 101s tests. Default: 1. 101s --minimum-test-reads MINIMUM_TEST_READS 101s Number of reads required at a position to perform 101s significance testing or contribute to model 101s estimation. Default: 50 101s --statistic-type {ks,u,t} 101s Type of statistical test to apply. Default: "ks" 101s --store-p-value Store p-value instead of effect-size statistic. 101s Statistics are D-statistic (KS-test), deviation from 101s even common language effect size (u-test), and Cohen's 101s D (t-test). 101s 101s Output Argument: 101s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 101s Number of the most significant sites to store for 101s faster access. If a longer list of most significant 101s sites is required the list must be re-computed from 101s all batches. Very large values can increase RAM usage. 101s Default: 100000 101s 101s Multiprocessing Arguments: 101s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 101s Size of regions over which to multiprocesses statistic 101s computation. For very deep samples a smaller value is 101s recommmended in order to control memory consumption. 101s Default: 10000 101s --processes PROCESSES 101s Number of processes. Default: 1 101s 101s FAST5 Data Arguments: 101s --corrected-group CORRECTED_GROUP 101s FAST5 group created by resquiggle command. Default: 101s RawGenomeCorrected_000 101s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 101s FAST5 subgroup(s) (under /Analyses/[--basecall- 101s group]/) containing basecalls and created within 101s [--corrected-group] containing re-squiggle results. 101s Default: ['BaseCalled_template'] 101s 101s Miscellaneous Arguments: 101s --quiet, -q Don't print status information. 101s --help, -h Print this help message and exit 101s usage: tombo detect_modifications aggregate_per_read_stats 101s --per-read-statistics-filename 101s PER_READ_STATISTICS_FILENAME 101s --statistics-filename 101s STATISTICS_FILENAME 101s --single-read-threshold 101s SINGLE_READ_THRESHOLD 101s [SINGLE_READ_THRESHOLD ...] 101s [--minimum-test-reads MINIMUM_TEST_READS] 101s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 101s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 101s [--processes PROCESSES] 101s [--corrected-group CORRECTED_GROUP] 101s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 101s [--quiet] [--help] 101s 101s Required Argument: 101s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 101s Binary file containing per-read statistics from 101s statistical testing. 101s --statistics-filename STATISTICS_FILENAME 101s File to save/load genomic base anchored statistics. 101s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 101s P-value or log likelihood ratio threshold when 101s computing fraction of significant reads at each 101s genomic position. If two values are provided, 101s statistics between these values are not considered. 101s 101s Significance Test Arguments: 101s --minimum-test-reads MINIMUM_TEST_READS 101s Number of reads required at a position to perform 101s significance testing or contribute to model 101s estimation. Default: 1 101s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 101s Dampen fraction modified estimates for low coverage 101s sites. Two parameters are unmodified and modified 101s pseudo read counts. This is equivalent to a beta prior 101s on the fraction estimate. Set to "0 0" to disable 101s dampened fraction estimation. Default: [2, 0] 101s 101s Output Argument: 101s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 101s Number of the most significant sites to store for 101s faster access. If a longer list of most significant 101s sites is required the list must be re-computed from 101s all batches. Very large values can increase RAM usage. 101s Default: 100000 101s 101s Multiprocessing Arguments: 101s --processes PROCESSES 101s Number of processes. Default: 1 101s 101s FAST5 Data Arguments: 101s --corrected-group CORRECTED_GROUP 101s FAST5 group created by resquiggle command. Default: 101s RawGenomeCorrected_000 101s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 101s FAST5 subgroup(s) (under /Analyses/[--basecall- 101s group]/) containing basecalls and created within 101s [--corrected-group] containing re-squiggle results. 101s Default: ['BaseCalled_template'] 101s 101s Miscellaneous Arguments: 101s --quiet, -q Don't print status information. 101s --help, -h Print this help message and exit 101s usage: tombo text_output browser_files 101s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 101s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 101s [--statistics-filename STATISTICS_FILENAME] 101s [--genome-fasta GENOME_FASTA] 101s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 101s [--browser-file-basename BROWSER_FILE_BASENAME] 101s [--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} ...]] 101s [--corrected-group CORRECTED_GROUP] 101s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 101s [--quiet] [--help] 101s 101s Data Arguments: 101s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 101s Directories containing fast5 files. 101s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 101s Set of directories containing fast5 files for control 101s reads, containing only canonical nucleotides. 101s --statistics-filename STATISTICS_FILENAME 101s File to save/load genomic base anchored statistics. 101s 101s Statistic Motif Filter Arguments: 101s --genome-fasta GENOME_FASTA 101s FASTA file used to re-squiggle. For faster sequence 101s access. 101s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 101s Ground truth, motif centered, modified base 101s descriptions for output filtering. Format descriptions 101s as: "motif:mod_pos:name". The mod_pos indicates the 101s modified base within the motif (1-based index). 101s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 101s output for identification of E. coli dam and dcm 101s methylation. 101s 101s Output Arguments: 101s --browser-file-basename BROWSER_FILE_BASENAME 101s Basename for output browser files. Two files (plus and 101s minus strand) will be produced for each --file-types 101s supplied. Filenames formatted as "[browser-file- 101s basename].[file- 101s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 101s Default: tombo_results 101s --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} ...] 