0s autopkgtest [18:05:22]: starting date and time: 2025-03-15 18:05:22+0000 0s autopkgtest [18:05:22]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [18:05:22]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7jjtj5us/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.229 lxd-armhf-10.145.243.229:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [18:05:43]: testbed dpkg architecture: armhf 23s autopkgtest [18:05:45]: testbed apt version: 2.9.33 27s autopkgtest [18:05:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 30s autopkgtest [18:05:51]: testbed release detected to be: None 37s autopkgtest [18:05:59]: updating testbed package index (apt update) 39s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 39s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 39s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 40s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 40s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 40s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 40s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 40s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 41s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 41s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 41s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 41s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 58s Get:16 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 58s Get:17 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 60s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 61s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 62s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 62s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 78s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 80s Fetched 41.0 MB in 41s (1005 kB/s) 81s Reading package lists... 87s autopkgtest [18:06:49]: upgrading testbed (apt dist-upgrade and autopurge) 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 90s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 90s Starting 2 pkgProblemResolver with broken count: 0 90s Done 91s Entering ResolveByKeep 91s 91s Calculating upgrade... 92s The following packages will be upgraded: 92s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 92s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s Need to get 8683 kB of archives. 92s After this operation, 23.6 kB of additional disk space will be used. 92s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 95s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 96s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 100s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 100s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 101s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 101s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 102s Preconfiguring packages ... 102s Fetched 8683 kB in 9s (938 kB/s) 102s (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 ... 64655 files and directories currently installed.) 102s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 102s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 102s Setting up libc6:armhf (2.41-1ubuntu2) ... 103s (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 ... 64655 files and directories currently installed.) 103s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 103s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 103s Setting up libc-bin (2.41-1ubuntu2) ... 103s (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 ... 64655 files and directories currently installed.) 103s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 103s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 103s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 103s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 103s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 103s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 104s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 104s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 104s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 104s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 104s Setting up sos (4.9.0-5) ... 105s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 105s Setting up locales (2.41-1ubuntu2) ... 106s Generating locales (this might take a while)... 108s en_US.UTF-8... done 108s Generation complete. 108s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 108s Setting up strace (6.13+ds-1ubuntu1) ... 108s Processing triggers for man-db (2.13.0-1) ... 109s Processing triggers for systemd (257.3-1ubuntu3) ... 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Starting pkgProblemResolver with broken count: 0 113s Starting 2 pkgProblemResolver with broken count: 0 113s Done 113s Solving dependencies... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s autopkgtest [18:07:17]: rebooting testbed after setup commands that affected boot 155s autopkgtest [18:07:57]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 179s autopkgtest [18:08:21]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 215s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build2 (dsc) [2291 B] 215s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build2 (tar) [22.3 MB] 215s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build2 (diff) [9628 B] 215s gpgv: Signature made Tue Mar 4 15:27:30 2025 UTC 215s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 215s gpgv: Can't check signature: No public key 215s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7build2.dsc: no acceptable signature found 216s autopkgtest [18:08:58]: testing package tombo version 1.5.1-7build2 218s autopkgtest [18:09:00]: build not needed 221s autopkgtest [18:09:03]: test run-unit-test: preparing testbed 223s Reading package lists... 223s Building dependency tree... 223s Reading state information... 224s Starting pkgProblemResolver with broken count: 0 225s Starting 2 pkgProblemResolver with broken count: 0 225s Done 225s The following NEW packages will be installed: 225s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 225s libhdf5-310 libhdf5-hl-310 libjs-jquery libjs-mathjax libjs-sphinxdoc 225s libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 python3-decorator 225s python3-h5py python3-h5py-serial python3-mappy python3-numpy 225s python3-numpy-dev python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 226s tombo-doc 226s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 226s Need to get 60.9 MB of archives. 226s After this operation, 182 MB of additional disk space will be used. 226s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-lato all 2.015-1 [2781 kB] 228s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy-dev armhf 1:2.2.3+ds-5 [141 kB] 228s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 228s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 229s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 230s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:2.2.3+ds-5 [3725 kB] 233s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 234s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 235s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 235s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 235s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-310 armhf 1.14.5+repack-3 [1410 kB] 236s Get:12 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-310 armhf 1.14.5+repack-3 [58.8 kB] 236s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 236s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 236s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 8.1.3-4 [30.9 kB] 236s Get:16 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 236s Get:17 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 236s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 236s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.13.0-1 [1113 kB] 236s Get:20 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.13.0-1 [7978 B] 236s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mappy armhf 2.27+dfsg-1build2 [174 kB] 236s Get:22 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-tqdm all 4.67.1-2 [92.5 kB] 236s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 237s Get:24 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.14.1-4ubuntu2 [16.7 MB] 247s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf tombo armhf 1.5.1-7build2 [455 kB] 248s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 253s Get:27 http://ftpmaster.internal/ubuntu plucky/universe armhf tombo-doc all 1.5.1-7build2 [21.7 MB] 273s Fetched 60.9 MB in 47s (1294 kB/s) 273s Selecting previously unselected package fonts-lato. 273s (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 ... 