1s autopkgtest [11:18:10]: starting date and time: 2024-11-13 11:18:10+0000 1s autopkgtest [11:18:10]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 1s autopkgtest [11:18:10]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1ruymew0/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@bos03-arm64-40.secgroup --name adt-plucky-arm64-tombo-20241113-111809-juju-7f2275-prod-proposed-migration-environment-2-e63c8840-7608-4e02-8b9a-05e541b802a2 --image adt/ubuntu-plucky-arm64-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/ 114s autopkgtest [11:20:03]: testbed dpkg architecture: arm64 114s autopkgtest [11:20:03]: testbed apt version: 2.9.8 114s autopkgtest [11:20:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 115s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 115s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 115s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 115s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 115s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 116s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 116s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 116s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 116s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 116s Fetched 1794 kB in 1s (1958 kB/s) 116s Reading package lists... 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 120s Calculating upgrade... 120s The following NEW packages will be installed: 120s python3.13-gdbm 120s The following packages will be upgraded: 120s libpython3-stdlib python3 python3-gdbm python3-minimal 120s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 120s Need to get 101 kB of archives. 120s After this operation, 141 kB of additional disk space will be used. 120s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 120s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 120s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 120s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 121s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 121s Fetched 101 kB in 0s (289 kB/s) 121s (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 ... 79924 files and directories currently installed.) 121s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 121s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 121s Setting up python3-minimal (3.12.7-1) ... 122s (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 ... 79924 files and directories currently installed.) 122s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 122s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 122s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 122s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 122s Selecting previously unselected package python3.13-gdbm. 122s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 122s Unpacking python3.13-gdbm (3.13.0-2) ... 122s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 122s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 122s Setting up python3.13-gdbm (3.13.0-2) ... 122s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 122s Setting up python3 (3.12.7-1) ... 122s Setting up python3-gdbm:arm64 (3.12.7-1) ... 122s Processing triggers for man-db (2.12.1-3) ... 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 125s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 125s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 125s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 126s Reading package lists... 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 127s Calculating upgrade... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s autopkgtest [11:20:20]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 132s autopkgtest [11:20:21]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 135s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (dsc) [2291 B] 135s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (tar) [22.3 MB] 135s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (diff) [7100 B] 135s gpgv: Signature made Wed Apr 10 17:15:32 2024 UTC 135s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 135s gpgv: Can't check signature: No public key 135s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6build1.dsc: no acceptable signature found 135s autopkgtest [11:20:24]: testing package tombo version 1.5.1-6build1 136s autopkgtest [11:20:25]: build not needed 137s autopkgtest [11:20:26]: test run-unit-test: preparing testbed 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Starting pkgProblemResolver with broken count: 0 139s Starting 2 pkgProblemResolver with broken count: 0 139s Done 140s The following additional packages will be installed: 140s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 140s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 140s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 140s python3-decorator python3-h5py python3-h5py-serial python3-mappy 140s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 140s tombo-doc 140s Suggested packages: 140s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 140s gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 140s Recommended packages: 140s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 140s python3-rpy2 140s The following NEW packages will be installed: 140s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 140s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 140s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 140s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 140s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 140s tombo-doc 140s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 140s Need to get 60.5 MB/60.5 MB of archives. 140s After this operation, 194 MB of additional disk space will be used. 140s Get:1 /tmp/autopkgtest.2qzGz1/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 140s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB] 141s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 141s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 141s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 141s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 141s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 141s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 141s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 141s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 141s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 141s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 141s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 141s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 141s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 141s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 141s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 141s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 141s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-5ubuntu1 [1064 kB] 142s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 142s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mappy arm64 2.27+dfsg-1 [167 kB] 142s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.0-1 [91.6 kB] 142s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 142s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 142s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 tombo arm64 1.5.1-6build1 [446 kB] 142s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 143s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 tombo-doc all 1.5.1-6build1 [21.7 MB] 144s Fetched 60.5 MB in 3s (17.8 MB/s) 144s Selecting previously unselected package fonts-lato. 144s (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 ... 79931 files and directories currently installed.) 144s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 144s Unpacking fonts-lato (2.015-1) ... 144s Selecting previously unselected package fonts-font-awesome. 144s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 144s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 144s Selecting previously unselected package fonts-mathjax. 144s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 144s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 145s Selecting previously unselected package libaec0:arm64. 145s Preparing to unpack .../03-libaec0_1.1.3-1_arm64.deb ... 145s Unpacking libaec0:arm64 (1.1.3-1) ... 145s Selecting previously unselected package libblas3:arm64. 145s Preparing to unpack .../04-libblas3_3.12.0-3build2_arm64.deb ... 145s Unpacking libblas3:arm64 (3.12.0-3build2) ... 145s Selecting previously unselected package libgfortran5:arm64. 145s Preparing to unpack .../05-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 145s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 145s Selecting previously unselected package libsz2:arm64. 145s Preparing to unpack .../06-libsz2_1.1.3-1_arm64.deb ... 145s Unpacking libsz2:arm64 (1.1.3-1) ... 145s Selecting previously unselected package libhdf5-103-1t64:arm64. 145s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 145s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 145s Selecting previously unselected package libhdf5-hl-100t64:arm64. 145s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 145s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 145s Selecting previously unselected package libjs-jquery. 145s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 145s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 145s Selecting previously unselected package libjs-underscore. 145s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 145s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 145s Selecting previously unselected package libjs-sphinxdoc. 145s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-4_all.deb ... 145s Unpacking libjs-sphinxdoc (7.4.7-4) ... 145s Selecting previously unselected package liblapack3:arm64. 145s Preparing to unpack .../12-liblapack3_3.12.0-3build2_arm64.deb ... 145s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 145s Selecting previously unselected package liblbfgsb0:arm64. 145s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 145s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 145s Selecting previously unselected package liblzf1:arm64. 145s Preparing to unpack .../14-liblzf1_3.6-4_arm64.deb ... 145s Unpacking liblzf1:arm64 (3.6-4) ... 145s Selecting previously unselected package python3-decorator. 145s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 145s Unpacking python3-decorator (5.1.1-5) ... 145s Selecting previously unselected package python3-numpy. 145s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 145s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 145s Selecting previously unselected package python3-h5py-serial. 145s Preparing to unpack .../17-python3-h5py-serial_3.11.0-5ubuntu1_arm64.deb ... 