101s Data types of genome browser files to produce. 101s Produced coverage files are in bedGraph format, while 101s all other file types will be in wiggle format 101s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 101s Default: "coverage" 101s 101s FAST5 Data Arguments: 101s --corrected-group CORRECTED_GROUP 101s FAST5 group created by resquiggle command. Default: 101s RawGenomeCorrected_000 101s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 101s FAST5 subgroup(s) (under /Analyses/[--basecall- 101s group]/) containing basecalls and created within 101s [--corrected-group] containing re-squiggle results. 101s Default: ['BaseCalled_template'] 101s 101s Miscellaneous Arguments: 101s --quiet, -q Don't print status information. 101s --help, -h Print this help message and exit 101s usage: tombo text_output signif_sequence_context --statistics-filename 101s STATISTICS_FILENAME 101s [--genome-fasta GENOME_FASTA] 101s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 101s [--num-regions NUM_REGIONS] 101s [--num-bases NUM_BASES] 101s [--sequences-filename SEQUENCES_FILENAME] 101s [--corrected-group CORRECTED_GROUP] 101s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 101s [--quiet] [--help] 101s 101s Required Argument: 101s --statistics-filename STATISTICS_FILENAME 101s File to save/load genomic base anchored statistics. 101s 101s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 101s --genome-fasta GENOME_FASTA 101s FASTA file used to re-squiggle. For faster sequence 101s access. 101s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 101s Directories containing fast5 files. 101s 101s Region Selection Arguments: 101s --num-regions NUM_REGIONS 101s Number of regions to plot. Default: 100 101s --num-bases NUM_BASES 101s Number of bases to plot/output. Default: 15 101s 101s Output Arguments: 101s --sequences-filename SEQUENCES_FILENAME 101s File for sequences from selected regions. Sequences 101s will be stored in FASTA format. Default: 101s tombo_results.significant_regions.fasta. 101s 101s FAST5 Data Arguments: 101s --corrected-group CORRECTED_GROUP 101s FAST5 group created by resquiggle command. Default: 101s RawGenomeCorrected_000 101s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 101s FAST5 subgroup(s) (under /Analyses/[--basecall- 101s group]/) containing basecalls and created within 101s [--corrected-group] containing re-squiggle results. 101s Default: ['BaseCalled_template'] 101s 101s Miscellaneous Arguments: 101s --quiet, -q Don't print status information. 101s --help, -h Print this help message and exit 102s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 102s [FAST5_BASEDIRS ...] 102s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 102s [--plot-standard-model] 102s [--plot-alternate-model {dam,CpG,5mC,dcm,6mA}] 102s [--overplot-threshold OVERPLOT_THRESHOLD] 102s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 102s [--num-regions NUM_REGIONS] 102s [--num-bases NUM_BASES] 102s [--pdf-filename PDF_FILENAME] 102s [--corrected-group CORRECTED_GROUP] 102s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 102s [--quiet] [--help] 102s 102s Required Argument: 102s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 102s Directories containing fast5 files. 102s 102s Comparison Arguments: 102s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 102s Set of directories containing fast5 files for control 102s reads, containing only canonical nucleotides. 102s --plot-standard-model 102s Add default standard model distribution to the plot. 102s --plot-alternate-model {dam,CpG,5mC,dcm,6mA} 102s Add alternative model distribution to the plot. 102s 102s Overplotting Arguments: 102s --overplot-threshold OVERPLOT_THRESHOLD 102s Coverage level to trigger alternative plot type 102s instead of raw signal. Default: 50 102s --overplot-type {Downsample,Boxplot,Quantile,Density} 102s Plot type for regions with higher coverage. Default: 102s Downsample 102s 102s Plotting Region Arguments: 102s --num-regions NUM_REGIONS 102s Number of regions to plot. Default: 10 102s --num-bases NUM_BASES 102s Number of bases to plot/output. Default: 21 102s 102s Output Argument: 102s --pdf-filename PDF_FILENAME 102s PDF filename to store plot(s). Default: 102s tombo_results.max_coverage.pdf 102s 102s FAST5 Data Arguments: 102s --corrected-group CORRECTED_GROUP 102s FAST5 group created by resquiggle command. Default: 102s RawGenomeCorrected_000 102s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 102s FAST5 subgroup(s) (under /Analyses/[--basecall- 102s group]/) containing basecalls and created within 102s [--corrected-group] containing re-squiggle results. 102s Default: ['BaseCalled_template'] 102s 102s Miscellaneous Arguments: 102s --quiet, -q Don't print status information. 102s --help, -h Print this help message and exit 102s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 102s [FAST5_BASEDIRS ...] --genome-locations 102s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 102s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 102s [--plot-standard-model] 102s [--plot-alternate-model {6mA,CpG,5mC,dam,dcm}] 102s [--overplot-threshold OVERPLOT_THRESHOLD] 102s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 102s [--num-bases NUM_BASES] 102s [--pdf-filename PDF_FILENAME] 102s [--corrected-group CORRECTED_GROUP] 102s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 102s [--quiet] [--help] 102s 102s Required Arguments: 102s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 102s Directories containing fast5 files. 102s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 102s Genomic locations at which to plot signal. Format 102s locations as "chrm:position[:strand] 102s [chrm2:position2[:strand2] ...]" (strand not 102s applicable for all applications) 102s 102s Comparison Arguments: 102s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 102s Set of directories containing fast5 files for control 102s reads, containing only canonical nucleotides. 