64655 files and directories currently installed.) 273s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 273s Unpacking fonts-lato (2.015-1) ... 273s Selecting previously unselected package python3-numpy-dev:armhf. 273s Preparing to unpack .../01-python3-numpy-dev_1%3a2.2.3+ds-5_armhf.deb ... 273s Unpacking python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 273s Selecting previously unselected package libblas3:armhf. 273s Preparing to unpack .../02-libblas3_3.12.1-2_armhf.deb ... 273s Unpacking libblas3:armhf (3.12.1-2) ... 273s Selecting previously unselected package libgfortran5:armhf. 273s Preparing to unpack .../03-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 273s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 273s Selecting previously unselected package liblapack3:armhf. 273s Preparing to unpack .../04-liblapack3_3.12.1-2_armhf.deb ... 273s Unpacking liblapack3:armhf (3.12.1-2) ... 274s Selecting previously unselected package python3-numpy. 274s Preparing to unpack .../05-python3-numpy_1%3a2.2.3+ds-5_armhf.deb ... 274s Unpacking python3-numpy (1:2.2.3+ds-5) ... 274s Selecting previously unselected package fonts-font-awesome. 274s Preparing to unpack .../06-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 274s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 274s Selecting previously unselected package fonts-mathjax. 274s Preparing to unpack .../07-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 274s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 274s Selecting previously unselected package libaec0:armhf. 274s Preparing to unpack .../08-libaec0_1.1.3-1_armhf.deb ... 274s Unpacking libaec0:armhf (1.1.3-1) ... 274s Selecting previously unselected package libsz2:armhf. 274s Preparing to unpack .../09-libsz2_1.1.3-1_armhf.deb ... 274s Unpacking libsz2:armhf (1.1.3-1) ... 274s Selecting previously unselected package libhdf5-310:armhf. 274s Preparing to unpack .../10-libhdf5-310_1.14.5+repack-3_armhf.deb ... 274s Unpacking libhdf5-310:armhf (1.14.5+repack-3) ... 274s Selecting previously unselected package libhdf5-hl-310:armhf. 274s Preparing to unpack .../11-libhdf5-hl-310_1.14.5+repack-3_armhf.deb ... 274s Unpacking libhdf5-hl-310:armhf (1.14.5+repack-3) ... 274s Selecting previously unselected package libjs-jquery. 274s Preparing to unpack .../12-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 274s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 274s Selecting previously unselected package libjs-underscore. 274s Preparing to unpack .../13-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 274s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 274s Selecting previously unselected package libjs-sphinxdoc. 274s Preparing to unpack .../14-libjs-sphinxdoc_8.1.3-4_all.deb ... 274s Unpacking libjs-sphinxdoc (8.1.3-4) ... 274s Selecting previously unselected package liblbfgsb0:armhf. 274s Preparing to unpack .../15-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 274s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 274s Selecting previously unselected package liblzf1:armhf. 274s Preparing to unpack .../16-liblzf1_3.6-4_armhf.deb ... 274s Unpacking liblzf1:armhf (3.6-4) ... 274s Selecting previously unselected package python3-decorator. 274s Preparing to unpack .../17-python3-decorator_5.1.1-5_all.deb ... 274s Unpacking python3-decorator (5.1.1-5) ... 274s Selecting previously unselected package python3-h5py-serial. 274s Preparing to unpack .../18-python3-h5py-serial_3.13.0-1_armhf.deb ... 274s Unpacking python3-h5py-serial (3.13.0-1) ... 275s Selecting previously unselected package python3-h5py. 275s Preparing to unpack .../19-python3-h5py_3.13.0-1_all.deb ... 275s Unpacking python3-h5py (3.13.0-1) ... 275s Selecting previously unselected package python3-mappy. 275s Preparing to unpack .../20-python3-mappy_2.27+dfsg-1build2_armhf.deb ... 275s Unpacking python3-mappy (2.27+dfsg-1build2) ... 275s Selecting previously unselected package python3-tqdm. 275s Preparing to unpack .../21-python3-tqdm_4.67.1-2_all.deb ... 275s Unpacking python3-tqdm (4.67.1-2) ... 275s Selecting previously unselected package sphinx-rtd-theme-common. 275s Preparing to unpack .../22-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 275s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 275s Selecting previously unselected package python3-scipy. 275s Preparing to unpack .../23-python3-scipy_1.14.1-4ubuntu2_armhf.deb ... 275s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 275s Selecting previously unselected package tombo. 275s Preparing to unpack .../24-tombo_1.5.1-7build2_armhf.deb ... 275s Unpacking tombo (1.5.1-7build2) ... 275s Selecting previously unselected package libjs-mathjax. 275s Preparing to unpack .../25-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 275s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 276s Selecting previously unselected package tombo-doc. 276s Preparing to unpack .../26-tombo-doc_1.5.1-7build2_all.deb ... 276s Unpacking tombo-doc (1.5.1-7build2) ... 276s Setting up fonts-lato (2.015-1) ... 276s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 276s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 276s Setting up python3-tqdm (4.67.1-2) ... 276s Setting up python3-mappy (2.27+dfsg-1build2) ... 276s Setting up libaec0:armhf (1.1.3-1) ... 276s Setting up python3-decorator (5.1.1-5) ... 277s Setting up libblas3:armhf (3.12.1-2) ... 277s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 277s Setting up liblzf1:armhf (3.6-4) ... 277s Setting up python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 277s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 277s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 277s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 277s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 277s Setting up libsz2:armhf (1.1.3-1) ... 277s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 277s Setting up liblapack3:armhf (3.12.1-2) ... 277s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 277s Setting up python3-numpy (1:2.2.3+ds-5) ... 279s Setting up libjs-sphinxdoc (8.1.3-4) ... 279s Setting up tombo-doc (1.5.1-7build2) ... 279s Setting up libhdf5-310:armhf (1.14.5+repack-3) ... 279s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 279s Setting up libhdf5-hl-310:armhf (1.14.5+repack-3) ... 279s Setting up python3-scipy (1.14.1-4ubuntu2) ... 283s Setting up python3-h5py-serial (3.13.0-1) ... 283s Setting up python3-h5py (3.13.0-1) ... 283s Setting up tombo (1.5.1-7build2) ... 284s Processing triggers for man-db (2.13.0-1) ... 284s Processing triggers for libc-bin (2.41-1ubuntu2) ... 302s autopkgtest [18:10:24]: test run-unit-test: [----------------------- 304s ********* Testing help commands ********** 304s usage: tombo [-h] [-v] 304s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} ... 304s 304s ********** Tombo ********* 304s 304s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 304s 304s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 304s 304s Tombo command groups (additional help available within each command group): 304s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 304s preprocess Pre-process nanopore reads for Tombo processing. 304s filter Apply filter to Tombo index file for specified criterion. 304s detect_modifications Perform statistical testing to detect non-standard nucleotides. 304s text_output Output Tombo results in text files. 304s build_model Create canonical and alternative base Tombo models. 304s plot Save plots to visualize raw nanopore signal or testing results. 304s 304s options: 304s -h, --help show this help message and exit 304s -v, --version show Tombo version and exit. 304s usage: tombo resquiggle [--dna] [--rna] 304s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 304s [--q-score Q_SCORE] 304s [--signal-matching-score SIGNAL_MATCHING_SCORE] 304s [--processes PROCESSES] 304s [--corrected-group CORRECTED_GROUP] 304s [--basecall-group BASECALL_GROUP] 304s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 304s [--overwrite] 304s [--failed-reads-filename FAILED_READS_FILENAME] 304s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 304s [--print-advanced-arguments] [--quiet] [--help] 304s fast5s_basedir reference 304s 304s Required Arguments: 304s fast5s_basedir Directory containing fast5 files. All files ending in 304s "fast5" found recursively within this base directory 304s will be processed. 304s reference Reference genome/transcriptome FASTA file or minimap2 304s index (with "map-ont" preset) for mapping. 