145s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 145s Selecting previously unselected package python3-h5py. 145s Preparing to unpack .../18-python3-h5py_3.11.0-5ubuntu1_all.deb ... 145s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 145s Selecting previously unselected package python3-mappy. 145s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1_arm64.deb ... 145s Unpacking python3-mappy (2.27+dfsg-1) ... 145s Selecting previously unselected package python3-tqdm. 146s Preparing to unpack .../20-python3-tqdm_4.67.0-1_all.deb ... 146s Unpacking python3-tqdm (4.67.0-1) ... 146s Selecting previously unselected package sphinx-rtd-theme-common. 146s Preparing to unpack .../21-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 146s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 146s Selecting previously unselected package python3-scipy. 146s Preparing to unpack .../22-python3-scipy_1.13.1-5_arm64.deb ... 146s Unpacking python3-scipy (1.13.1-5) ... 146s Selecting previously unselected package tombo. 146s Preparing to unpack .../23-tombo_1.5.1-6build1_arm64.deb ... 146s Unpacking tombo (1.5.1-6build1) ... 146s Selecting previously unselected package libjs-mathjax. 146s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 146s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 147s Selecting previously unselected package tombo-doc. 147s Preparing to unpack .../25-tombo-doc_1.5.1-6build1_all.deb ... 147s Unpacking tombo-doc (1.5.1-6build1) ... 147s Selecting previously unselected package autopkgtest-satdep. 147s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 147s Unpacking autopkgtest-satdep (0) ... 147s Setting up fonts-lato (2.015-1) ... 147s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 147s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 147s Setting up python3-tqdm (4.67.0-1) ... 147s Setting up python3-mappy (2.27+dfsg-1) ... 147s Setting up libaec0:arm64 (1.1.3-1) ... 147s Setting up python3-decorator (5.1.1-5) ... 147s Setting up libblas3:arm64 (3.12.0-3build2) ... 147s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 147s Setting up liblzf1:arm64 (3.6-4) ... 147s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 147s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 147s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 147s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 147s Setting up libsz2:arm64 (1.1.3-1) ... 148s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 148s Setting up liblapack3:arm64 (3.12.0-3build2) ... 148s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 148s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 150s Setting up libjs-sphinxdoc (7.4.7-4) ... 150s Setting up tombo-doc (1.5.1-6build1) ... 150s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 150s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 150s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 150s Setting up python3-scipy (1.13.1-5) ... 155s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 155s Setting up python3-h5py (3.11.0-5ubuntu1) ... 155s Setting up tombo (1.5.1-6build1) ... 155s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 155s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 155s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 155s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 155s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 155s re.match('\+', fastq_rec[2]) is None): 155s Setting up autopkgtest-satdep (0) ... 155s Processing triggers for man-db (2.12.1-3) ... 156s Processing triggers for libc-bin (2.40-1ubuntu3) ... 161s (Reading database ... 87133 files and directories currently installed.) 161s Removing autopkgtest-satdep (0) ... 162s autopkgtest [11:20:51]: test run-unit-test: [----------------------- 162s ********* Testing help commands ********** 162s usage: tombo [-h] [-v] 162s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 162s ... 162s 162s ********** Tombo ********* 162s 162s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 162s 162s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 162s 162s Tombo command groups (additional help available within each command group): 162s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 162s preprocess Pre-process nanopore reads for Tombo processing. 162s filter Apply filter to Tombo index file for specified criterion. 162s detect_modifications Perform statistical testing to detect non-standard nucleotides. 162s text_output Output Tombo results in text files. 162s build_model Create canonical and alternative base Tombo models. 162s plot Save plots to visualize raw nanopore signal or testing results. 162s 162s options: 162s -h, --help show this help message and exit 162s -v, --version show Tombo version and exit. 163s usage: tombo resquiggle [--dna] [--rna] 163s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 163s [--q-score Q_SCORE] 163s [--signal-matching-score SIGNAL_MATCHING_SCORE] 163s [--processes PROCESSES] 163s [--corrected-group CORRECTED_GROUP] 163s [--basecall-group BASECALL_GROUP] 163s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 163s [--overwrite] 163s [--failed-reads-filename FAILED_READS_FILENAME] 163s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 163s [--print-advanced-arguments] [--quiet] [--help] 163s fast5s_basedir reference 163s 163s Required Arguments: 163s fast5s_basedir Directory containing fast5 files. All files ending in 163s "fast5" found recursively within this base directory 163s will be processed. 163s reference Reference genome/transcriptome FASTA file or minimap2 163s index (with "map-ont" preset) for mapping. 163s 163s Model Parameters: 163s --dna Explicitly select canonical DNA model. Default: 163s Automatically determine from FAST5s 163s --rna Explicitly select canonical RNA model. Default: 163s Automatically determine from FAST5s 163s 163s Read Filtering Argument: 163s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 163s Filter reads based on observations per base percentile 163s thresholds. Format thresholds as "percentile:thresh 163s [pctl2:thresh2 ...]". For example to filter reads with 163s 99th pctl > 200 obs/base or max > 5k obs/base use 163s "99:200 100:5000". 163s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 163s Default: 0.000000 163s --signal-matching-score SIGNAL_MATCHING_SCORE 163s Observed to expected signal matching score (higher 163s score indicates poor matching). Sample type defaults: 163s RNA : 2 || DNA : 1.1 163s 163s Multiprocessing Arguments: 163s --processes PROCESSES 163s Number of processes. Default: 1 163s 163s FAST5 Data Arguments: 163s --corrected-group CORRECTED_GROUP 163s FAST5 group created by resquiggle command. Default: 163s RawGenomeCorrected_000 163s --basecall-group BASECALL_GROUP 163s FAST5 group obtain original basecalls (under Analyses 163s group). Default: Basecall_1D_000 163s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 163s FAST5 subgroup(s) (under /Analyses/[--basecall- 163s group]/) containing basecalls and created within 163s [--corrected-group] containing re-squiggle results. 163s Default: ['BaseCalled_template'] 163s --overwrite Overwrite previous corrected group in FAST5 files. 163s Note: only effects --corrected-group or --new- 163s corrected-group. 163s 163s Input/Output Arguments: 163s --failed-reads-filename FAILED_READS_FILENAME 163s Output failed read filenames with assoicated error. 163s Default: Do not store failed reads. 163s --num-most-common-errors NUM_MOST_COMMON_ERRORS 163s Dynamically show this many most common errors so far 163s through run. Default: 0; Just show progress 163s 163s Advanced Arguments: 163s --print-advanced-arguments 163s Print advanced re-squiggle arguments and exit. 163s 163s Miscellaneous Arguments: 163s --quiet, -q Don't print status information. 163s --help, -h Print this help message and exit 163s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 163s --fastq-filenames 163s FASTQ_FILENAMES 163s [FASTQ_FILENAMES ...] 163s [--basecall-group BASECALL_GROUP] 163s [--basecall-subgroup BASECALL_SUBGROUP] 163s [--overwrite] 163s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 163s [--processes PROCESSES] 163s [--quiet] [--help] 163s 163s Required Arguments: 163s --fast5-basedir FAST5_BASEDIR 163s Directory containing fast5 files. 163s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 163s FASTQ filenames containing basecalls to be added to 163s raw FAST5 files. 163s 163s FAST5 Data Arguments: 163s --basecall-group BASECALL_GROUP 163s FAST5 group obtain original basecalls (under Analyses 163s group). Default: Basecall_1D_000 163s --basecall-subgroup BASECALL_SUBGROUP 163s FAST5 subgroup (under /Analyses/[--basecall-group]/) 163s under which to store basecalls from FASTQs. Default: 163s BaseCalled_template 163s --overwrite Overwrite previous corrected group in FAST5 files. 163s Note: only effects --corrected-group or --new- 163s corrected-group. 163s 163s Sequencing Summary Argument: 163s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 163s Sequencing summary filenames produced by albacore. 163s These can make annotation of raw FAST5 files with 163s FASTQ sequence much faster. 163s 163s Multiprocessing Argument: 163s --processes PROCESSES 163s Number of processes. Default: 1 163s 163s Miscellaneous Arguments: 163s --quiet, -q Don't print status information. 163s --help, -h Print this help message and exit 163s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 163s [FAST5_BASEDIRS ...] 163s [--corrected-group CORRECTED_GROUP] 163s [--quiet] [--help] 163s 163s Required Argument: 163s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 163s Directories containing fast5 files. 163s 163s FAST5 Data Argument: 163s --corrected-group CORRECTED_GROUP 163s FAST5 group created by resquiggle command. Default: 163s RawGenomeCorrected_000 163s 163s Miscellaneous Arguments: 163s --quiet, -q Don't print status information. 163s --help, -h Print this help message and exit 163s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 163s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 163s [--corrected-group CORRECTED_GROUP] [--quiet] 163s [--help] 163s 163s Required Argument: 163s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 163s Directories containing fast5 files. 163s 163s Read Filtering Argument: 163s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 163s Filter reads based on observations per base percentile 163s thresholds. Format thresholds as "percentile:thresh 163s [pctl2:thresh2 ...]". For example to filter reads with 163s 99th pctl > 200 obs/base or max > 5k obs/base use 163s "99:200 100:5000". 163s 163s FAST5 Data Argument: 163s --corrected-group CORRECTED_GROUP 163s FAST5 group created by resquiggle command. Default: 163s RawGenomeCorrected_000 163s 163s Miscellaneous Arguments: 163s --quiet, -q Don't print status information. 163s --help, -h Print this help message and exit 163s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 163s [FAST5_BASEDIRS ...] 