102s --plot-standard-model 102s Add default standard model distribution to the plot. 102s --plot-alternate-model {6mA,CpG,5mC,dam,dcm} 102s Add alternative model distribution to the plot. 102s 102s Overplotting Arguments: 102s --overplot-threshold OVERPLOT_THRESHOLD 102s Coverage level to trigger alternative plot type 102s instead of raw signal. Default: 50 102s --overplot-type {Downsample,Boxplot,Quantile,Density} 102s Plot type for regions with higher coverage. Default: 102s Downsample 102s 102s Plotting Region Argument: 102s --num-bases NUM_BASES 102s Number of bases to plot/output. Default: 21 102s 102s Output Argument: 102s --pdf-filename PDF_FILENAME 102s PDF filename to store plot(s). Default: 102s tombo_results.genome_locations.pdf 102s 102s FAST5 Data Arguments: 102s --corrected-group CORRECTED_GROUP 102s FAST5 group created by resquiggle command. Default: 102s RawGenomeCorrected_000 102s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 102s FAST5 subgroup(s) (under /Analyses/[--basecall- 102s group]/) containing basecalls and created within 102s [--corrected-group] containing re-squiggle results. 102s Default: ['BaseCalled_template'] 102s 102s Miscellaneous Arguments: 102s --quiet, -q Don't print status information. 102s --help, -h Print this help message and exit 102s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 102s [FAST5_BASEDIRS ...] --motif MOTIF 102s --genome-fasta GENOME_FASTA 102s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 102s [--plot-standard-model] 102s [--plot-alternate-model {dcm,6mA,5mC,dam,CpG}] 102s [--overplot-threshold OVERPLOT_THRESHOLD] 102s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 102s [--num-regions NUM_REGIONS] 102s [--num-bases NUM_BASES] [--deepest-coverage] 102s [--pdf-filename PDF_FILENAME] 102s [--corrected-group CORRECTED_GROUP] 102s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 102s [--quiet] [--help] 102s 102s Required Arguments: 102s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 102s Directories containing fast5 files. 102s --motif MOTIF Motif of interest at which to plot signal and 102s statsitics. Supports IUPAC single letter codes (use T 102s for RNA). 102s --genome-fasta GENOME_FASTA 102s FASTA file used to re-squiggle. For faster sequence 102s access. 102s 102s Comparison Arguments: 102s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 102s Set of directories containing fast5 files for control 102s reads, containing only canonical nucleotides. 102s --plot-standard-model 102s Add default standard model distribution to the plot. 102s --plot-alternate-model {dcm,6mA,5mC,dam,CpG} 102s Add alternative model distribution to the plot. 102s 102s Overplotting Arguments: 102s --overplot-threshold OVERPLOT_THRESHOLD 102s Coverage level to trigger alternative plot type 102s instead of raw signal. Default: 50 102s --overplot-type {Downsample,Boxplot,Quantile,Density} 102s Plot type for regions with higher coverage. Default: 102s Downsample 102s 102s Plotting Region Arguments: 102s --num-regions NUM_REGIONS 102s Number of regions to plot. Default: 10 102s --num-bases NUM_BASES 102s Number of bases to plot/output. Default: 21 102s --deepest-coverage Plot the deepest coverage regions. 102s 102s Output Argument: 102s --pdf-filename PDF_FILENAME 102s PDF filename to store plot(s). Default: 102s tombo_results.motif_centered.pdf 102s 102s FAST5 Data Arguments: 102s --corrected-group CORRECTED_GROUP 102s FAST5 group created by resquiggle command. Default: 102s RawGenomeCorrected_000 102s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 102s FAST5 subgroup(s) (under /Analyses/[--basecall- 102s group]/) containing basecalls and created within 102s [--corrected-group] containing re-squiggle results. 102s Default: ['BaseCalled_template'] 102s 102s Miscellaneous Arguments: 102s --quiet, -q Don't print status information. 102s --help, -h Print this help message and exit 102s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 102s [FAST5_BASEDIRS ...] --control-fast5-basedirs 102s CONTROL_FAST5_BASEDIRS 102s [CONTROL_FAST5_BASEDIRS ...] 102s [--overplot-threshold OVERPLOT_THRESHOLD] 102s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 102s [--num-regions NUM_REGIONS] 102s [--num-bases NUM_BASES] 102s [--pdf-filename PDF_FILENAME] 102s [--sequences-filename SEQUENCES_FILENAME] 102s [--corrected-group CORRECTED_GROUP] 102s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 102s [--quiet] [--help] 102s 102s Required Arguments: 102s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 102s Directories containing fast5 files. 102s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 102s Set of directories containing fast5 files for control 102s reads, containing only canonical nucleotides. 102s 102s Overplotting Arguments: 102s --overplot-threshold OVERPLOT_THRESHOLD 102s Coverage level to trigger alternative plot type 102s instead of raw signal. Default: 50 102s --overplot-type {Downsample,Boxplot,Quantile,Density} 102s Plot type for regions with higher coverage. Default: 102s Downsample 102s 102s Plotting Region Arguments: 102s --num-regions NUM_REGIONS 102s Number of regions to plot. Default: 10 102s --num-bases NUM_BASES 102s Number of bases to plot/output. Default: 21 102s 102s Output Arguments: 102s --pdf-filename PDF_FILENAME 102s PDF filename to store plot(s). Default: 102s tombo_results.max_difference.pdf 102s --sequences-filename SEQUENCES_FILENAME 102s File for sequences from selected regions. Sequences 102s will be stored in FASTA format. Default: None. 102s 102s FAST5 Data Arguments: 102s --corrected-group CORRECTED_GROUP 102s FAST5 group created by resquiggle command. Default: 102s RawGenomeCorrected_000 102s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 102s FAST5 subgroup(s) (under /Analyses/[--basecall- 102s group]/) containing basecalls and created within 102s [--corrected-group] containing re-squiggle results. 102s Default: ['BaseCalled_template'] 102s 102s Miscellaneous Arguments: 102s --quiet, -q Don't print status information. 