304s 304s Model Parameters: 304s --dna Explicitly select canonical DNA model. Default: 304s Automatically determine from FAST5s 304s --rna Explicitly select canonical RNA model. Default: 304s Automatically determine from FAST5s 304s 304s Read Filtering Argument: 304s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 304s Filter reads based on observations per base percentile 304s thresholds. Format thresholds as "percentile:thresh 304s [pctl2:thresh2 ...]". For example to filter reads with 304s 99th pctl > 200 obs/base or max > 5k obs/base use 304s "99:200 100:5000". 304s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 304s Default: 0.000000 304s --signal-matching-score SIGNAL_MATCHING_SCORE 304s Observed to expected signal matching score (higher 304s score indicates poor matching). Sample type defaults: 304s RNA : 2 || DNA : 1.1 304s 304s Multiprocessing Arguments: 304s --processes PROCESSES 304s Number of processes. Default: 1 304s 304s FAST5 Data Arguments: 304s --corrected-group CORRECTED_GROUP 304s FAST5 group created by resquiggle command. Default: 304s RawGenomeCorrected_000 304s --basecall-group BASECALL_GROUP 304s FAST5 group obtain original basecalls (under Analyses 304s group). Default: Basecall_1D_000 304s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 304s FAST5 subgroup(s) (under /Analyses/[--basecall- 304s group]/) containing basecalls and created within 304s [--corrected-group] containing re-squiggle results. 304s Default: ['BaseCalled_template'] 304s --overwrite Overwrite previous corrected group in FAST5 files. 304s Note: only effects --corrected-group or --new- 304s corrected-group. 304s 304s Input/Output Arguments: 304s --failed-reads-filename FAILED_READS_FILENAME 304s Output failed read filenames with assoicated error. 304s Default: Do not store failed reads. 304s --num-most-common-errors NUM_MOST_COMMON_ERRORS 304s Dynamically show this many most common errors so far 304s through run. Default: 0; Just show progress 304s 304s Advanced Arguments: 304s --print-advanced-arguments 304s Print advanced re-squiggle arguments and exit. 304s 304s Miscellaneous Arguments: 304s --quiet, -q Don't print status information. 304s --help, -h Print this help message and exit 305s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 305s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 305s [--basecall-group BASECALL_GROUP] 305s [--basecall-subgroup BASECALL_SUBGROUP] 305s [--overwrite] 305s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 305s [--processes PROCESSES] 305s [--quiet] [--help] 305s 305s Required Arguments: 305s --fast5-basedir FAST5_BASEDIR 305s Directory containing fast5 files. 305s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 305s FASTQ filenames containing basecalls to be added to 305s raw FAST5 files. 305s 305s FAST5 Data Arguments: 305s --basecall-group BASECALL_GROUP 305s FAST5 group obtain original basecalls (under Analyses 305s group). Default: Basecall_1D_000 305s --basecall-subgroup BASECALL_SUBGROUP 305s FAST5 subgroup (under /Analyses/[--basecall-group]/) 305s under which to store basecalls from FASTQs. Default: 305s BaseCalled_template 305s --overwrite Overwrite previous corrected group in FAST5 files. 305s Note: only effects --corrected-group or --new- 305s corrected-group. 305s 305s Sequencing Summary Argument: 305s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 305s Sequencing summary filenames produced by albacore. 305s These can make annotation of raw FAST5 files with 305s FASTQ sequence much faster. 305s 305s Multiprocessing Argument: 305s --processes PROCESSES 305s Number of processes. Default: 1 305s 305s Miscellaneous Arguments: 305s --quiet, -q Don't print status information. 305s --help, -h Print this help message and exit 305s usage: tombo filter clear_filters 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s [--corrected-group CORRECTED_GROUP] 305s [--quiet] [--help] 305s 305s Required Argument: 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s Directories containing fast5 files. 305s 305s FAST5 Data Argument: 305s --corrected-group CORRECTED_GROUP 305s FAST5 group created by resquiggle command. Default: 305s RawGenomeCorrected_000 305s 305s Miscellaneous Arguments: 305s --quiet, -q Don't print status information. 305s --help, -h Print this help message and exit 305s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 305s [--corrected-group CORRECTED_GROUP] [--quiet] 305s [--help] 305s 305s Required Argument: 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s Directories containing fast5 files. 305s 305s Read Filtering Argument: 305s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 305s Filter reads based on observations per base percentile 305s thresholds. Format thresholds as "percentile:thresh 305s [pctl2:thresh2 ...]". For example to filter reads with 305s 99th pctl > 200 obs/base or max > 5k obs/base use 305s "99:200 100:5000". 305s 305s FAST5 Data Argument: 305s --corrected-group CORRECTED_GROUP 305s FAST5 group created by resquiggle command. Default: 305s RawGenomeCorrected_000 305s 305s Miscellaneous Arguments: 305s --quiet, -q Don't print status information. 305s --help, -h Print this help message and exit 305s usage: tombo filter level_coverage 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s [--percent-to-filter PERCENT_TO_FILTER] 305s [--corrected-group CORRECTED_GROUP] 305s [--quiet] [--help] 305s 305s Required Arguments: 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s Directories containing fast5 files. 305s 305s Read Filtering Argument: 305s --percent-to-filter PERCENT_TO_FILTER 305s Percentage of all reads to filter. Reads are randomly 305s selected weighted according to the approximate 305s coverage at the mapped genomic location. This can be 305s useful in modeling and testing. Default: 10.000000 305s 305s FAST5 Data Arguments: 305s --corrected-group CORRECTED_GROUP 305s FAST5 group created by resquiggle command. Default: 305s RawGenomeCorrected_000 305s 305s Miscellaneous Arguments: 305s --quiet, -q Don't print status information. 305s --help, -h Print this help message and exit 305s usage: tombo filter q_score 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s [--q-score Q_SCORE] 305s [--corrected-group CORRECTED_GROUP] 305s [--basecall-group BASECALL_GROUP] [--quiet] 305s [--help] 305s 305s Required Arguments: 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s Directories containing fast5 files. 305s 305s Read Filtering Argument: 305s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 305s Default: 7.000000 305s 305s FAST5 Data Arguments: 305s --corrected-group CORRECTED_GROUP 305s FAST5 group created by resquiggle command. Default: 305s RawGenomeCorrected_000 305s --basecall-group BASECALL_GROUP 305s FAST5 group obtain original basecalls (under Analyses 305s group). Default: Basecall_1D_000 305s 305s Miscellaneous Arguments: 305s --quiet, -q Don't print status information. 305s --help, -h Print this help message and exit 305s usage: tombo filter raw_signal_matching 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s --signal-matching-score SIGNAL_MATCHING_SCORE 305s [--corrected-group CORRECTED_GROUP] 305s [--quiet] [--help] 305s 305s Required Arguments: 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s Directories containing fast5 files. 305s --signal-matching-score SIGNAL_MATCHING_SCORE 305s Observed to expected signal matching score (higher 305s score indicates poor matching). Sample type defaults: 305s RNA : 2 || DNA : 1.1 305s 305s FAST5 Data Arguments: 305s --corrected-group CORRECTED_GROUP 305s FAST5 group created by resquiggle command. Default: 305s RawGenomeCorrected_000 305s 305s Miscellaneous Arguments: 305s --quiet, -q Don't print status information. 305s --help, -h Print this help message and exit 305s usage: tombo filter genome_locations 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 305s [--include-partial-overlap] 305s [--corrected-group CORRECTED_GROUP] 305s [--quiet] [--help] 305s 305s Required Arguments: 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s Directories containing fast5 files. 305s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 305s Filter out reads not falling completely within include 305s regions. Omit start and end coordinates to include an 305s entire chromosome/sequence record. Format regions as 305s "chrm[:start-end] [chrm2[:start2-end2] ...]". 305s 305s Filter Argument: 305s --include-partial-overlap 305s Include reads that partially overlap the specified 305s region. Default: Only include reads completely 305s contained in a specified region 305s 305s FAST5 Data Argument: 305s --corrected-group CORRECTED_GROUP 305s FAST5 group created by resquiggle command. Default: 305s RawGenomeCorrected_000 305s 305s Miscellaneous Arguments: 305s --quiet, -q Don't print status information. 