163s [--percent-to-filter PERCENT_TO_FILTER] 163s [--corrected-group CORRECTED_GROUP] 163s [--quiet] [--help] 163s 163s Required Arguments: 163s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 163s Directories containing fast5 files. 163s 163s Read Filtering Argument: 163s --percent-to-filter PERCENT_TO_FILTER 163s Percentage of all reads to filter. Reads are randomly 163s selected weighted according to the approximate 163s coverage at the mapped genomic location. This can be 163s useful in modeling and testing. Default: 10.000000 163s 163s FAST5 Data Arguments: 163s --corrected-group CORRECTED_GROUP 163s FAST5 group created by resquiggle command. Default: 163s RawGenomeCorrected_000 163s 163s Miscellaneous Arguments: 163s --quiet, -q Don't print status information. 163s --help, -h Print this help message and exit 163s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 163s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 163s [--corrected-group CORRECTED_GROUP] 163s [--basecall-group BASECALL_GROUP] [--quiet] 163s [--help] 163s 163s Required Arguments: 163s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 163s Directories containing fast5 files. 163s 163s Read Filtering Argument: 163s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 163s Default: 7.000000 163s 163s FAST5 Data Arguments: 163s --corrected-group CORRECTED_GROUP 163s FAST5 group created by resquiggle command. Default: 163s RawGenomeCorrected_000 163s --basecall-group BASECALL_GROUP 163s FAST5 group obtain original basecalls (under Analyses 163s group). Default: Basecall_1D_000 163s 163s Miscellaneous Arguments: 163s --quiet, -q Don't print status information. 163s --help, -h Print this help message and exit 163s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 163s [FAST5_BASEDIRS ...] 163s --signal-matching-score 163s SIGNAL_MATCHING_SCORE 163s [--corrected-group CORRECTED_GROUP] 163s [--quiet] [--help] 163s 163s Required Arguments: 163s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 163s Directories containing fast5 files. 163s --signal-matching-score SIGNAL_MATCHING_SCORE 163s Observed to expected signal matching score (higher 163s score indicates poor matching). Sample type defaults: 163s RNA : 2 || DNA : 1.1 163s 163s FAST5 Data Arguments: 163s --corrected-group CORRECTED_GROUP 163s FAST5 group created by resquiggle command. Default: 163s RawGenomeCorrected_000 163s 163s Miscellaneous Arguments: 163s --quiet, -q Don't print status information. 163s --help, -h Print this help message and exit 163s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 163s [FAST5_BASEDIRS ...] 163s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 163s [--include-partial-overlap] 163s [--corrected-group CORRECTED_GROUP] 163s [--quiet] [--help] 163s 163s Required Arguments: 163s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 163s Directories containing fast5 files. 163s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 163s Filter out reads not falling completely within include 163s regions. Omit start and end coordinates to include an 163s entire chromosome/sequence record. Format regions as 163s "chrm[:start-end] [chrm2[:start2-end2] ...]". 163s 163s Filter Argument: 163s --include-partial-overlap 163s Include reads that partially overlap the specified 163s region. Default: Only include reads completely 163s contained in a specified region 163s 163s FAST5 Data Argument: 163s --corrected-group CORRECTED_GROUP 163s FAST5 group created by resquiggle command. Default: 163s RawGenomeCorrected_000 163s 163s Miscellaneous Arguments: 163s --quiet, -q Don't print status information. 163s --help, -h Print this help message and exit 163s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 163s [FAST5_BASEDIRS ...] 163s --statistics-file-basename 163s STATISTICS_FILE_BASENAME [--dna] 163s [--rna] 163s [--fishers-method-context FISHERS_METHOD_CONTEXT] 163s [--minimum-test-reads MINIMUM_TEST_READS] 163s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 163s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 163s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 163s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 163s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 163s [--processes PROCESSES] 163s [--corrected-group CORRECTED_GROUP] 163s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 163s [--quiet] [--help] 163s 163s Required Argument: 163s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 163s Directories containing fast5 files. 163s --statistics-file-basename STATISTICS_FILE_BASENAME 163s File base name to save base by base statistics from 163s testing. Filenames will be [--statistics-file- 163s basename].[--alternate-bases]?.tombo.stats 163s 163s Comparison Model Arguments: 163s --dna Explicitly select canonical DNA model. Default: 163s Automatically determine from FAST5s 163s --rna Explicitly select canonical RNA model. Default: 163s Automatically determine from FAST5s 163s 163s Significance Test Arguments: 163s --fishers-method-context FISHERS_METHOD_CONTEXT 163s Number of context bases up and downstream over which 163s to compute Fisher's method combined p-values. Note: 163s Not applicable for alternative model likelihood ratio 163s tests. Default: 1. 163s --minimum-test-reads MINIMUM_TEST_READS 163s Number of reads required at a position to perform 163s significance testing or contribute to model 163s estimation. Default: 1 163s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 163s P-value threshold when computing fraction of 163s significant reads at each genomic position. If two 163s values are provided, statistics between these values 163s are not considered. Default thresholds: DNA:0.15-0.5 , 163s RNA:0.05-0.4 163s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 163s Dampen fraction modified estimates for low coverage 163s sites. Two parameters are unmodified and modified 163s pseudo read counts. This is equivalent to a beta prior 163s on the fraction estimate. Set to "0 0" to disable 163s dampened fraction estimation. Default: [2, 0] 163s 163s Output Argument: 163s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 163s Base for binary files containing per-read statistics 163s from statistical testing. Filenames will be [--per- 163s read-statistics-basename].[--alternate- 163s bases]?.tombo.per_read_stats 163s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 163s Number of the most significant sites to store for 163s faster access. If a longer list of most significant 163s sites is required the list must be re-computed from 163s all batches. Very large values can increase RAM usage. 163s Default: 100000 163s 163s Multiprocessing Arguments: 163s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 163s Size of regions over which to multiprocesses statistic 163s computation. For very deep samples a smaller value is 163s recommmended in order to control memory consumption. 163s Default: 10000 163s --processes PROCESSES 163s Number of processes. Default: 1 163s 163s FAST5 Data Arguments: 163s --corrected-group CORRECTED_GROUP 163s FAST5 group created by resquiggle command. Default: 163s RawGenomeCorrected_000 163s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 163s FAST5 subgroup(s) (under /Analyses/[--basecall- 163s group]/) containing basecalls and created within 163s [--corrected-group] containing re-squiggle results. 163s Default: ['BaseCalled_template'] 163s 163s Miscellaneous Arguments: 163s --quiet, -q Don't print status information. 163s --help, -h Print this help message and exit 164s usage: tombo detect_modifications alternative_model 164s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 164s [--statistics-file-basename STATISTICS_FILE_BASENAME] 164s [--alternate-bases {6mA,5mC,dcm,CpG,dam} [{6mA,5mC,dcm,CpG,dam} ...]] 164s [--print-available-models] 164s [--dna] [--rna] 164s [--minimum-test-reads MINIMUM_TEST_READS] 164s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 164s [--standard-log-likelihood-ratio] 164s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 164s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 164s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 164s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 164s [--processes PROCESSES] 164s [--corrected-group CORRECTED_GROUP] 164s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 164s [--quiet] [--help] 164s 164s Required Argument: 164s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 164s Directories containing fast5 files. 164s --statistics-file-basename STATISTICS_FILE_BASENAME 164s File base name to save base by base statistics from 164s testing. Filenames will be [--statistics-file- 164s basename].[--alternate-bases]?.tombo.stats 164s --alternate-bases {6mA,5mC,dcm,CpG,dam} [{6mA,5mC,dcm,CpG,dam} ...] 164s Default non-standard base model for testing (not 164s required if user created --alternate-model-filenames 164s is provided). 164s 164s Comparison Arguments: 164s --print-available-models 164s Print available alternative models and exit. 164s --dna Explicitly select canonical DNA model. Default: 164s Automatically determine from FAST5s 164s --rna Explicitly select canonical RNA model. Default: 164s Automatically determine from FAST5s 164s 164s Significance Test Arguments: 164s --minimum-test-reads MINIMUM_TEST_READS 164s Number of reads required at a position to perform 164s significance testing or contribute to model 164s estimation. Default: 1 164s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 164s Log likelihood ratio threshold when computing fraction 164s of significant reads at each genomic position. If two 164s values are provided, statistics between these values 164s are not considered. Default thresholds: DNA:-1.5-2.5 , 164s RNA:-2.5-2.5 164s --standard-log-likelihood-ratio 164s Use a standard log likelihood ratio (LLR) statistic. 164s Default is to use an outlier-robust LLR-like 164s statistic. Detail in full online documentation. 164s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 164s Dampen fraction modified estimates for low coverage 164s sites. Two parameters are unmodified and modified 164s pseudo read counts. This is equivalent to a beta prior 164s on the fraction estimate. Set to "0 0" to disable 164s dampened fraction estimation. Default: [2, 0] 164s 164s Output Argument: 164s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 164s Base for binary files containing per-read statistics 164s from statistical testing. Filenames will be [--per- 164s read-statistics-basename].[--alternate- 164s bases]?.tombo.per_read_stats 164s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 164s Number of the most significant sites to store for 164s faster access. If a longer list of most significant 164s sites is required the list must be re-computed from 164s all batches. Very large values can increase RAM usage. 