102s --help, -h Print this help message and exit 102s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 102s [FAST5_BASEDIRS ...] --statistics-filename 102s STATISTICS_FILENAME 102s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 102s [--plot-standard-model] 102s [--plot-alternate-model {dcm,5mC,dam,CpG,6mA}] 102s [--overplot-threshold OVERPLOT_THRESHOLD] 102s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 102s [--num-regions NUM_REGIONS] 102s [--num-bases NUM_BASES] 102s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 102s [--pdf-filename PDF_FILENAME] 102s [--sequences-filename SEQUENCES_FILENAME] 102s [--corrected-group CORRECTED_GROUP] 102s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 102s [--quiet] [--help] 102s 102s Required Arguments: 102s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 102s Directories containing fast5 files. 102s --statistics-filename STATISTICS_FILENAME 102s File to save/load genomic base anchored statistics. 102s 102s Comparison Arguments: 102s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 102s Set of directories containing fast5 files for control 102s reads, containing only canonical nucleotides. 102s --plot-standard-model 102s Add default standard model distribution to the plot. 102s --plot-alternate-model {dcm,5mC,dam,CpG,6mA} 102s Add alternative model distribution to the plot. 102s 102s Overplotting Arguments: 102s --overplot-threshold OVERPLOT_THRESHOLD 102s Coverage level to trigger alternative plot type 102s instead of raw signal. Default: 50 102s --overplot-type {Downsample,Boxplot,Quantile,Density} 102s Plot type for regions with higher coverage. Default: 102s Downsample 102s 102s Plotting Region Arguments: 102s --num-regions NUM_REGIONS 102s Number of regions to plot. Default: 10 102s --num-bases NUM_BASES 102s Number of bases to plot/output. Default: 21 102s 102s Statistical Argument: 102s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 102s Dampen fraction modified estimates for low coverage 102s sites. Two parameters are unmodified and modified 102s pseudo read counts. This is equivalent to a beta prior 102s on the fraction estimate. Set to "0 0" to disable 102s dampened fraction estimation. Default: [2, 0] 102s 102s Output Arguments: 102s --pdf-filename PDF_FILENAME 102s PDF filename to store plot(s). Default: 102s tombo_results.significant_difference.pdf 102s --sequences-filename SEQUENCES_FILENAME 102s File for sequences from selected regions. Sequences 102s will be stored in FASTA format. Default: None. 102s 102s FAST5 Data Arguments: 102s --corrected-group CORRECTED_GROUP 102s FAST5 group created by resquiggle command. Default: 102s RawGenomeCorrected_000 102s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 102s FAST5 subgroup(s) (under /Analyses/[--basecall- 102s group]/) containing basecalls and created within 102s [--corrected-group] containing re-squiggle results. 102s Default: ['BaseCalled_template'] 102s 102s Miscellaneous Arguments: 102s --quiet, -q Don't print status information. 102s --help, -h Print this help message and exit 102s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 102s [FAST5_BASEDIRS ...] --motif MOTIF 102s --statistics-filename STATISTICS_FILENAME 102s --genome-fasta GENOME_FASTA 102s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 102s [--plot-standard-model] 102s [--plot-alternate-model {dam,6mA,dcm,5mC,CpG}] 102s [--overplot-threshold OVERPLOT_THRESHOLD] 102s [--num-regions NUM_REGIONS] 102s [--num-context NUM_CONTEXT] 102s [--num-statistics NUM_STATISTICS] 102s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 102s [--pdf-filename PDF_FILENAME] 102s [--corrected-group CORRECTED_GROUP] 102s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 102s [--quiet] [--help] 102s 102s Required Arguments: 102s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 102s Directories containing fast5 files. 102s --motif MOTIF Motif of interest at which to plot signal and 102s statsitics. Supports IUPAC single letter codes (use T 102s for RNA). 102s --statistics-filename STATISTICS_FILENAME 102s File to save/load genomic base anchored statistics. 102s --genome-fasta GENOME_FASTA 102s FASTA file used to re-squiggle. For faster sequence 102s access. 102s 102s Comparison Arguments: 102s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 102s Set of directories containing fast5 files for control 102s reads, containing only canonical nucleotides. 102s --plot-standard-model 102s Add default standard model distribution to the plot. 102s --plot-alternate-model {dam,6mA,dcm,5mC,CpG} 102s Add alternative model distribution to the plot. 102s 102s Overplotting Argument: 102s --overplot-threshold OVERPLOT_THRESHOLD 102s Coverage level to trigger alternative plot type 102s instead of raw signal. Default: 50 102s 102s Plotting Region Arguments: 102s --num-regions NUM_REGIONS 102s Number of regions to plot. Default: 3 102s --num-context NUM_CONTEXT 102s Number of context bases around motif. Default: 5 102s --num-statistics NUM_STATISTICS 102s Number of motif centered regions to include in 102s statistic distributions. Default: 200 102s 102s Statistical Argument: 102s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 102s Dampen fraction modified estimates for low coverage 102s sites. Two parameters are unmodified and modified 102s pseudo read counts. This is equivalent to a beta prior 102s on the fraction estimate. Set to "0 0" to disable 102s dampened fraction estimation. Default: [2, 0] 102s 102s Output Argument: 102s --pdf-filename PDF_FILENAME 102s PDF filename to store plot(s). Default: 102s tombo_results.motif_statistics.pdf 102s 102s FAST5 Data Arguments: 102s --corrected-group CORRECTED_GROUP 102s FAST5 group created by resquiggle command. Default: 102s RawGenomeCorrected_000 102s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 102s FAST5 subgroup(s) (under /Analyses/[--basecall- 102s group]/) containing basecalls and created within 102s [--corrected-group] containing re-squiggle results. 102s Default: ['BaseCalled_template'] 102s 102s Miscellaneous Arguments: 102s --quiet, -q Don't print status information. 102s --help, -h Print this help message and exit 102s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 102s [GENOME_LOCATIONS ...] 102s --per-read-statistics-filename 102s PER_READ_STATISTICS_FILENAME 102s [--genome-fasta GENOME_FASTA] 102s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 102s [--num-reads NUM_READS] [--num-bases NUM_BASES] 102s [--box-center] [--pdf-filename PDF_FILENAME] 102s [--corrected-group CORRECTED_GROUP] 102s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 102s [--quiet] [--help] 102s 102s Required Arguments: 102s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 102s Genomic locations at which to plot signal. Format 102s locations as "chrm:position[:strand] 102s [chrm2:position2[:strand2] ...]" (strand not 102s applicable for all applications) 102s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 102s Binary file containing per-read statistics from 102s statistical testing. 