305s --help, -h Print this help message and exit 305s usage: tombo detect_modifications de_novo 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s --statistics-file-basename STATISTICS_FILE_BASENAME 305s [--dna] [--rna] 305s [--fishers-method-context FISHERS_METHOD_CONTEXT] 305s [--minimum-test-reads MINIMUM_TEST_READS] 305s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 305s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 305s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 305s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 305s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 305s [--processes PROCESSES] 305s [--corrected-group CORRECTED_GROUP] 305s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 305s [--quiet] [--help] 305s 305s Required Argument: 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s Directories containing fast5 files. 305s --statistics-file-basename STATISTICS_FILE_BASENAME 305s File base name to save base by base statistics from 305s testing. Filenames will be [--statistics-file- 305s basename].[--alternate-bases]?.tombo.stats 305s 305s Comparison Model Arguments: 305s --dna Explicitly select canonical DNA model. Default: 305s Automatically determine from FAST5s 305s --rna Explicitly select canonical RNA model. Default: 305s Automatically determine from FAST5s 305s 305s Significance Test Arguments: 305s --fishers-method-context FISHERS_METHOD_CONTEXT 305s Number of context bases up and downstream over which 305s to compute Fisher's method combined p-values. Note: 305s Not applicable for alternative model likelihood ratio 305s tests. Default: 1. 305s --minimum-test-reads MINIMUM_TEST_READS 305s Number of reads required at a position to perform 305s significance testing or contribute to model 305s estimation. Default: 1 305s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 305s P-value threshold when computing fraction of 305s significant reads at each genomic position. If two 305s values are provided, statistics between these values 305s are not considered. Default thresholds: DNA:0.15-0.5 , 305s RNA:0.05-0.4 305s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 305s Dampen fraction modified estimates for low coverage 305s sites. Two parameters are unmodified and modified 305s pseudo read counts. This is equivalent to a beta prior 305s on the fraction estimate. Set to "0 0" to disable 305s dampened fraction estimation. Default: [2, 0] 305s 305s Output Argument: 305s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 305s Base for binary files containing per-read statistics 305s from statistical testing. Filenames will be [--per- 305s read-statistics-basename].[--alternate- 305s bases]?.tombo.per_read_stats 305s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 305s Number of the most significant sites to store for 305s faster access. If a longer list of most significant 305s sites is required the list must be re-computed from 305s all batches. Very large values can increase RAM usage. 305s Default: 100000 305s 305s Multiprocessing Arguments: 305s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 305s Size of regions over which to multiprocesses statistic 305s computation. For very deep samples a smaller value is 305s recommmended in order to control memory consumption. 305s Default: 10000 305s --processes PROCESSES 305s Number of processes. Default: 1 305s 305s FAST5 Data Arguments: 305s --corrected-group CORRECTED_GROUP 305s FAST5 group created by resquiggle command. Default: 305s RawGenomeCorrected_000 305s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 305s FAST5 subgroup(s) (under /Analyses/[--basecall- 305s group]/) containing basecalls and created within 305s [--corrected-group] containing re-squiggle results. 305s Default: ['BaseCalled_template'] 305s 305s Miscellaneous Arguments: 305s --quiet, -q Don't print status information. 305s --help, -h Print this help message and exit 305s usage: tombo detect_modifications alternative_model 305s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 305s [--statistics-file-basename STATISTICS_FILE_BASENAME] 305s [--alternate-bases {dam,5mC,dcm,CpG,6mA} [{dam,5mC,dcm,CpG,6mA} ...]] 305s [--print-available-models] 305s [--dna] [--rna] 305s [--minimum-test-reads MINIMUM_TEST_READS] 305s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 305s [--standard-log-likelihood-ratio] 305s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 305s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 305s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 305s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 305s [--processes PROCESSES] 305s [--corrected-group CORRECTED_GROUP] 305s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 305s [--quiet] [--help] 305s 305s Required Argument: 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s Directories containing fast5 files. 305s --statistics-file-basename STATISTICS_FILE_BASENAME 305s File base name to save base by base statistics from 305s testing. Filenames will be [--statistics-file- 305s basename].[--alternate-bases]?.tombo.stats 305s --alternate-bases {dam,5mC,dcm,CpG,6mA} [{dam,5mC,dcm,CpG,6mA} ...] 305s Default non-standard base model for testing (not 305s required if user created --alternate-model-filenames 305s is provided). 305s 305s Comparison Arguments: 305s --print-available-models 305s Print available alternative models and exit. 305s --dna Explicitly select canonical DNA model. Default: 305s Automatically determine from FAST5s 305s --rna Explicitly select canonical RNA model. Default: 305s Automatically determine from FAST5s 305s 305s Significance Test Arguments: 305s --minimum-test-reads MINIMUM_TEST_READS 305s Number of reads required at a position to perform 305s significance testing or contribute to model 305s estimation. Default: 1 305s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 305s Log likelihood ratio threshold when computing fraction 305s of significant reads at each genomic position. If two 305s values are provided, statistics between these values 305s are not considered. Default thresholds: DNA:-1.5-2.5 , 305s RNA:-2.5-2.5 305s --standard-log-likelihood-ratio 305s Use a standard log likelihood ratio (LLR) statistic. 305s Default is to use an outlier-robust LLR-like 305s statistic. Detail in full online documentation. 305s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 305s Dampen fraction modified estimates for low coverage 305s sites. Two parameters are unmodified and modified 305s pseudo read counts. This is equivalent to a beta prior 305s on the fraction estimate. Set to "0 0" to disable 305s dampened fraction estimation. Default: [2, 0] 305s 305s Output Argument: 305s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 305s Base for binary files containing per-read statistics 305s from statistical testing. Filenames will be [--per- 305s read-statistics-basename].[--alternate- 305s bases]?.tombo.per_read_stats 305s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 305s Number of the most significant sites to store for 305s faster access. If a longer list of most significant 305s sites is required the list must be re-computed from 305s all batches. Very large values can increase RAM usage. 305s Default: 100000 305s 305s Multiprocessing Arguments: 305s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 305s Size of regions over which to multiprocesses statistic 305s computation. For very deep samples a smaller value is 305s recommmended in order to control memory consumption. 305s Default: 10000 305s --processes PROCESSES 305s Number of processes. Default: 1 305s 305s FAST5 Data Arguments: 305s --corrected-group CORRECTED_GROUP 305s FAST5 group created by resquiggle command. Default: 305s RawGenomeCorrected_000 305s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 305s FAST5 subgroup(s) (under /Analyses/[--basecall- 305s group]/) containing basecalls and created within 305s [--corrected-group] containing re-squiggle results. 305s Default: ['BaseCalled_template'] 305s 305s Miscellaneous Arguments: 305s --quiet, -q Don't print status information. 