164s Default: 100000 164s 164s Multiprocessing Arguments: 164s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 164s Size of regions over which to multiprocesses statistic 164s computation. For very deep samples a smaller value is 164s recommmended in order to control memory consumption. 164s Default: 10000 164s --processes PROCESSES 164s Number of processes. Default: 1 164s 164s FAST5 Data Arguments: 164s --corrected-group CORRECTED_GROUP 164s FAST5 group created by resquiggle command. Default: 164s RawGenomeCorrected_000 164s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 164s FAST5 subgroup(s) (under /Analyses/[--basecall- 164s group]/) containing basecalls and created within 164s [--corrected-group] containing re-squiggle results. 164s Default: ['BaseCalled_template'] 164s 164s Miscellaneous Arguments: 164s --quiet, -q Don't print status information. 164s --help, -h Print this help message and exit 164s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 164s FAST5_BASEDIRS 164s [FAST5_BASEDIRS ...] 164s --statistics-file-basename 164s STATISTICS_FILE_BASENAME 164s --control-fast5-basedirs 164s CONTROL_FAST5_BASEDIRS 164s [CONTROL_FAST5_BASEDIRS ...] 164s [--sample-only-estimates] 164s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 164s [--dna] [--rna] 164s [--fishers-method-context FISHERS_METHOD_CONTEXT] 164s [--minimum-test-reads MINIMUM_TEST_READS] 164s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 164s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 164s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 164s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 164s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 164s [--processes PROCESSES] 164s [--corrected-group CORRECTED_GROUP] 164s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 164s [--quiet] [--help] 164s 164s Required Argument: 164s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 164s Directories containing fast5 files. 164s --statistics-file-basename STATISTICS_FILE_BASENAME 164s File base name to save base by base statistics from 164s testing. Filenames will be [--statistics-file- 164s basename].[--alternate-bases]?.tombo.stats 164s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 164s Set of directories containing fast5 files for control 164s reads, containing only canonical nucleotides. 164s 164s Model Prior Arguments: 164s --sample-only-estimates 164s Only use canonical sample to estimate expected signal 164s level and spread. Default: Use canonical model to 164s improve estimtates (esp. for low coverage regions) 164s using baysian posterior estimates. 164s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 164s Prior weights (one each for mean and spread) applied 164s to canonical base model for estimating posterior model 164s parameters for sample comparison. Default: [5, 40] 164s --dna Explicitly select canonical DNA model. Default: 164s Automatically determine from FAST5s 164s --rna Explicitly select canonical RNA model. Default: 164s Automatically determine from FAST5s 164s 164s Significance Test Arguments: 164s --fishers-method-context FISHERS_METHOD_CONTEXT 164s Number of context bases up and downstream over which 164s to compute Fisher's method combined p-values. Note: 164s Not applicable for alternative model likelihood ratio 164s tests. Default: 1. 164s --minimum-test-reads MINIMUM_TEST_READS 164s Number of reads required at a position to perform 164s significance testing or contribute to model 164s estimation. Default: 1 164s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 164s P-value threshold when computing fraction of 164s significant reads at each genomic position. If two 164s values are provided, statistics between these values 164s are not considered. Default thresholds: DNA:0.15-0.5 , 164s RNA:0.05-0.4 164s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 164s Dampen fraction modified estimates for low coverage 164s sites. Two parameters are unmodified and modified 164s pseudo read counts. This is equivalent to a beta prior 164s on the fraction estimate. Set to "0 0" to disable 164s dampened fraction estimation. Default: [2, 0] 164s 164s Output Argument: 164s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 164s Base for binary files containing per-read statistics 164s from statistical testing. Filenames will be [--per- 164s read-statistics-basename].[--alternate- 164s bases]?.tombo.per_read_stats 164s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 164s Number of the most significant sites to store for 164s faster access. If a longer list of most significant 164s sites is required the list must be re-computed from 164s all batches. Very large values can increase RAM usage. 164s Default: 100000 164s 164s Multiprocessing Arguments: 164s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 164s Size of regions over which to multiprocesses statistic 164s computation. For very deep samples a smaller value is 164s recommmended in order to control memory consumption. 164s Default: 10000 164s --processes PROCESSES 164s Number of processes. Default: 1 164s 164s FAST5 Data Arguments: 164s --corrected-group CORRECTED_GROUP 164s FAST5 group created by resquiggle command. Default: 164s RawGenomeCorrected_000 164s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 164s FAST5 subgroup(s) (under /Analyses/[--basecall- 164s group]/) containing basecalls and created within 164s [--corrected-group] containing re-squiggle results. 164s Default: ['BaseCalled_template'] 164s 164s Miscellaneous Arguments: 164s --quiet, -q Don't print status information. 164s --help, -h Print this help message and exit 164s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 164s FAST5_BASEDIRS 164s [FAST5_BASEDIRS ...] 164s --statistics-file-basename 164s STATISTICS_FILE_BASENAME 164s --alternate-fast5-basedirs 164s ALTERNATE_FAST5_BASEDIRS 164s [ALTERNATE_FAST5_BASEDIRS ...] 164s [--fishers-method-context FISHERS_METHOD_CONTEXT] 164s [--minimum-test-reads MINIMUM_TEST_READS] 164s [--statistic-type {ks,u,t}] 164s [--store-p-value] 164s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 164s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 164s [--processes PROCESSES] 164s [--corrected-group CORRECTED_GROUP] 164s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 164s [--quiet] [--help] 164s 164s Required Argument: 164s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 164s Directories containing fast5 files. 164s --statistics-file-basename STATISTICS_FILE_BASENAME 164s File base name to save base by base statistics from 164s testing. Filenames will be [--statistics-file- 164s basename].[--alternate-bases]?.tombo.stats 164s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 164s Set of directories containing fast5 files for 164s alternate set of reads. 164s 164s Significance Test Arguments: 164s --fishers-method-context FISHERS_METHOD_CONTEXT 164s Number of context bases up and downstream over which 164s to compute Fisher's method combined p-values. Note: 164s Not applicable for alternative model likelihood ratio 164s tests. Default: 1. 164s --minimum-test-reads MINIMUM_TEST_READS 164s Number of reads required at a position to perform 164s significance testing or contribute to model 164s estimation. Default: 50 164s --statistic-type {ks,u,t} 164s Type of statistical test to apply. Default: "ks" 164s --store-p-value Store p-value instead of effect-size statistic. 164s Statistics are D-statistic (KS-test), deviation from 164s even common language effect size (u-test), and Cohen's 164s D (t-test). 164s 164s Output Argument: 164s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 164s Number of the most significant sites to store for 164s faster access. If a longer list of most significant 164s sites is required the list must be re-computed from 164s all batches. Very large values can increase RAM usage. 164s Default: 100000 164s 164s Multiprocessing Arguments: 164s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 164s Size of regions over which to multiprocesses statistic 164s computation. For very deep samples a smaller value is 164s recommmended in order to control memory consumption. 164s Default: 10000 164s --processes PROCESSES 164s Number of processes. Default: 1 164s 164s FAST5 Data Arguments: 164s --corrected-group CORRECTED_GROUP 164s FAST5 group created by resquiggle command. Default: 164s RawGenomeCorrected_000 164s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 164s FAST5 subgroup(s) (under /Analyses/[--basecall- 164s group]/) containing basecalls and created within 164s [--corrected-group] containing re-squiggle results. 164s Default: ['BaseCalled_template'] 164s 164s Miscellaneous Arguments: 164s --quiet, -q Don't print status information. 164s --help, -h Print this help message and exit 164s usage: tombo detect_modifications aggregate_per_read_stats 164s --per-read-statistics-filename 164s PER_READ_STATISTICS_FILENAME 164s --statistics-filename 164s STATISTICS_FILENAME 164s --single-read-threshold 164s SINGLE_READ_THRESHOLD 164s [SINGLE_READ_THRESHOLD ...] 164s [--minimum-test-reads MINIMUM_TEST_READS] 164s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 164s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 164s [--processes PROCESSES] 164s [--corrected-group CORRECTED_GROUP] 164s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 164s [--quiet] [--help] 164s 164s Required Argument: 164s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 164s Binary file containing per-read statistics from 164s statistical testing. 164s --statistics-filename STATISTICS_FILENAME 164s File to save/load genomic base anchored statistics. 164s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 164s P-value or log likelihood ratio threshold when 164s computing fraction of significant reads at each 164s genomic position. If two values are provided, 164s statistics between these values are not considered. 164s 164s Significance Test Arguments: 164s --minimum-test-reads MINIMUM_TEST_READS 164s Number of reads required at a position to perform 164s significance testing or contribute to model 164s estimation. Default: 1 164s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 164s Dampen fraction modified estimates for low coverage 164s sites. Two parameters are unmodified and modified 164s pseudo read counts. This is equivalent to a beta prior 164s on the fraction estimate. Set to "0 0" to disable 164s dampened fraction estimation. Default: [2, 0] 164s 164s Output Argument: 164s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 164s Number of the most significant sites to store for 164s faster access. If a longer list of most significant 164s sites is required the list must be re-computed from 164s all batches. Very large values can increase RAM usage. 