102s 102s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 102s --genome-fasta GENOME_FASTA 102s FASTA file used to re-squiggle. For faster sequence 102s access. 102s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 102s Directories containing fast5 files. 102s 102s Plotting Region Arguments: 102s --num-reads NUM_READS 102s Number of reads to plot. Default: 100 102s --num-bases NUM_BASES 102s Number of bases to plot/output. Default: 51 102s --box-center Plot a box around the central base. 102s 102s Output Argument: 102s --pdf-filename PDF_FILENAME 102s PDF filename to store plot(s). Default: 102s tombo_results.per_read_stats.pdf 102s 102s FAST5 Data Arguments: 102s --corrected-group CORRECTED_GROUP 102s FAST5 group created by resquiggle command. Default: 102s RawGenomeCorrected_000 102s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 102s FAST5 subgroup(s) (under /Analyses/[--basecall- 102s group]/) containing basecalls and created within 102s [--corrected-group] containing re-squiggle results. 102s Default: ['BaseCalled_template'] 102s 102s Miscellaneous Arguments: 102s --quiet, -q Don't print status information. 102s --help, -h Print this help message and exit 102s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 102s [STATISTICS_FILENAMES ...] 102s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 102s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 102s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 102s [--genome-fasta GENOME_FASTA] 102s [--pdf-filename PDF_FILENAME] 102s [--statistics-per-block STATISTICS_PER_BLOCK] 102s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 102s [--quiet] [--help] 102s 102s Required Argument: 102s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 102s Files to load genomic base anchored statistics. 102s 102s Ground Truth Arguments (provide bed files or motifs): 102s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 102s Modification description and bed format files 102s containing single base locations of ground truth 102s modified sites. Bed files should contain 6 fields 102s including strand. Format descriptions as 102s "mod_name:locs.bed". Example: "CpG 102s bisulfite":bisulfite_locs.bed 102s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 102s Bed format files containing single base locations of 102s ground truth unmodified sites. Bed files should 102s contain 6 fields including strand. 102s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 102s Ground truth, motif centered, modified base 102s descriptions for computing ROC and PR curves. Each 102s statistics file is associated with a set of motif 102s descriptions. Format descriptions as: 102s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 102s mod_pos indicates the alternate-base within the motif 102s (1-based index). Example: CCWGG:2:"dcm 102s 5mC"::GATC:2:"dam 6mA" would assess the performance of 102s a single Tombo statistics file for identification of 102s E. coli dam and dcm methylation. 102s --genome-fasta GENOME_FASTA 102s FASTA file used to re-squiggle. For faster sequence 102s access. 102s 102s Output Arguments: 102s --pdf-filename PDF_FILENAME 102s PDF filename to store plot(s). Default: 102s tombo_results.roc.pdf 102s 102s Down-sampling Arguments: 102s --statistics-per-block STATISTICS_PER_BLOCK 102s Number of randomly selected per-read, per-base 102s statistics to extract from each genomic block for 102s plotting. Default: Include all stats 102s --total-statistics-limit TOTAL_STATISTICS_LIMIT 102s Total per-read statistics to be extracted for 102s plotting. Avoids memory overflow for large runs. 102s Default: 5000000 102s 102s Miscellaneous Arguments: 102s --quiet, -q Don't print status information. 102s --help, -h Print this help message and exit 102s usage: tombo plot per_read_roc --per-read-statistics-filenames 102s PER_READ_STATISTICS_FILENAMES 102s [PER_READ_STATISTICS_FILENAMES ...] 102s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 102s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 102s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 102s [--genome-fasta GENOME_FASTA] 102s [--statistics-per-block STATISTICS_PER_BLOCK] 102s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 102s [--pdf-filename PDF_FILENAME] [--quiet] 102s [--help] 102s 102s Required Argument: 102s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 102s Binary files containing per-read statistics from 102s statistical testing. 102s 102s Ground Truth Arguments (provide bed files or motifs): 102s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 102s Modification description and bed format files 102s containing single base locations of ground truth 102s modified sites. Bed files should contain 6 fields 102s including strand. Format descriptions as 102s "mod_name:locs.bed". Example: "CpG 102s bisulfite":bisulfite_locs.bed 102s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 102s Bed format files containing single base locations of 102s ground truth unmodified sites. Bed files should 102s contain 6 fields including strand. 102s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 102s Ground truth, motif centered, modified base 102s descriptions for computing ROC and PR curves. Each 102s statistics file is associated with a set of motif 102s descriptions. Format descriptions as: 102s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 102s mod_pos indicates the alternate-base within the motif 102s (1-based index). Example: CCWGG:2:"dcm 102s 5mC"::GATC:2:"dam 6mA" would assess the performance of 102s a single Tombo statistics file for identification of 102s E. coli dam and dcm methylation. 102s --genome-fasta GENOME_FASTA 102s FASTA file used to re-squiggle. For faster sequence 102s access. 