305s --help, -h Print this help message and exit 305s usage: tombo detect_modifications model_sample_compare 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s --statistics-file-basename STATISTICS_FILE_BASENAME 305s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 305s [--sample-only-estimates] 305s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 305s [--dna] [--rna] 305s [--fishers-method-context FISHERS_METHOD_CONTEXT] 305s [--minimum-test-reads MINIMUM_TEST_READS] 305s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 305s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 305s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 305s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 305s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 305s [--processes PROCESSES] 305s [--corrected-group CORRECTED_GROUP] 305s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 305s [--quiet] [--help] 305s 305s Required Argument: 305s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 305s Directories containing fast5 files. 305s --statistics-file-basename STATISTICS_FILE_BASENAME 305s File base name to save base by base statistics from 305s testing. Filenames will be [--statistics-file- 305s basename].[--alternate-bases]?.tombo.stats 305s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 305s Set of directories containing fast5 files for control 305s reads, containing only canonical nucleotides. 305s 305s Model Prior Arguments: 305s --sample-only-estimates 305s Only use canonical sample to estimate expected signal 305s level and spread. Default: Use canonical model to 305s improve estimtates (esp. for low coverage regions) 305s using baysian posterior estimates. 305s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 305s Prior weights (one each for mean and spread) applied 305s to canonical base model for estimating posterior model 305s parameters for sample comparison. Default: [5, 40] 305s --dna Explicitly select canonical DNA model. Default: 305s Automatically determine from FAST5s 305s --rna Explicitly select canonical RNA model. Default: 305s Automatically determine from FAST5s 305s 305s Significance Test Arguments: 305s --fishers-method-context FISHERS_METHOD_CONTEXT 305s Number of context bases up and downstream over which 305s to compute Fisher's method combined p-values. Note: 305s Not applicable for alternative model likelihood ratio 305s tests. Default: 1. 305s --minimum-test-reads MINIMUM_TEST_READS 305s Number of reads required at a position to perform 305s significance testing or contribute to model 305s estimation. Default: 1 305s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 305s P-value threshold when computing fraction of 305s significant reads at each genomic position. If two 305s values are provided, statistics between these values 305s are not considered. Default thresholds: DNA:0.15-0.5 , 305s RNA:0.05-0.4 305s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 305s Dampen fraction modified estimates for low coverage 305s sites. Two parameters are unmodified and modified 305s pseudo read counts. This is equivalent to a beta prior 305s on the fraction estimate. Set to "0 0" to disable 305s dampened fraction estimation. Default: [2, 0] 305s 305s Output Argument: 305s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 305s Base for binary files containing per-read statistics 305s from statistical testing. Filenames will be [--per- 305s read-statistics-basename].[--alternate- 305s bases]?.tombo.per_read_stats 305s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 305s Number of the most significant sites to store for 305s faster access. If a longer list of most significant 305s sites is required the list must be re-computed from 305s all batches. Very large values can increase RAM usage. 305s Default: 100000 305s 305s Multiprocessing Arguments: 305s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 305s Size of regions over which to multiprocesses statistic 305s computation. For very deep samples a smaller value is 305s recommmended in order to control memory consumption. 305s Default: 10000 305s --processes PROCESSES 305s Number of processes. Default: 1 305s 305s FAST5 Data Arguments: 305s --corrected-group CORRECTED_GROUP 305s FAST5 group created by resquiggle command. Default: 305s RawGenomeCorrected_000 305s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 305s FAST5 subgroup(s) (under /Analyses/[--basecall- 305s group]/) containing basecalls and created within 305s [--corrected-group] containing re-squiggle results. 305s Default: ['BaseCalled_template'] 305s 305s Miscellaneous Arguments: 305s --quiet, -q Don't print status information. 305s --help, -h Print this help message and exit 306s usage: tombo detect_modifications level_sample_compare 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s --statistics-file-basename STATISTICS_FILE_BASENAME 306s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 306s [--fishers-method-context FISHERS_METHOD_CONTEXT] 306s [--minimum-test-reads MINIMUM_TEST_READS] 306s [--statistic-type {ks,u,t}] 306s [--store-p-value] 306s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 306s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 306s [--processes PROCESSES] 306s [--corrected-group CORRECTED_GROUP] 306s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 306s [--quiet] [--help] 306s 306s Required Argument: 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s Directories containing fast5 files. 306s --statistics-file-basename STATISTICS_FILE_BASENAME 306s File base name to save base by base statistics from 306s testing. Filenames will be [--statistics-file- 306s basename].[--alternate-bases]?.tombo.stats 306s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 306s Set of directories containing fast5 files for 306s alternate set of reads. 306s 306s Significance Test Arguments: 306s --fishers-method-context FISHERS_METHOD_CONTEXT 306s Number of context bases up and downstream over which 306s to compute Fisher's method combined p-values. Note: 306s Not applicable for alternative model likelihood ratio 306s tests. Default: 1. 306s --minimum-test-reads MINIMUM_TEST_READS 306s Number of reads required at a position to perform 306s significance testing or contribute to model 306s estimation. Default: 50 306s --statistic-type {ks,u,t} 306s Type of statistical test to apply. Default: "ks" 306s --store-p-value Store p-value instead of effect-size statistic. 306s Statistics are D-statistic (KS-test), deviation from 306s even common language effect size (u-test), and Cohen's 306s D (t-test). 306s 306s Output Argument: 306s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 306s Number of the most significant sites to store for 306s faster access. If a longer list of most significant 306s sites is required the list must be re-computed from 306s all batches. Very large values can increase RAM usage. 306s Default: 100000 306s 306s Multiprocessing Arguments: 306s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 306s Size of regions over which to multiprocesses statistic 306s computation. For very deep samples a smaller value is 306s recommmended in order to control memory consumption. 306s Default: 10000 306s --processes PROCESSES 306s Number of processes. Default: 1 306s 306s FAST5 Data Arguments: 306s --corrected-group CORRECTED_GROUP 306s FAST5 group created by resquiggle command. Default: 306s RawGenomeCorrected_000 306s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 306s FAST5 subgroup(s) (under /Analyses/[--basecall- 306s group]/) containing basecalls and created within 306s [--corrected-group] containing re-squiggle results. 306s Default: ['BaseCalled_template'] 306s 306s Miscellaneous Arguments: 306s --quiet, -q Don't print status information. 306s --help, -h Print this help message and exit 306s usage: tombo detect_modifications aggregate_per_read_stats 306s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 306s --statistics-filename STATISTICS_FILENAME 306s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 306s [--minimum-test-reads MINIMUM_TEST_READS] 306s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 306s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 306s [--processes PROCESSES] 306s [--corrected-group CORRECTED_GROUP] 306s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 306s [--quiet] [--help] 306s 306s Required Argument: 306s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 306s Binary file containing per-read statistics from 306s statistical testing. 306s --statistics-filename STATISTICS_FILENAME 306s File to save/load genomic base anchored statistics. 306s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 306s P-value or log likelihood ratio threshold when 306s computing fraction of significant reads at each 306s genomic position. If two values are provided, 306s statistics between these values are not considered. 