164s Default: 100000 164s 164s Multiprocessing Arguments: 164s --processes PROCESSES 164s Number of processes. Default: 1 164s 164s FAST5 Data Arguments: 164s --corrected-group CORRECTED_GROUP 164s FAST5 group created by resquiggle command. Default: 164s RawGenomeCorrected_000 164s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 164s FAST5 subgroup(s) (under /Analyses/[--basecall- 164s group]/) containing basecalls and created within 164s [--corrected-group] containing re-squiggle results. 164s Default: ['BaseCalled_template'] 164s 164s Miscellaneous Arguments: 164s --quiet, -q Don't print status information. 164s --help, -h Print this help message and exit 164s usage: tombo text_output browser_files 164s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 164s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 164s [--statistics-filename STATISTICS_FILENAME] 164s [--genome-fasta GENOME_FASTA] 164s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 164s [--browser-file-basename BROWSER_FILE_BASENAME] 164s [--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} ...]] 164s [--corrected-group CORRECTED_GROUP] 164s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 164s [--quiet] [--help] 164s 164s Data Arguments: 164s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 164s Directories containing fast5 files. 164s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 164s Set of directories containing fast5 files for control 164s reads, containing only canonical nucleotides. 164s --statistics-filename STATISTICS_FILENAME 164s File to save/load genomic base anchored statistics. 164s 164s Statistic Motif Filter Arguments: 164s --genome-fasta GENOME_FASTA 164s FASTA file used to re-squiggle. For faster sequence 164s access. 164s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 164s Ground truth, motif centered, modified base 164s descriptions for output filtering. Format descriptions 164s as: "motif:mod_pos:name". The mod_pos indicates the 164s modified base within the motif (1-based index). 164s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 164s output for identification of E. coli dam and dcm 164s methylation. 164s 164s Output Arguments: 164s --browser-file-basename BROWSER_FILE_BASENAME 164s Basename for output browser files. Two files (plus and 164s minus strand) will be produced for each --file-types 164s supplied. Filenames formatted as "[browser-file- 164s basename].[file- 164s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 164s Default: tombo_results 164s --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} ...] 164s Data types of genome browser files to produce. 164s Produced coverage files are in bedGraph format, while 164s all other file types will be in wiggle format 164s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 164s Default: "coverage" 164s 164s FAST5 Data Arguments: 164s --corrected-group CORRECTED_GROUP 164s FAST5 group created by resquiggle command. Default: 164s RawGenomeCorrected_000 164s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 164s FAST5 subgroup(s) (under /Analyses/[--basecall- 164s group]/) containing basecalls and created within 164s [--corrected-group] containing re-squiggle results. 164s Default: ['BaseCalled_template'] 164s 164s Miscellaneous Arguments: 164s --quiet, -q Don't print status information. 164s --help, -h Print this help message and exit 164s usage: tombo text_output signif_sequence_context --statistics-filename 164s STATISTICS_FILENAME 164s [--genome-fasta GENOME_FASTA] 164s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 164s [--num-regions NUM_REGIONS] 164s [--num-bases NUM_BASES] 164s [--sequences-filename SEQUENCES_FILENAME] 164s [--corrected-group CORRECTED_GROUP] 164s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 164s [--quiet] [--help] 164s 164s Required Argument: 164s --statistics-filename STATISTICS_FILENAME 164s File to save/load genomic base anchored statistics. 164s 164s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 164s --genome-fasta GENOME_FASTA 164s FASTA file used to re-squiggle. For faster sequence 164s access. 164s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 164s Directories containing fast5 files. 164s 164s Region Selection Arguments: 164s --num-regions NUM_REGIONS 164s Number of regions to plot. Default: 100 164s --num-bases NUM_BASES 164s Number of bases to plot/output. Default: 15 164s 164s Output Arguments: 164s --sequences-filename SEQUENCES_FILENAME 164s File for sequences from selected regions. Sequences 164s will be stored in FASTA format. Default: 164s tombo_results.significant_regions.fasta. 164s 164s FAST5 Data Arguments: 164s --corrected-group CORRECTED_GROUP 164s FAST5 group created by resquiggle command. Default: 164s RawGenomeCorrected_000 164s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 164s FAST5 subgroup(s) (under /Analyses/[--basecall- 164s group]/) containing basecalls and created within 164s [--corrected-group] containing re-squiggle results. 164s Default: ['BaseCalled_template'] 164s 164s Miscellaneous Arguments: 164s --quiet, -q Don't print status information. 164s --help, -h Print this help message and exit 164s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 164s [FAST5_BASEDIRS ...] 164s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 164s [--plot-standard-model] 164s [--plot-alternate-model {dam,6mA,5mC,dcm,CpG}] 164s [--overplot-threshold OVERPLOT_THRESHOLD] 164s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 164s [--num-regions NUM_REGIONS] 164s [--num-bases NUM_BASES] 164s [--pdf-filename PDF_FILENAME] 164s [--corrected-group CORRECTED_GROUP] 164s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 164s [--quiet] [--help] 164s 164s Required Argument: 164s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 164s Directories containing fast5 files. 164s 164s Comparison Arguments: 164s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 164s Set of directories containing fast5 files for control 164s reads, containing only canonical nucleotides. 164s --plot-standard-model 164s Add default standard model distribution to the plot. 164s --plot-alternate-model {dam,6mA,5mC,dcm,CpG} 164s Add alternative model distribution to the plot. 164s 164s Overplotting Arguments: 164s --overplot-threshold OVERPLOT_THRESHOLD 164s Coverage level to trigger alternative plot type 164s instead of raw signal. Default: 50 164s --overplot-type {Downsample,Boxplot,Quantile,Density} 164s Plot type for regions with higher coverage. Default: 164s Downsample 164s 164s Plotting Region Arguments: 164s --num-regions NUM_REGIONS 164s Number of regions to plot. Default: 10 164s --num-bases NUM_BASES 164s Number of bases to plot/output. Default: 21 164s 164s Output Argument: 164s --pdf-filename PDF_FILENAME 164s PDF filename to store plot(s). Default: 164s tombo_results.max_coverage.pdf 164s 164s FAST5 Data Arguments: 164s --corrected-group CORRECTED_GROUP 164s FAST5 group created by resquiggle command. Default: 164s RawGenomeCorrected_000 164s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 164s FAST5 subgroup(s) (under /Analyses/[--basecall- 164s group]/) containing basecalls and created within 164s [--corrected-group] containing re-squiggle results. 164s Default: ['BaseCalled_template'] 164s 164s Miscellaneous Arguments: 164s --quiet, -q Don't print status information. 164s --help, -h Print this help message and exit 164s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 164s [FAST5_BASEDIRS ...] --genome-locations 164s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 164s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 164s [--plot-standard-model] 164s [--plot-alternate-model {dam,5mC,6mA,dcm,CpG}] 164s [--overplot-threshold OVERPLOT_THRESHOLD] 164s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 164s [--num-bases NUM_BASES] 164s [--pdf-filename PDF_FILENAME] 164s [--corrected-group CORRECTED_GROUP] 164s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 164s [--quiet] [--help] 164s 164s Required Arguments: 164s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 164s Directories containing fast5 files. 164s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 164s Genomic locations at which to plot signal. Format 164s locations as "chrm:position[:strand] 164s [chrm2:position2[:strand2] ...]" (strand not 164s applicable for all applications) 164s 164s Comparison Arguments: 164s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 164s Set of directories containing fast5 files for control 164s reads, containing only canonical nucleotides. 164s --plot-standard-model 164s Add default standard model distribution to the plot. 164s --plot-alternate-model {dam,5mC,6mA,dcm,CpG} 164s Add alternative model distribution to the plot. 164s 164s Overplotting Arguments: 164s --overplot-threshold OVERPLOT_THRESHOLD 164s Coverage level to trigger alternative plot type 164s instead of raw signal. Default: 50 164s --overplot-type {Downsample,Boxplot,Quantile,Density} 164s Plot type for regions with higher coverage. Default: 164s Downsample 164s 164s Plotting Region Argument: 164s --num-bases NUM_BASES 164s Number of bases to plot/output. Default: 21 164s 164s Output Argument: 164s --pdf-filename PDF_FILENAME 164s PDF filename to store plot(s). Default: 164s tombo_results.genome_locations.pdf 164s 164s FAST5 Data Arguments: 164s --corrected-group CORRECTED_GROUP 164s FAST5 group created by resquiggle command. Default: 164s RawGenomeCorrected_000 164s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 164s FAST5 subgroup(s) (under /Analyses/[--basecall- 164s group]/) containing basecalls and created within 164s [--corrected-group] containing re-squiggle results. 164s Default: ['BaseCalled_template'] 164s 164s Miscellaneous Arguments: 164s --quiet, -q Don't print status information. 164s --help, -h Print this help message and exit 164s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 164s [FAST5_BASEDIRS ...] --motif MOTIF 164s --genome-fasta GENOME_FASTA 164s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 164s [--plot-standard-model] 164s [--plot-alternate-model {6mA,dam,dcm,CpG,5mC}] 164s [--overplot-threshold OVERPLOT_THRESHOLD] 164s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 164s [--num-regions NUM_REGIONS] 164s [--num-bases NUM_BASES] [--deepest-coverage] 164s [--pdf-filename PDF_FILENAME] 164s [--corrected-group CORRECTED_GROUP] 164s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 164s [--quiet] [--help] 164s 164s Required Arguments: 164s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 164s Directories containing fast5 files. 164s --motif MOTIF Motif of interest at which to plot signal and 164s statsitics. Supports IUPAC single letter codes (use T 164s for RNA). 164s --genome-fasta GENOME_FASTA 164s FASTA file used to re-squiggle. For faster sequence 164s access. 164s 164s Comparison Arguments: 164s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 164s Set of directories containing fast5 files for control 164s reads, containing only canonical nucleotides. 