102s 102s Down-sampling Arguments: 102s --statistics-per-block STATISTICS_PER_BLOCK 102s Number of randomly selected per-read, per-base 102s statistics to extract from each genomic block for 102s plotting. Default: 100000 102s --total-statistics-limit TOTAL_STATISTICS_LIMIT 102s Total per-read statistics to be extracted for 102s plotting. Avoids memory overflow for large runs. 102s Default: 5000000 102s 102s Output Arguments: 102s --pdf-filename PDF_FILENAME 102s PDF filename to store plot(s). Default: 102s tombo_results.per_reads_roc.pdf 102s 102s Miscellaneous Arguments: 102s --quiet, -q Don't print status information. 102s --help, -h Print this help message and exit 102s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 102s [--upstream-bases {0,1,2,3,4}] 102s [--downstream-bases {0,1,2,3,4}] [--read-mean] 102s [--num-kmer-threshold NUM_KMER_THRESHOLD] 102s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 102s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 102s [--corrected-group CORRECTED_GROUP] 102s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 102s [--quiet] [--help] 102s 102s Required Argument: 102s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 102s Directories containing fast5 files. 102s 102s Data Processing Arguments: 102s --upstream-bases {0,1,2,3,4} 102s Upstream bases in k-mer. Default: 1 102s --downstream-bases {0,1,2,3,4} 102s Downstream bases in k-mer. Default: 2 102s --read-mean Plot k-mer means across whole reads as opposed to 102s individual k-mer event levels. 102s --num-kmer-threshold NUM_KMER_THRESHOLD 102s Observations of each k-mer required to include a read 102s in read level averages. Default: 1 102s 102s Plotting Region Arguments: 102s --num-reads NUM_READS 102s Number of reads to plot. Default: 100 102s 102s Output Arguments: 102s --pdf-filename PDF_FILENAME 102s PDF filename to store plot(s). Default: 102s tombo_results.kmer_distribution.pdf 102s --r-data-filename R_DATA_FILENAME 102s Filename to save R data structure. Default: Don't save 102s --dont-plot Don't plot result. Useful to produce only R data file. 102s 102s FAST5 Data Arguments: 102s --corrected-group CORRECTED_GROUP 102s FAST5 group created by resquiggle command. Default: 102s RawGenomeCorrected_000 102s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 102s FAST5 subgroup(s) (under /Analyses/[--basecall- 102s group]/) containing basecalls and created within 102s [--corrected-group] containing re-squiggle results. 102s Default: ['BaseCalled_template'] 102s 102s Miscellaneous Arguments: 102s --quiet, -q Don't print status information. 102s --help, -h Print this help message and exit 102s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 102s [FAST5_BASEDIRS ...] 102s --control-fast5-basedirs 102s CONTROL_FAST5_BASEDIRS 102s [CONTROL_FAST5_BASEDIRS ...] 102s --statistics-filename 102s STATISTICS_FILENAME 102s [--genome-fasta GENOME_FASTA] 102s [--processes PROCESSES] 102s [--num-regions NUM_REGIONS] 102s [--num-bases NUM_BASES] 102s [--slide-span SLIDE_SPAN] 102s [--pdf-filename PDF_FILENAME] 102s [--r-data-filename R_DATA_FILENAME] 102s [--corrected-group CORRECTED_GROUP] 102s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 102s [--quiet] [--help] 102s 102s Required Arguments: 102s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 102s Directories containing fast5 files. 102s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 102s Set of directories containing fast5 files for control 102s reads, containing only canonical nucleotides. 102s --statistics-filename STATISTICS_FILENAME 102s File to save/load genomic base anchored statistics. 102s 102s FASTA Sequence Argument: 102s --genome-fasta GENOME_FASTA 102s FASTA file used to re-squiggle. For faster sequence 102s access. 102s 102s Multiprocessing Argument: 102s --processes PROCESSES 102s Number of processes. Default: 1 102s 102s Plotting Region Arguments: 102s --num-regions NUM_REGIONS 102s Number of regions to plot. Default: 10 102s --num-bases NUM_BASES 102s Number of bases to plot/output. Default: 21 102s --slide-span SLIDE_SPAN 102s Number of bases offset over which to search when 102s computing distances for signal cluster plotting. 102s Default: 0 (exact position) 102s 102s Output Arguments: 102s --pdf-filename PDF_FILENAME 102s PDF filename to store plot(s). Default: 102s tombo_results.signal_clusters.pdf 102s --r-data-filename R_DATA_FILENAME 102s Filename to save R data structure. Default: Don't save 102s 102s FAST5 Data Arguments: 102s --corrected-group CORRECTED_GROUP 102s FAST5 group created by resquiggle command. Default: 102s RawGenomeCorrected_000 102s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 102s FAST5 subgroup(s) (under /Analyses/[--basecall- 102s group]/) containing basecalls and created within 102s [--corrected-group] containing re-squiggle results. 102s Default: ['BaseCalled_template'] 102s 102s Miscellaneous Arguments: 102s --quiet, -q Don't print status information. 102s --help, -h Print this help message and exit 103s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 103s 103s Required Arguments: 103s fast5s_basedir Directory containing fast5 files. All files ending in 103s "fast5" found recursively within this base directory will be 103s processed. 103s 103s Miscellaneous Arguments: 103s --quiet, -q Don't print status information. 103s --help, -h Print this help message and exit 103s usage: tombo build_model event_resquiggle 103s [--minimap2-executable MINIMAP2_EXECUTABLE] 103s [--minimap2-index MINIMAP2_INDEX] 103s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 103s [--graphmap-executable GRAPHMAP_EXECUTABLE] 103s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 103s [--normalization-type {median,pA,pA_raw,none}] 103s [--pore-model-filename PORE_MODEL_FILENAME] 103s [--outlier-threshold OUTLIER_THRESHOLD] 103s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 103s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 103s [--timeout TIMEOUT] 103s [--cpts-limit CPTS_LIMIT] 103s [--skip-index] [--overwrite] 103s [--failed-reads-filename FAILED_READS_FILENAME] 103s [--include-event-stdev] 103s [--corrected-group CORRECTED_GROUP] 103s [--basecall-group BASECALL_GROUP] 103s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 103s [--processes PROCESSES] 103s [--align-processes ALIGN_PROCESSES] 103s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 103s [--resquiggle-processes RESQUIGGLE_PROCESSES] 103s [--quiet] [--help] 103s fast5s_basedir reference_fasta 103s 103s Required Arguments: 103s fast5s_basedir Directory containing fast5 files. All files ending in 103s "fast5" found recursively within this base directory 103s will be processed. 