306s 306s Significance Test Arguments: 306s --minimum-test-reads MINIMUM_TEST_READS 306s Number of reads required at a position to perform 306s significance testing or contribute to model 306s estimation. Default: 1 306s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 306s Dampen fraction modified estimates for low coverage 306s sites. Two parameters are unmodified and modified 306s pseudo read counts. This is equivalent to a beta prior 306s on the fraction estimate. Set to "0 0" to disable 306s dampened fraction estimation. Default: [2, 0] 306s 306s Output Argument: 306s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 306s Number of the most significant sites to store for 306s faster access. If a longer list of most significant 306s sites is required the list must be re-computed from 306s all batches. Very large values can increase RAM usage. 306s Default: 100000 306s 306s Multiprocessing Arguments: 306s --processes PROCESSES 306s Number of processes. Default: 1 306s 306s FAST5 Data Arguments: 306s --corrected-group CORRECTED_GROUP 306s FAST5 group created by resquiggle command. Default: 306s RawGenomeCorrected_000 306s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 306s FAST5 subgroup(s) (under /Analyses/[--basecall- 306s group]/) containing basecalls and created within 306s [--corrected-group] containing re-squiggle results. 306s Default: ['BaseCalled_template'] 306s 306s Miscellaneous Arguments: 306s --quiet, -q Don't print status information. 306s --help, -h Print this help message and exit 306s usage: tombo text_output browser_files 306s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 306s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 306s [--statistics-filename STATISTICS_FILENAME] 306s [--genome-fasta GENOME_FASTA] 306s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 306s [--browser-file-basename BROWSER_FILE_BASENAME] 306s [--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} ...]] 306s [--corrected-group CORRECTED_GROUP] 306s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 306s [--quiet] [--help] 306s 306s Data Arguments: 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s Directories containing fast5 files. 306s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 306s Set of directories containing fast5 files for control 306s reads, containing only canonical nucleotides. 306s --statistics-filename STATISTICS_FILENAME 306s File to save/load genomic base anchored statistics. 306s 306s Statistic Motif Filter Arguments: 306s --genome-fasta GENOME_FASTA 306s FASTA file used to re-squiggle. For faster sequence 306s access. 306s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 306s Ground truth, motif centered, modified base 306s descriptions for output filtering. Format descriptions 306s as: "motif:mod_pos:name". The mod_pos indicates the 306s modified base within the motif (1-based index). 306s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 306s output for identification of E. coli dam and dcm 306s methylation. 306s 306s Output Arguments: 306s --browser-file-basename BROWSER_FILE_BASENAME 306s Basename for output browser files. Two files (plus and 306s minus strand) will be produced for each --file-types 306s supplied. Filenames formatted as "[browser-file- 306s basename].[file- 306s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 306s Default: tombo_results 306s --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} ...] 306s Data types of genome browser files to produce. 306s Produced coverage files are in bedGraph format, while 306s all other file types will be in wiggle format 306s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 306s Default: "coverage" 306s 306s FAST5 Data Arguments: 306s --corrected-group CORRECTED_GROUP 306s FAST5 group created by resquiggle command. Default: 306s RawGenomeCorrected_000 306s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 306s FAST5 subgroup(s) (under /Analyses/[--basecall- 306s group]/) containing basecalls and created within 306s [--corrected-group] containing re-squiggle results. 306s Default: ['BaseCalled_template'] 306s 306s Miscellaneous Arguments: 306s --quiet, -q Don't print status information. 306s --help, -h Print this help message and exit 306s usage: tombo text_output signif_sequence_context 306s --statistics-filename STATISTICS_FILENAME 306s [--genome-fasta GENOME_FASTA] 306s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 306s [--num-regions NUM_REGIONS] 306s [--num-bases NUM_BASES] 306s [--sequences-filename SEQUENCES_FILENAME] 306s [--corrected-group CORRECTED_GROUP] 306s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 306s [--quiet] [--help] 306s 306s Required Argument: 306s --statistics-filename STATISTICS_FILENAME 306s File to save/load genomic base anchored statistics. 306s 306s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 306s --genome-fasta GENOME_FASTA 306s FASTA file used to re-squiggle. For faster sequence 306s access. 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s Directories containing fast5 files. 306s 306s Region Selection Arguments: 306s --num-regions NUM_REGIONS 306s Number of regions to plot. Default: 100 306s --num-bases NUM_BASES 306s Number of bases to plot/output. Default: 15 306s 306s Output Arguments: 306s --sequences-filename SEQUENCES_FILENAME 306s File for sequences from selected regions. Sequences 306s will be stored in FASTA format. Default: 306s tombo_results.significant_regions.fasta. 306s 306s FAST5 Data Arguments: 306s --corrected-group CORRECTED_GROUP 306s FAST5 group created by resquiggle command. Default: 306s RawGenomeCorrected_000 306s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 306s FAST5 subgroup(s) (under /Analyses/[--basecall- 306s group]/) containing basecalls and created within 306s [--corrected-group] containing re-squiggle results. 306s Default: ['BaseCalled_template'] 306s 306s Miscellaneous Arguments: 306s --quiet, -q Don't print status information. 306s --help, -h Print this help message and exit 306s usage: tombo plot max_coverage 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 306s [--plot-standard-model] 306s [--plot-alternate-model {dcm,dam,6mA,CpG,5mC}] 306s [--overplot-threshold OVERPLOT_THRESHOLD] 306s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 306s [--num-regions NUM_REGIONS] 306s [--num-bases NUM_BASES] 306s [--pdf-filename PDF_FILENAME] 306s [--corrected-group CORRECTED_GROUP] 306s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 306s [--quiet] [--help] 306s 306s Required Argument: 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s Directories containing fast5 files. 306s 306s Comparison Arguments: 306s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 306s Set of directories containing fast5 files for control 306s reads, containing only canonical nucleotides. 306s --plot-standard-model 306s Add default standard model distribution to the plot. 306s --plot-alternate-model {dcm,dam,6mA,CpG,5mC} 306s Add alternative model distribution to the plot. 306s 306s Overplotting Arguments: 306s --overplot-threshold OVERPLOT_THRESHOLD 306s Coverage level to trigger alternative plot type 306s instead of raw signal. Default: 50 306s --overplot-type {Downsample,Boxplot,Quantile,Density} 306s Plot type for regions with higher coverage. Default: 306s Downsample 306s 306s Plotting Region Arguments: 306s --num-regions NUM_REGIONS 306s Number of regions to plot. Default: 10 306s --num-bases NUM_BASES 306s Number of bases to plot/output. Default: 21 306s 306s Output Argument: 306s --pdf-filename PDF_FILENAME 306s PDF filename to store plot(s). Default: 306s tombo_results.max_coverage.pdf 306s 306s FAST5 Data Arguments: 306s --corrected-group CORRECTED_GROUP 306s FAST5 group created by resquiggle command. Default: 306s RawGenomeCorrected_000 306s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 306s FAST5 subgroup(s) (under /Analyses/[--basecall- 306s group]/) containing basecalls and created within 306s [--corrected-group] containing re-squiggle results. 306s Default: ['BaseCalled_template'] 306s 306s Miscellaneous Arguments: 306s --quiet, -q Don't print status information. 306s --help, -h Print this help message and exit 306s usage: tombo plot genome_locations 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 306s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 306s [--plot-standard-model] 306s [--plot-alternate-model {dam,5mC,dcm,CpG,6mA}] 306s [--overplot-threshold OVERPLOT_THRESHOLD] 306s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 306s [--num-bases NUM_BASES] 306s [--pdf-filename PDF_FILENAME] 306s [--corrected-group CORRECTED_GROUP] 306s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 306s [--quiet] [--help] 306s 306s Required Arguments: 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s Directories containing fast5 files. 