164s --plot-standard-model 164s Add default standard model distribution to the plot. 164s --plot-alternate-model {6mA,dam,dcm,CpG,5mC} 164s Add alternative model distribution to the plot. 164s 164s Overplotting Arguments: 164s --overplot-threshold OVERPLOT_THRESHOLD 164s Coverage level to trigger alternative plot type 164s instead of raw signal. Default: 50 164s --overplot-type {Downsample,Boxplot,Quantile,Density} 164s Plot type for regions with higher coverage. Default: 164s Downsample 164s 164s Plotting Region Arguments: 164s --num-regions NUM_REGIONS 164s Number of regions to plot. Default: 10 164s --num-bases NUM_BASES 164s Number of bases to plot/output. Default: 21 164s --deepest-coverage Plot the deepest coverage regions. 164s 164s Output Argument: 164s --pdf-filename PDF_FILENAME 164s PDF filename to store plot(s). Default: 164s tombo_results.motif_centered.pdf 164s 164s FAST5 Data Arguments: 164s --corrected-group CORRECTED_GROUP 164s FAST5 group created by resquiggle command. Default: 164s RawGenomeCorrected_000 164s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 164s FAST5 subgroup(s) (under /Analyses/[--basecall- 164s group]/) containing basecalls and created within 164s [--corrected-group] containing re-squiggle results. 164s Default: ['BaseCalled_template'] 164s 164s Miscellaneous Arguments: 164s --quiet, -q Don't print status information. 164s --help, -h Print this help message and exit 165s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 165s [FAST5_BASEDIRS ...] --control-fast5-basedirs 165s CONTROL_FAST5_BASEDIRS 165s [CONTROL_FAST5_BASEDIRS ...] 165s [--overplot-threshold OVERPLOT_THRESHOLD] 165s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 165s [--num-regions NUM_REGIONS] 165s [--num-bases NUM_BASES] 165s [--pdf-filename PDF_FILENAME] 165s [--sequences-filename SEQUENCES_FILENAME] 165s [--corrected-group CORRECTED_GROUP] 165s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 165s [--quiet] [--help] 165s 165s Required Arguments: 165s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s Directories containing fast5 files. 165s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 165s Set of directories containing fast5 files for control 165s reads, containing only canonical nucleotides. 165s 165s Overplotting Arguments: 165s --overplot-threshold OVERPLOT_THRESHOLD 165s Coverage level to trigger alternative plot type 165s instead of raw signal. Default: 50 165s --overplot-type {Downsample,Boxplot,Quantile,Density} 165s Plot type for regions with higher coverage. Default: 165s Downsample 165s 165s Plotting Region Arguments: 165s --num-regions NUM_REGIONS 165s Number of regions to plot. Default: 10 165s --num-bases NUM_BASES 165s Number of bases to plot/output. Default: 21 165s 165s Output Arguments: 165s --pdf-filename PDF_FILENAME 165s PDF filename to store plot(s). Default: 165s tombo_results.max_difference.pdf 165s --sequences-filename SEQUENCES_FILENAME 165s File for sequences from selected regions. Sequences 165s will be stored in FASTA format. Default: None. 165s 165s FAST5 Data Arguments: 165s --corrected-group CORRECTED_GROUP 165s FAST5 group created by resquiggle command. Default: 165s RawGenomeCorrected_000 165s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 165s FAST5 subgroup(s) (under /Analyses/[--basecall- 165s group]/) containing basecalls and created within 165s [--corrected-group] containing re-squiggle results. 165s Default: ['BaseCalled_template'] 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 165s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 165s [FAST5_BASEDIRS ...] --statistics-filename 165s STATISTICS_FILENAME 165s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 165s [--plot-standard-model] 165s [--plot-alternate-model {dcm,6mA,CpG,dam,5mC}] 165s [--overplot-threshold OVERPLOT_THRESHOLD] 165s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 165s [--num-regions NUM_REGIONS] 165s [--num-bases NUM_BASES] 165s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 165s [--pdf-filename PDF_FILENAME] 165s [--sequences-filename SEQUENCES_FILENAME] 165s [--corrected-group CORRECTED_GROUP] 165s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 165s [--quiet] [--help] 165s 165s Required Arguments: 165s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s Directories containing fast5 files. 165s --statistics-filename STATISTICS_FILENAME 165s File to save/load genomic base anchored statistics. 165s 165s Comparison Arguments: 165s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 165s Set of directories containing fast5 files for control 165s reads, containing only canonical nucleotides. 165s --plot-standard-model 165s Add default standard model distribution to the plot. 165s --plot-alternate-model {dcm,6mA,CpG,dam,5mC} 165s Add alternative model distribution to the plot. 165s 165s Overplotting Arguments: 165s --overplot-threshold OVERPLOT_THRESHOLD 165s Coverage level to trigger alternative plot type 165s instead of raw signal. Default: 50 165s --overplot-type {Downsample,Boxplot,Quantile,Density} 165s Plot type for regions with higher coverage. Default: 165s Downsample 165s 165s Plotting Region Arguments: 165s --num-regions NUM_REGIONS 165s Number of regions to plot. Default: 10 165s --num-bases NUM_BASES 165s Number of bases to plot/output. Default: 21 165s 165s Statistical Argument: 165s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 165s Dampen fraction modified estimates for low coverage 165s sites. Two parameters are unmodified and modified 165s pseudo read counts. This is equivalent to a beta prior 165s on the fraction estimate. Set to "0 0" to disable 165s dampened fraction estimation. Default: [2, 0] 165s 165s Output Arguments: 165s --pdf-filename PDF_FILENAME 165s PDF filename to store plot(s). Default: 165s tombo_results.significant_difference.pdf 165s --sequences-filename SEQUENCES_FILENAME 165s File for sequences from selected regions. Sequences 165s will be stored in FASTA format. Default: None. 165s 165s FAST5 Data Arguments: 165s --corrected-group CORRECTED_GROUP 165s FAST5 group created by resquiggle command. Default: 165s RawGenomeCorrected_000 165s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 165s FAST5 subgroup(s) (under /Analyses/[--basecall- 165s group]/) containing basecalls and created within 165s [--corrected-group] containing re-squiggle results. 165s Default: ['BaseCalled_template'] 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 165s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 165s [FAST5_BASEDIRS ...] --motif MOTIF 165s --statistics-filename STATISTICS_FILENAME 165s --genome-fasta GENOME_FASTA 165s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 165s [--plot-standard-model] 165s [--plot-alternate-model {CpG,dam,6mA,dcm,5mC}] 165s [--overplot-threshold OVERPLOT_THRESHOLD] 165s [--num-regions NUM_REGIONS] 165s [--num-context NUM_CONTEXT] 165s [--num-statistics NUM_STATISTICS] 165s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 165s [--pdf-filename PDF_FILENAME] 165s [--corrected-group CORRECTED_GROUP] 165s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 165s [--quiet] [--help] 165s 165s Required Arguments: 165s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s Directories containing fast5 files. 165s --motif MOTIF Motif of interest at which to plot signal and 165s statsitics. Supports IUPAC single letter codes (use T 165s for RNA). 165s --statistics-filename STATISTICS_FILENAME 165s File to save/load genomic base anchored statistics. 165s --genome-fasta GENOME_FASTA 165s FASTA file used to re-squiggle. For faster sequence 165s access. 165s 165s Comparison Arguments: 165s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 165s Set of directories containing fast5 files for control 165s reads, containing only canonical nucleotides. 165s --plot-standard-model 165s Add default standard model distribution to the plot. 165s --plot-alternate-model {CpG,dam,6mA,dcm,5mC} 165s Add alternative model distribution to the plot. 165s 165s Overplotting Argument: 165s --overplot-threshold OVERPLOT_THRESHOLD 165s Coverage level to trigger alternative plot type 165s instead of raw signal. Default: 50 165s 165s Plotting Region Arguments: 165s --num-regions NUM_REGIONS 165s Number of regions to plot. Default: 3 165s --num-context NUM_CONTEXT 165s Number of context bases around motif. Default: 5 165s --num-statistics NUM_STATISTICS 165s Number of motif centered regions to include in 165s statistic distributions. Default: 200 165s 165s Statistical Argument: 165s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 165s Dampen fraction modified estimates for low coverage 165s sites. Two parameters are unmodified and modified 165s pseudo read counts. This is equivalent to a beta prior 165s on the fraction estimate. Set to "0 0" to disable 165s dampened fraction estimation. Default: [2, 0] 165s 165s Output Argument: 165s --pdf-filename PDF_FILENAME 165s PDF filename to store plot(s). Default: 165s tombo_results.motif_statistics.pdf 165s 165s FAST5 Data Arguments: 165s --corrected-group CORRECTED_GROUP 165s FAST5 group created by resquiggle command. Default: 165s RawGenomeCorrected_000 165s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 165s FAST5 subgroup(s) (under /Analyses/[--basecall- 165s group]/) containing basecalls and created within 165s [--corrected-group] containing re-squiggle results. 165s Default: ['BaseCalled_template'] 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 165s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 165s [GENOME_LOCATIONS ...] 165s --per-read-statistics-filename 165s PER_READ_STATISTICS_FILENAME 165s [--genome-fasta GENOME_FASTA] 165s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 165s [--num-reads NUM_READS] [--num-bases NUM_BASES] 165s [--box-center] [--pdf-filename PDF_FILENAME] 165s [--corrected-group CORRECTED_GROUP] 165s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 165s [--quiet] [--help] 165s 165s Required Arguments: 165s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 165s Genomic locations at which to plot signal. Format 165s locations as "chrm:position[:strand] 165s [chrm2:position2[:strand2] ...]" (strand not 165s applicable for all applications) 165s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 165s Binary file containing per-read statistics from 165s statistical testing. 165s 165s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 165s --genome-fasta GENOME_FASTA 165s FASTA file used to re-squiggle. For faster sequence 165s access. 165s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s Directories containing fast5 files. 