103s reference_fasta Reference genome/transcriptome FASTA file for mapping. 103s 103s Mapper Arguments (One mapper is required): 103s --minimap2-executable MINIMAP2_EXECUTABLE 103s Path to minimap2 executable. 103s --minimap2-index MINIMAP2_INDEX 103s Path to minimap2 index (with map-ont preset) file 103s corresponding to the [genome_fasta] provided. 103s --bwa-mem-executable BWA_MEM_EXECUTABLE 103s Path to bwa-mem executable. 103s --graphmap-executable GRAPHMAP_EXECUTABLE 103s Path to graphmap executable. 103s --alignment-batch-size ALIGNMENT_BATCH_SIZE 103s Number of reads included in each alignment call. Note: 103s A new system mapping call is made for each batch 103s (including loading of the genome), so it is advised to 103s use larger values for larger genomes. Default: 1000 103s 103s Signal Processing Arguments: 103s --normalization-type {median,pA,pA_raw,none} 103s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 103s as in the ONT events (using offset, range and 103s digitization), "pA": k-mer-based correction for pA 103s drift as in nanopolish (requires [--pore-model- 103s filename]), "median": median and MAD from raw signal. 103s Default: median 103s --pore-model-filename PORE_MODEL_FILENAME 103s File containing kmer model parameters (level_mean and 103s level_stdv) used in order to compute kmer-based 103s corrected pA values. E.g. https://github.com/jts/nanop 103s olish/blob/master/etc/r9- 103s models/template_median68pA.5mers.model 103s --outlier-threshold OUTLIER_THRESHOLD 103s Windosrize the signal at this number of scale values. 103s Negative value disables outlier clipping. Default: 103s 5.000000 103s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 103s Specify the 2 parameters for segmentation 1) running 103s neighboring windows width 2) minimum raw observations 103s per genomic base. Sample type defaults: RNA : 12 6 || 103s DNA : 5 3 103s 103s Read Filtering Arguments: 103s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 103s Filter reads based on observations per base percentile 103s thresholds. Format thresholds as "percentile:thresh 103s [pctl2:thresh2 ...]". For example to filter reads with 103s 99th pctl > 200 obs/base or max > 5k obs/base use 103s "99:200 100:5000". 103s --timeout TIMEOUT Timeout in seconds for processing a single read. 103s Default: No timeout. 103s --cpts-limit CPTS_LIMIT 103s Maximum number of changepoints to find within a single 103s indel group. Default: No limit. 103s 103s Input/Output Arguments: 103s --skip-index Skip creation of tombo index. This drastically slows 103s downstream tombo commands. Default stores tombo index 103s named ".[--fast5-basedir].[--corrected- 103s group].tombo.index" to be loaded automatically for 103s downstream commands. 103s --overwrite Overwrite previous corrected group in FAST5 files. 103s Note: only effects --corrected-group or --new- 103s corrected-group. 103s --failed-reads-filename FAILED_READS_FILENAME 103s Output failed read filenames with assoicated error. 103s Default: Do not store failed reads. 103s --include-event-stdev 103s Include corrected event standard deviation in output 103s FAST5 data. 103s 103s FAST5 Data Arguments: 103s --corrected-group CORRECTED_GROUP 103s FAST5 group created by resquiggle command. Default: 103s RawGenomeCorrected_000 103s --basecall-group BASECALL_GROUP 103s FAST5 group obtain original basecalls (under Analyses 103s group). Default: Basecall_1D_000 103s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 103s FAST5 subgroup(s) (under /Analyses/[--basecall- 103s group]/) containing basecalls and created within 103s [--corrected-group] containing re-squiggle results. 103s Default: ['BaseCalled_template'] 103s 103s Multiprocessing Arguments: 103s --processes PROCESSES 103s Number of processes. Default: 2 103s --align-processes ALIGN_PROCESSES 103s Number of processes to use for parsing and aligning 103s original basecalls. Each process will independently 103s load the genome into memory, so use caution with 103s larger genomes (e.g. human). Default: 1 103s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 103s Number of threads to use for aligner system call. 103s Default: [--processes] / (2 * [--align-processes)] 103s --resquiggle-processes RESQUIGGLE_PROCESSES 103s Number of processes to use for resquiggle algorithm. 103s Default: [--processes] / 2 103s 103s Miscellaneous Arguments: 103s --quiet, -q Don't print status information. 103s --help, -h Print this help message and exit 103s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 103s [FAST5_BASEDIRS ...] 103s --tombo-model-filename 103s TOMBO_MODEL_FILENAME 103s [--estimate-mean] 103s [--kmer-specific-sd] 103s [--upstream-bases {0,1,2,3,4}] 103s [--downstream-bases {0,1,2,3,4}] 103s [--minimum-test-reads MINIMUM_TEST_READS] 103s [--coverage-threshold COVERAGE_THRESHOLD] 103s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 103s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 103s [--processes PROCESSES] 103s [--corrected-group CORRECTED_GROUP] 103s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 103s [--quiet] [--help] 103s 103s Required Arguments: 103s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 103s Directories containing fast5 files. 103s --tombo-model-filename TOMBO_MODEL_FILENAME 103s Filename to save Tombo model. 103s 103s Modeling Arguments: 103s --estimate-mean Use the mean instead of median for model level 103s estimation. Note: This can cause poor fits due to 103s outliers 103s --kmer-specific-sd Estimate standard deviation for each k-mers 103s individually. 