306s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 306s Genomic locations at which to plot signal. Format 306s locations as "chrm:position[:strand] 306s [chrm2:position2[:strand2] ...]" (strand not 306s applicable for all applications) 306s 306s Comparison Arguments: 306s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 306s Set of directories containing fast5 files for control 306s reads, containing only canonical nucleotides. 306s --plot-standard-model 306s Add default standard model distribution to the plot. 306s --plot-alternate-model {dam,5mC,dcm,CpG,6mA} 306s Add alternative model distribution to the plot. 306s 306s Overplotting Arguments: 306s --overplot-threshold OVERPLOT_THRESHOLD 306s Coverage level to trigger alternative plot type 306s instead of raw signal. Default: 50 306s --overplot-type {Downsample,Boxplot,Quantile,Density} 306s Plot type for regions with higher coverage. Default: 306s Downsample 306s 306s Plotting Region Argument: 306s --num-bases NUM_BASES 306s Number of bases to plot/output. Default: 21 306s 306s Output Argument: 306s --pdf-filename PDF_FILENAME 306s PDF filename to store plot(s). Default: 306s tombo_results.genome_locations.pdf 306s 306s FAST5 Data Arguments: 306s --corrected-group CORRECTED_GROUP 306s FAST5 group created by resquiggle command. Default: 306s RawGenomeCorrected_000 306s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 306s FAST5 subgroup(s) (under /Analyses/[--basecall- 306s group]/) containing basecalls and created within 306s [--corrected-group] containing re-squiggle results. 306s Default: ['BaseCalled_template'] 306s 306s Miscellaneous Arguments: 306s --quiet, -q Don't print status information. 306s --help, -h Print this help message and exit 306s usage: tombo plot motif_centered 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s --motif MOTIF --genome-fasta GENOME_FASTA 306s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 306s [--plot-standard-model] 306s [--plot-alternate-model {6mA,dam,CpG,dcm,5mC}] 306s [--overplot-threshold OVERPLOT_THRESHOLD] 306s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 306s [--num-regions NUM_REGIONS] 306s [--num-bases NUM_BASES] [--deepest-coverage] 306s [--pdf-filename PDF_FILENAME] 306s [--corrected-group CORRECTED_GROUP] 306s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 306s [--quiet] [--help] 306s 306s Required Arguments: 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s Directories containing fast5 files. 306s --motif MOTIF Motif of interest at which to plot signal and 306s statsitics. Supports IUPAC single letter codes (use T 306s for RNA). 306s --genome-fasta GENOME_FASTA 306s FASTA file used to re-squiggle. For faster sequence 306s access. 306s 306s Comparison Arguments: 306s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 306s Set of directories containing fast5 files for control 306s reads, containing only canonical nucleotides. 306s --plot-standard-model 306s Add default standard model distribution to the plot. 306s --plot-alternate-model {6mA,dam,CpG,dcm,5mC} 306s Add alternative model distribution to the plot. 306s 306s Overplotting Arguments: 306s --overplot-threshold OVERPLOT_THRESHOLD 306s Coverage level to trigger alternative plot type 306s instead of raw signal. Default: 50 306s --overplot-type {Downsample,Boxplot,Quantile,Density} 306s Plot type for regions with higher coverage. Default: 306s Downsample 306s 306s Plotting Region Arguments: 306s --num-regions NUM_REGIONS 306s Number of regions to plot. Default: 10 306s --num-bases NUM_BASES 306s Number of bases to plot/output. Default: 21 306s --deepest-coverage Plot the deepest coverage regions. 306s 306s Output Argument: 306s --pdf-filename PDF_FILENAME 306s PDF filename to store plot(s). Default: 306s tombo_results.motif_centered.pdf 306s 306s FAST5 Data Arguments: 306s --corrected-group CORRECTED_GROUP 306s FAST5 group created by resquiggle command. Default: 306s RawGenomeCorrected_000 306s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 306s FAST5 subgroup(s) (under /Analyses/[--basecall- 306s group]/) containing basecalls and created within 306s [--corrected-group] containing re-squiggle results. 306s Default: ['BaseCalled_template'] 306s 306s Miscellaneous Arguments: 306s --quiet, -q Don't print status information. 306s --help, -h Print this help message and exit 306s usage: tombo plot max_difference 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 306s [--overplot-threshold OVERPLOT_THRESHOLD] 306s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 306s [--num-regions NUM_REGIONS] 306s [--num-bases NUM_BASES] 306s [--pdf-filename PDF_FILENAME] 306s [--sequences-filename SEQUENCES_FILENAME] 306s [--corrected-group CORRECTED_GROUP] 306s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 306s [--quiet] [--help] 306s 306s Required Arguments: 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s Directories containing fast5 files. 306s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 306s Set of directories containing fast5 files for control 306s reads, containing only canonical nucleotides. 306s 306s Overplotting Arguments: 306s --overplot-threshold OVERPLOT_THRESHOLD 306s Coverage level to trigger alternative plot type 306s instead of raw signal. Default: 50 306s --overplot-type {Downsample,Boxplot,Quantile,Density} 306s Plot type for regions with higher coverage. Default: 306s Downsample 306s 306s Plotting Region Arguments: 306s --num-regions NUM_REGIONS 306s Number of regions to plot. Default: 10 306s --num-bases NUM_BASES 306s Number of bases to plot/output. Default: 21 306s 306s Output Arguments: 306s --pdf-filename PDF_FILENAME 306s PDF filename to store plot(s). Default: 306s tombo_results.max_difference.pdf 306s --sequences-filename SEQUENCES_FILENAME 306s File for sequences from selected regions. Sequences 306s will be stored in FASTA format. Default: None. 306s 306s FAST5 Data Arguments: 306s --corrected-group CORRECTED_GROUP 306s FAST5 group created by resquiggle command. Default: 306s RawGenomeCorrected_000 306s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 306s FAST5 subgroup(s) (under /Analyses/[--basecall- 306s group]/) containing basecalls and created within 306s [--corrected-group] containing re-squiggle results. 306s Default: ['BaseCalled_template'] 306s 306s Miscellaneous Arguments: 306s --quiet, -q Don't print status information. 306s --help, -h Print this help message and exit 306s usage: tombo plot most_significant 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s --statistics-filename STATISTICS_FILENAME 306s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 306s [--plot-standard-model] 306s [--plot-alternate-model {dcm,5mC,CpG,6mA,dam}] 306s [--overplot-threshold OVERPLOT_THRESHOLD] 306s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 306s [--num-regions NUM_REGIONS] 306s [--num-bases NUM_BASES] 306s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 306s [--pdf-filename PDF_FILENAME] 306s [--sequences-filename SEQUENCES_FILENAME] 306s [--corrected-group CORRECTED_GROUP] 306s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 306s [--quiet] [--help] 306s 306s Required Arguments: 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s Directories containing fast5 files. 306s --statistics-filename STATISTICS_FILENAME 306s File to save/load genomic base anchored statistics. 306s 306s Comparison Arguments: 306s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 306s Set of directories containing fast5 files for control 306s reads, containing only canonical nucleotides. 306s --plot-standard-model 306s Add default standard model distribution to the plot. 306s --plot-alternate-model {dcm,5mC,CpG,6mA,dam} 306s Add alternative model distribution to the plot. 306s 306s Overplotting Arguments: 306s --overplot-threshold OVERPLOT_THRESHOLD 306s Coverage level to trigger alternative plot type 306s instead of raw signal. Default: 50 306s --overplot-type {Downsample,Boxplot,Quantile,Density} 306s Plot type for regions with higher coverage. Default: 306s Downsample 306s 306s Plotting Region Arguments: 306s --num-regions NUM_REGIONS 306s Number of regions to plot. Default: 10 306s --num-bases NUM_BASES 306s Number of bases to plot/output. Default: 21 306s 306s Statistical Argument: 306s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 306s Dampen fraction modified estimates for low coverage 306s sites. Two parameters are unmodified and modified 306s pseudo read counts. This is equivalent to a beta prior 306s on the fraction estimate. Set to "0 0" to disable 306s dampened fraction estimation. Default: [2, 0] 306s 306s Output Arguments: 306s --pdf-filename PDF_FILENAME 306s PDF filename to store plot(s). Default: 306s tombo_results.significant_difference.pdf 306s --sequences-filename SEQUENCES_FILENAME 306s File for sequences from selected regions. Sequences 306s will be stored in FASTA format. Default: None. 306s 306s FAST5 Data Arguments: 306s --corrected-group CORRECTED_GROUP 306s FAST5 group created by resquiggle command. Default: 306s RawGenomeCorrected_000 306s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 306s FAST5 subgroup(s) (under /Analyses/[--basecall- 306s group]/) containing basecalls and created within 306s [--corrected-group] containing re-squiggle results. 