165s 165s Plotting Region Arguments: 165s --num-reads NUM_READS 165s Number of reads to plot. Default: 100 165s --num-bases NUM_BASES 165s Number of bases to plot/output. Default: 51 165s --box-center Plot a box around the central base. 165s 165s Output Argument: 165s --pdf-filename PDF_FILENAME 165s PDF filename to store plot(s). Default: 165s tombo_results.per_read_stats.pdf 165s 165s FAST5 Data Arguments: 165s --corrected-group CORRECTED_GROUP 165s FAST5 group created by resquiggle command. Default: 165s RawGenomeCorrected_000 165s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 165s FAST5 subgroup(s) (under /Analyses/[--basecall- 165s group]/) containing basecalls and created within 165s [--corrected-group] containing re-squiggle results. 165s Default: ['BaseCalled_template'] 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 165s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 165s [STATISTICS_FILENAMES ...] 165s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 165s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 165s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 165s [--genome-fasta GENOME_FASTA] 165s [--pdf-filename PDF_FILENAME] 165s [--statistics-per-block STATISTICS_PER_BLOCK] 165s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 165s [--quiet] [--help] 165s 165s Required Argument: 165s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 165s Files to load genomic base anchored statistics. 165s 165s Ground Truth Arguments (provide bed files or motifs): 165s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 165s Modification description and bed format files 165s containing single base locations of ground truth 165s modified sites. Bed files should contain 6 fields 165s including strand. Format descriptions as 165s "mod_name:locs.bed". Example: "CpG 165s bisulfite":bisulfite_locs.bed 165s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 165s Bed format files containing single base locations of 165s ground truth unmodified sites. Bed files should 165s contain 6 fields including strand. 165s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 165s Ground truth, motif centered, modified base 165s descriptions for computing ROC and PR curves. Each 165s statistics file is associated with a set of motif 165s descriptions. Format descriptions as: 165s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 165s mod_pos indicates the alternate-base within the motif 165s (1-based index). Example: CCWGG:2:"dcm 165s 5mC"::GATC:2:"dam 6mA" would assess the performance of 165s a single Tombo statistics file for identification of 165s E. coli dam and dcm methylation. 165s --genome-fasta GENOME_FASTA 165s FASTA file used to re-squiggle. For faster sequence 165s access. 165s 165s Output Arguments: 165s --pdf-filename PDF_FILENAME 165s PDF filename to store plot(s). Default: 165s tombo_results.roc.pdf 165s 165s Down-sampling Arguments: 165s --statistics-per-block STATISTICS_PER_BLOCK 165s Number of randomly selected per-read, per-base 165s statistics to extract from each genomic block for 165s plotting. Default: Include all stats 165s --total-statistics-limit TOTAL_STATISTICS_LIMIT 165s Total per-read statistics to be extracted for 165s plotting. Avoids memory overflow for large runs. 165s Default: 5000000 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 165s usage: tombo plot per_read_roc --per-read-statistics-filenames 165s PER_READ_STATISTICS_FILENAMES 165s [PER_READ_STATISTICS_FILENAMES ...] 165s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 165s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 165s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 165s [--genome-fasta GENOME_FASTA] 165s [--statistics-per-block STATISTICS_PER_BLOCK] 165s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 165s [--pdf-filename PDF_FILENAME] [--quiet] 165s [--help] 165s 165s Required Argument: 165s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 165s Binary files containing per-read statistics from 165s statistical testing. 165s 165s Ground Truth Arguments (provide bed files or motifs): 165s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 165s Modification description and bed format files 165s containing single base locations of ground truth 165s modified sites. Bed files should contain 6 fields 165s including strand. Format descriptions as 165s "mod_name:locs.bed". Example: "CpG 165s bisulfite":bisulfite_locs.bed 165s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 165s Bed format files containing single base locations of 165s ground truth unmodified sites. Bed files should 165s contain 6 fields including strand. 165s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 165s Ground truth, motif centered, modified base 165s descriptions for computing ROC and PR curves. Each 165s statistics file is associated with a set of motif 165s descriptions. Format descriptions as: 165s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 165s mod_pos indicates the alternate-base within the motif 165s (1-based index). Example: CCWGG:2:"dcm 165s 5mC"::GATC:2:"dam 6mA" would assess the performance of 165s a single Tombo statistics file for identification of 165s E. coli dam and dcm methylation. 165s --genome-fasta GENOME_FASTA 165s FASTA file used to re-squiggle. For faster sequence 165s access. 165s 165s Down-sampling Arguments: 165s --statistics-per-block STATISTICS_PER_BLOCK 165s Number of randomly selected per-read, per-base 165s statistics to extract from each genomic block for 165s plotting. Default: 100000 165s --total-statistics-limit TOTAL_STATISTICS_LIMIT 165s Total per-read statistics to be extracted for 165s plotting. Avoids memory overflow for large runs. 165s Default: 5000000 165s 165s Output Arguments: 165s --pdf-filename PDF_FILENAME 165s PDF filename to store plot(s). Default: 165s tombo_results.per_reads_roc.pdf 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 165s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s [--upstream-bases {0,1,2,3,4}] 165s [--downstream-bases {0,1,2,3,4}] [--read-mean] 165s [--num-kmer-threshold NUM_KMER_THRESHOLD] 165s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 165s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 165s [--corrected-group CORRECTED_GROUP] 165s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 165s [--quiet] [--help] 165s 165s Required Argument: 165s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s Directories containing fast5 files. 165s 165s Data Processing Arguments: 165s --upstream-bases {0,1,2,3,4} 165s Upstream bases in k-mer. Default: 1 165s --downstream-bases {0,1,2,3,4} 165s Downstream bases in k-mer. Default: 2 165s --read-mean Plot k-mer means across whole reads as opposed to 165s individual k-mer event levels. 165s --num-kmer-threshold NUM_KMER_THRESHOLD 165s Observations of each k-mer required to include a read 165s in read level averages. Default: 1 165s 165s Plotting Region Arguments: 165s --num-reads NUM_READS 165s Number of reads to plot. Default: 100 165s 165s Output Arguments: 165s --pdf-filename PDF_FILENAME 165s PDF filename to store plot(s). Default: 165s tombo_results.kmer_distribution.pdf 165s --r-data-filename R_DATA_FILENAME 165s Filename to save R data structure. Default: Don't save 165s --dont-plot Don't plot result. Useful to produce only R data file. 165s 165s FAST5 Data Arguments: 165s --corrected-group CORRECTED_GROUP 165s FAST5 group created by resquiggle command. Default: 165s RawGenomeCorrected_000 165s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 165s FAST5 subgroup(s) (under /Analyses/[--basecall- 165s group]/) containing basecalls and created within 165s [--corrected-group] containing re-squiggle results. 165s Default: ['BaseCalled_template'] 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 165s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 165s [FAST5_BASEDIRS ...] 165s --control-fast5-basedirs 165s CONTROL_FAST5_BASEDIRS 165s [CONTROL_FAST5_BASEDIRS ...] 165s --statistics-filename 165s STATISTICS_FILENAME 165s [--genome-fasta GENOME_FASTA] 165s [--processes PROCESSES] 165s [--num-regions NUM_REGIONS] 165s [--num-bases NUM_BASES] 165s [--slide-span SLIDE_SPAN] 165s [--pdf-filename PDF_FILENAME] 165s [--r-data-filename R_DATA_FILENAME] 165s [--corrected-group CORRECTED_GROUP] 165s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 165s [--quiet] [--help] 165s 165s Required Arguments: 165s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s Directories containing fast5 files. 165s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 165s Set of directories containing fast5 files for control 165s reads, containing only canonical nucleotides. 165s --statistics-filename STATISTICS_FILENAME 165s File to save/load genomic base anchored statistics. 165s 165s FASTA Sequence Argument: 165s --genome-fasta GENOME_FASTA 165s FASTA file used to re-squiggle. For faster sequence 165s access. 165s 165s Multiprocessing Argument: 165s --processes PROCESSES 165s Number of processes. Default: 1 165s 165s Plotting Region Arguments: 165s --num-regions NUM_REGIONS 165s Number of regions to plot. Default: 10 165s --num-bases NUM_BASES 165s Number of bases to plot/output. Default: 21 165s --slide-span SLIDE_SPAN 165s Number of bases offset over which to search when 165s computing distances for signal cluster plotting. 165s Default: 0 (exact position) 165s 165s Output Arguments: 165s --pdf-filename PDF_FILENAME 165s PDF filename to store plot(s). Default: 165s tombo_results.signal_clusters.pdf 165s --r-data-filename R_DATA_FILENAME 165s Filename to save R data structure. Default: Don't save 165s 165s FAST5 Data Arguments: 165s --corrected-group CORRECTED_GROUP 165s FAST5 group created by resquiggle command. Default: 165s RawGenomeCorrected_000 165s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 165s FAST5 subgroup(s) (under /Analyses/[--basecall- 165s group]/) containing basecalls and created within 165s [--corrected-group] containing re-squiggle results. 165s Default: ['BaseCalled_template'] 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 165s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 165s 165s Required Arguments: 165s fast5s_basedir Directory containing fast5 files. All files ending in 165s "fast5" found recursively within this base directory will be 165s processed. 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 166s usage: tombo build_model event_resquiggle 166s [--minimap2-executable MINIMAP2_EXECUTABLE] 166s [--minimap2-index MINIMAP2_INDEX] 166s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 166s [--graphmap-executable GRAPHMAP_EXECUTABLE] 166s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 166s [--normalization-type {median,pA,pA_raw,none}] 166s [--pore-model-filename PORE_MODEL_FILENAME] 166s [--outlier-threshold OUTLIER_THRESHOLD] 166s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 166s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 166s [--timeout TIMEOUT] 166s [--cpts-limit CPTS_LIMIT] 166s [--skip-index] [--overwrite] 166s [--failed-reads-filename FAILED_READS_FILENAME] 166s [--include-event-stdev] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-group BASECALL_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--processes PROCESSES] 166s [--align-processes ALIGN_PROCESSES] 166s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 166s [--resquiggle-processes RESQUIGGLE_PROCESSES] 166s [--quiet] [--help] 166s fast5s_basedir reference_fasta 166s 166s Required Arguments: 166s fast5s_basedir Directory containing fast5 files. All files ending in 166s "fast5" found recursively within this base directory 166s will be processed. 