103s --upstream-bases {0,1,2,3,4} 103s Upstream bases in k-mer. Default: 1 103s --downstream-bases {0,1,2,3,4} 103s Downstream bases in k-mer. Default: 2 103s 103s Filtering Arguments: 103s --minimum-test-reads MINIMUM_TEST_READS 103s Number of reads required at a position to perform 103s significance testing or contribute to model 103s estimation. Default: 10 103s --coverage-threshold COVERAGE_THRESHOLD 103s Maximum mean coverage per region when estimating k-mer 103s model (limits compute time for deep samples). Default: 103s 100 103s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 103s Number of each k-mer observations required in order to 103s produce a reference (genomic locations for standard 103s reference and per-read for alternative reference). 103s Default: 5 103s 103s Multiprocessing Arguments: 103s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 103s Size of regions over which to multiprocesses statistic 103s computation. For very deep samples a smaller value is 103s recommmended in order to control memory consumption. 103s Default: 10000 103s --processes PROCESSES 103s Number of processes. Default: 1 103s 103s FAST5 Data Arguments: 103s --corrected-group CORRECTED_GROUP 103s FAST5 group created by resquiggle command. Default: 103s RawGenomeCorrected_000 103s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 103s FAST5 subgroup(s) (under /Analyses/[--basecall- 103s group]/) containing basecalls and created within 103s [--corrected-group] containing re-squiggle results. 103s Default: ['BaseCalled_template'] 103s 103s Miscellaneous Arguments: 103s --quiet, -q Don't print status information. 103s --help, -h Print this help message and exit 103s usage: tombo build_model estimate_alt_reference --alternate-model-filename 103s ALTERNATE_MODEL_FILENAME 103s --alternate-model-name 103s ALTERNATE_MODEL_NAME 103s --alternate-model-base 103s {A,C,G,T} 103s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 103s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 103s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 103s [--control-density-filename CONTROL_DENSITY_FILENAME] 103s [--dna] [--rna] 103s [--tombo-model-filename TOMBO_MODEL_FILENAME] 103s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 103s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 103s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 103s [--save-density-basename SAVE_DENSITY_BASENAME] 103s [--processes PROCESSES] 103s [--corrected-group CORRECTED_GROUP] 103s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 103s [--quiet] [--help] 103s 103s Required Arguments: 103s --alternate-model-filename ALTERNATE_MODEL_FILENAME 103s Tombo model for alternative likelihood ratio 103s significance testing. 103s --alternate-model-name ALTERNATE_MODEL_NAME 103s A short name to associate with this alternate model 103s (e.g. 5mC, 6mA, etc.). This text will be included in 103s output filenames when this model is used for testing. 103s --alternate-model-base {A,C,G,T} 103s Non-standard base is an alternative to this base. 103s 103s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 103s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 103s Directories containing fast5 files. 103s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 103s Set of directories containing fast5 files for control 103s reads, containing only canonical nucleotides. 103s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 103s File containing k-mer level kernel density estimates 103s for the alternative sample saved using --save-density- 103s basename. 103s --control-density-filename CONTROL_DENSITY_FILENAME 103s File containing k-mer level kernel density estimates 103s for the control sample saved using --save-density- 103s basename. 103s 103s Standard Model Arguments: 103s --dna Explicitly select canonical DNA model. Default: 103s Automatically determine from FAST5s 103s --rna Explicitly select canonical RNA model. Default: 103s Automatically determine from FAST5s 103s --tombo-model-filename TOMBO_MODEL_FILENAME 103s Tombo model filename. If no file is provided, the 103s default DNA or RNA Tombo model will be used. 103s 103s Model Fitting Arguments: 103s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 103s When esitmating the alternative base incorporation 103s rate, this percent of k-mers are assumed to have 103s significantly shifted signal so the alternative 103s distribution minimally overlaps the standard base 103s distribution. Default: 5.000000 103s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 103s Bandwidth applied when performing Gaussian kernal 103s density esitmation on standard and alternative base 103s signal distributions. Default: 0.050000 103s 103s Filtering Argument: 103s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 103s Number of each k-mer observations required in order to 103s produce a reference (genomic locations for standard 103s reference and per-read for alternative reference). 103s Default: 1000 103s 103s Output Argument: 103s --save-density-basename SAVE_DENSITY_BASENAME 103s Basename to save alternative model estimation density 103s estimation information. See scripts/debug_est_alt.R 103s for info use example. Default: Don't save. 103s 103s Multiprocessing Arguments: 103s --processes PROCESSES 103s Number of processes. Default: 1 103s 103s FAST5 Data Arguments: 103s --corrected-group CORRECTED_GROUP 103s FAST5 group created by resquiggle command. Default: 103s RawGenomeCorrected_000 103s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 103s FAST5 subgroup(s) (under /Analyses/[--basecall- 103s group]/) containing basecalls and created within 103s [--corrected-group] containing re-squiggle results. 103s Default: ['BaseCalled_template'] 103s 103s Miscellaneous Arguments: 103s --quiet, -q Don't print status information. 103s --help, -h Print this help message and exit 103s This test only tests the help system 103s There is an extensive test in 103s 103s tombo/tests/shell_tests.sh 103s 103s but this requires to download larger data 103s sets which is not done for the moment. 103s autopkgtest [09:13:07]: test run-unit-test: -----------------------] 103s autopkgtest [09:13:07]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 103s run-unit-test PASS 103s autopkgtest [09:13:07]: @@@@@@@@@@@@@@@@@@@@ summary 103s run-unit-test PASS 116s virt: nova [W] Skipping flock for amd64 116s virt: Creating nova instance adt-plucky-amd64-tombo-20241113-091124-juju-7f2275-prod-proposed-migration-environment-2-6e74b294-308d-4f2e-b67a-be72d4a69cb7 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)...