166s reference_fasta Reference genome/transcriptome FASTA file for mapping. 166s 166s Mapper Arguments (One mapper is required): 166s --minimap2-executable MINIMAP2_EXECUTABLE 166s Path to minimap2 executable. 166s --minimap2-index MINIMAP2_INDEX 166s Path to minimap2 index (with map-ont preset) file 166s corresponding to the [genome_fasta] provided. 166s --bwa-mem-executable BWA_MEM_EXECUTABLE 166s Path to bwa-mem executable. 166s --graphmap-executable GRAPHMAP_EXECUTABLE 166s Path to graphmap executable. 166s --alignment-batch-size ALIGNMENT_BATCH_SIZE 166s Number of reads included in each alignment call. Note: 166s A new system mapping call is made for each batch 166s (including loading of the genome), so it is advised to 166s use larger values for larger genomes. Default: 1000 166s 166s Signal Processing Arguments: 166s --normalization-type {median,pA,pA_raw,none} 166s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 166s as in the ONT events (using offset, range and 166s digitization), "pA": k-mer-based correction for pA 166s drift as in nanopolish (requires [--pore-model- 166s filename]), "median": median and MAD from raw signal. 166s Default: median 166s --pore-model-filename PORE_MODEL_FILENAME 166s File containing kmer model parameters (level_mean and 166s level_stdv) used in order to compute kmer-based 166s corrected pA values. E.g. https://github.com/jts/nanop 166s olish/blob/master/etc/r9- 166s models/template_median68pA.5mers.model 166s --outlier-threshold OUTLIER_THRESHOLD 166s Windosrize the signal at this number of scale values. 166s Negative value disables outlier clipping. Default: 166s 5.000000 166s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 166s Specify the 2 parameters for segmentation 1) running 166s neighboring windows width 2) minimum raw observations 166s per genomic base. Sample type defaults: RNA : 12 6 || 166s DNA : 5 3 166s 166s Read Filtering Arguments: 166s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 166s Filter reads based on observations per base percentile 166s thresholds. Format thresholds as "percentile:thresh 166s [pctl2:thresh2 ...]". For example to filter reads with 166s 99th pctl > 200 obs/base or max > 5k obs/base use 166s "99:200 100:5000". 166s --timeout TIMEOUT Timeout in seconds for processing a single read. 166s Default: No timeout. 166s --cpts-limit CPTS_LIMIT 166s Maximum number of changepoints to find within a single 166s indel group. Default: No limit. 166s 166s Input/Output Arguments: 166s --skip-index Skip creation of tombo index. This drastically slows 166s downstream tombo commands. Default stores tombo index 166s named ".[--fast5-basedir].[--corrected- 166s group].tombo.index" to be loaded automatically for 166s downstream commands. 166s --overwrite Overwrite previous corrected group in FAST5 files. 166s Note: only effects --corrected-group or --new- 166s corrected-group. 166s --failed-reads-filename FAILED_READS_FILENAME 166s Output failed read filenames with assoicated error. 166s Default: Do not store failed reads. 166s --include-event-stdev 166s Include corrected event standard deviation in output 166s FAST5 data. 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-group BASECALL_GROUP 166s FAST5 group obtain original basecalls (under Analyses 166s group). Default: Basecall_1D_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Multiprocessing Arguments: 166s --processes PROCESSES 166s Number of processes. Default: 2 166s --align-processes ALIGN_PROCESSES 166s Number of processes to use for parsing and aligning 166s original basecalls. Each process will independently 166s load the genome into memory, so use caution with 166s larger genomes (e.g. human). Default: 1 166s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 166s Number of threads to use for aligner system call. 166s Default: [--processes] / (2 * [--align-processes)] 166s --resquiggle-processes RESQUIGGLE_PROCESSES 166s Number of processes to use for resquiggle algorithm. 166s Default: [--processes] / 2 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 166s [FAST5_BASEDIRS ...] 166s --tombo-model-filename 166s TOMBO_MODEL_FILENAME 166s [--estimate-mean] 166s [--kmer-specific-sd] 166s [--upstream-bases {0,1,2,3,4}] 166s [--downstream-bases {0,1,2,3,4}] 166s [--minimum-test-reads MINIMUM_TEST_READS] 166s [--coverage-threshold COVERAGE_THRESHOLD] 166s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 166s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 166s [--processes PROCESSES] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Arguments: 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s --tombo-model-filename TOMBO_MODEL_FILENAME 166s Filename to save Tombo model. 166s 166s Modeling Arguments: 166s --estimate-mean Use the mean instead of median for model level 166s estimation. Note: This can cause poor fits due to 166s outliers 166s --kmer-specific-sd Estimate standard deviation for each k-mers 166s individually. 166s --upstream-bases {0,1,2,3,4} 166s Upstream bases in k-mer. Default: 1 166s --downstream-bases {0,1,2,3,4} 166s Downstream bases in k-mer. Default: 2 166s 166s Filtering Arguments: 166s --minimum-test-reads MINIMUM_TEST_READS 166s Number of reads required at a position to perform 166s significance testing or contribute to model 166s estimation. Default: 10 166s --coverage-threshold COVERAGE_THRESHOLD 166s Maximum mean coverage per region when estimating k-mer 166s model (limits compute time for deep samples). Default: 166s 100 166s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 166s Number of each k-mer observations required in order to 166s produce a reference (genomic locations for standard 166s reference and per-read for alternative reference). 166s Default: 5 166s 166s Multiprocessing Arguments: 166s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 166s Size of regions over which to multiprocesses statistic 166s computation. For very deep samples a smaller value is 166s recommmended in order to control memory consumption. 166s Default: 10000 166s --processes PROCESSES 166s Number of processes. Default: 1 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo build_model estimate_alt_reference --alternate-model-filename 166s ALTERNATE_MODEL_FILENAME 166s --alternate-model-name 166s ALTERNATE_MODEL_NAME 166s --alternate-model-base 166s {A,C,G,T} 166s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 166s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 166s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 166s [--control-density-filename CONTROL_DENSITY_FILENAME] 166s [--dna] [--rna] 166s [--tombo-model-filename TOMBO_MODEL_FILENAME] 166s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 166s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 166s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 166s [--save-density-basename SAVE_DENSITY_BASENAME] 166s [--processes PROCESSES] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Arguments: 166s --alternate-model-filename ALTERNATE_MODEL_FILENAME 166s Tombo model for alternative likelihood ratio 166s significance testing. 166s --alternate-model-name ALTERNATE_MODEL_NAME 166s A short name to associate with this alternate model 166s (e.g. 5mC, 6mA, etc.). This text will be included in 166s output filenames when this model is used for testing. 166s --alternate-model-base {A,C,G,T} 166s Non-standard base is an alternative to this base. 166s 166s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 166s Set of directories containing fast5 files for control 166s reads, containing only canonical nucleotides. 166s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 166s File containing k-mer level kernel density estimates 166s for the alternative sample saved using --save-density- 166s basename. 166s --control-density-filename CONTROL_DENSITY_FILENAME 166s File containing k-mer level kernel density estimates 166s for the control sample saved using --save-density- 166s basename. 166s 166s Standard Model Arguments: 166s --dna Explicitly select canonical DNA model. Default: 166s Automatically determine from FAST5s 166s --rna Explicitly select canonical RNA model. Default: 166s Automatically determine from FAST5s 166s --tombo-model-filename TOMBO_MODEL_FILENAME 166s Tombo model filename. If no file is provided, the 166s default DNA or RNA Tombo model will be used. 166s 166s Model Fitting Arguments: 166s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 166s When esitmating the alternative base incorporation 166s rate, this percent of k-mers are assumed to have 166s significantly shifted signal so the alternative 166s distribution minimally overlaps the standard base 166s distribution. Default: 5.000000 166s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 166s Bandwidth applied when performing Gaussian kernal 166s density esitmation on standard and alternative base 166s signal distributions. Default: 0.050000 166s 166s Filtering Argument: 166s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 166s Number of each k-mer observations required in order to 166s produce a reference (genomic locations for standard 166s reference and per-read for alternative reference). 166s Default: 1000 166s 166s Output Argument: 166s --save-density-basename SAVE_DENSITY_BASENAME 166s Basename to save alternative model estimation density 166s estimation information. See scripts/debug_est_alt.R 166s for info use example. Default: Don't save. 166s 166s Multiprocessing Arguments: 166s --processes PROCESSES 166s Number of processes. Default: 1 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s This test only tests the help system 166s There is an extensive test in 166s 166s tombo/tests/shell_tests.sh 166s 166s but this requires to download larger data 166s sets which is not done for the moment. 166s autopkgtest [11:20:55]: test run-unit-test: -----------------------] 167s run-unit-test PASS 167s autopkgtest [11:20:56]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 167s autopkgtest [11:20:56]: @@@@@@@@@@@@@@@@@@@@ summary 167s run-unit-test PASS 189s virt: nova [W] Skipping flock in bos03-arm64 189s virt: Creating nova instance adt-plucky-arm64-tombo-20241113-111809-juju-7f2275-prod-proposed-migration-environment-2-e63c8840-7608-4e02-8b9a-05e541b802a2 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...