306s Default: ['BaseCalled_template'] 306s 306s Miscellaneous Arguments: 306s --quiet, -q Don't print status information. 306s --help, -h Print this help message and exit 306s usage: tombo plot motif_with_stats 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s --motif MOTIF 306s --statistics-filename STATISTICS_FILENAME 306s --genome-fasta GENOME_FASTA 306s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 306s [--plot-standard-model] 306s [--plot-alternate-model {5mC,6mA,dam,CpG,dcm}] 306s [--overplot-threshold OVERPLOT_THRESHOLD] 306s [--num-regions NUM_REGIONS] 306s [--num-context NUM_CONTEXT] 306s [--num-statistics NUM_STATISTICS] 306s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 306s [--pdf-filename PDF_FILENAME] 306s [--corrected-group CORRECTED_GROUP] 306s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 306s [--quiet] [--help] 306s 306s Required Arguments: 306s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 306s Directories containing fast5 files. 306s --motif MOTIF Motif of interest at which to plot signal and 306s statsitics. Supports IUPAC single letter codes (use T 306s for RNA). 306s --statistics-filename STATISTICS_FILENAME 306s File to save/load genomic base anchored statistics. 306s --genome-fasta GENOME_FASTA 306s FASTA file used to re-squiggle. For faster sequence 306s access. 306s 306s Comparison Arguments: 306s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 306s Set of directories containing fast5 files for control 306s reads, containing only canonical nucleotides. 306s --plot-standard-model 306s Add default standard model distribution to the plot. 306s --plot-alternate-model {5mC,6mA,dam,CpG,dcm} 306s Add alternative model distribution to the plot. 306s 306s Overplotting Argument: 306s --overplot-threshold OVERPLOT_THRESHOLD 306s Coverage level to trigger alternative plot type 306s instead of raw signal. Default: 50 306s 306s Plotting Region Arguments: 306s --num-regions NUM_REGIONS 306s Number of regions to plot. Default: 3 306s --num-context NUM_CONTEXT 306s Number of context bases around motif. Default: 5 306s --num-statistics NUM_STATISTICS 306s Number of motif centered regions to include in 306s statistic distributions. Default: 200 306s 306s Statistical Argument: 306s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 306s Dampen fraction modified estimates for low coverage 306s sites. Two parameters are unmodified and modified 306s pseudo read counts. This is equivalent to a beta prior 306s on the fraction estimate. Set to "0 0" to disable 306s dampened fraction estimation. Default: [2, 0] 306s 306s Output Argument: 306s --pdf-filename PDF_FILENAME 306s PDF filename to store plot(s). Default: 306s tombo_results.motif_statistics.pdf 306s 306s FAST5 Data Arguments: 306s --corrected-group CORRECTED_GROUP 306s FAST5 group created by resquiggle command. Default: 306s RawGenomeCorrected_000 306s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 306s FAST5 subgroup(s) (under /Analyses/[--basecall- 306s group]/) containing basecalls and created within 306s [--corrected-group] containing re-squiggle results. 306s Default: ['BaseCalled_template'] 306s 306s Miscellaneous Arguments: 306s --quiet, -q Don't print status information. 306s --help, -h Print this help message and exit 307s usage: tombo plot per_read 307s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 307s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 307s [--genome-fasta GENOME_FASTA] 307s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 307s [--num-reads NUM_READS] [--num-bases NUM_BASES] 307s [--box-center] [--pdf-filename PDF_FILENAME] 307s [--corrected-group CORRECTED_GROUP] 307s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 307s [--quiet] [--help] 307s 307s Required Arguments: 307s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 307s Genomic locations at which to plot signal. Format 307s locations as "chrm:position[:strand] 307s [chrm2:position2[:strand2] ...]" (strand not 307s applicable for all applications) 307s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 307s Binary file containing per-read statistics from 307s statistical testing. 307s 307s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 307s --genome-fasta GENOME_FASTA 307s FASTA file used to re-squiggle. For faster sequence 307s access. 307s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 307s Directories containing fast5 files. 307s 307s Plotting Region Arguments: 307s --num-reads NUM_READS 307s Number of reads to plot. Default: 100 307s --num-bases NUM_BASES 307s Number of bases to plot/output. Default: 51 307s --box-center Plot a box around the central base. 307s 307s Output Argument: 307s --pdf-filename PDF_FILENAME 307s PDF filename to store plot(s). Default: 307s tombo_results.per_read_stats.pdf 307s 307s FAST5 Data Arguments: 307s --corrected-group CORRECTED_GROUP 307s FAST5 group created by resquiggle command. Default: 307s RawGenomeCorrected_000 307s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 307s FAST5 subgroup(s) (under /Analyses/[--basecall- 307s group]/) containing basecalls and created within 307s [--corrected-group] containing re-squiggle results. 307s Default: ['BaseCalled_template'] 307s 307s Miscellaneous Arguments: 307s --quiet, -q Don't print status information. 307s --help, -h Print this help message and exit 307s usage: tombo plot roc 307s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 307s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 307s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 307s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 307s [--genome-fasta GENOME_FASTA] 307s [--pdf-filename PDF_FILENAME] 307s [--statistics-per-block STATISTICS_PER_BLOCK] 307s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 307s [--quiet] [--help] 307s 307s Required Argument: 307s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 307s Files to load genomic base anchored statistics. 307s 307s Ground Truth Arguments (provide bed files or motifs): 307s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 307s Modification description and bed format files 307s containing single base locations of ground truth 307s modified sites. Bed files should contain 6 fields 307s including strand. Format descriptions as 307s "mod_name:locs.bed". Example: "CpG 307s bisulfite":bisulfite_locs.bed 307s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 307s Bed format files containing single base locations of 307s ground truth unmodified sites. Bed files should 307s contain 6 fields including strand. 307s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 307s Ground truth, motif centered, modified base 307s descriptions for computing ROC and PR curves. Each 307s statistics file is associated with a set of motif 307s descriptions. Format descriptions as: 307s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 307s mod_pos indicates the alternate-base within the motif 307s (1-based index). Example: CCWGG:2:"dcm 307s 5mC"::GATC:2:"dam 6mA" would assess the performance of 307s a single Tombo statistics file for identification of 307s E. coli dam and dcm methylation. 307s --genome-fasta GENOME_FASTA 307s FASTA file used to re-squiggle. For faster sequence 307s access. 307s 307s Output Arguments: 307s --pdf-filename PDF_FILENAME 307s PDF filename to store plot(s). Default: 307s tombo_results.roc.pdf 307s 307s Down-sampling Arguments: 307s --statistics-per-block STATISTICS_PER_BLOCK 307s Number of randomly selected per-read, per-base 307s statistics to extract from each genomic block for 307s plotting. Default: Include all stats 307s --total-statistics-limit TOTAL_STATISTICS_LIMIT 307s Total per-read statistics to be extracted for 307s plotting. Avoids memory overflow for large runs. 307s Default: 5000000 307s 307s Miscellaneous Arguments: 307s --quiet, -q Don't print status information. 307s --help, -h Print this help message and exit 307s usage: tombo plot per_read_roc 307s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 307s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 307s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 307s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 307s [--genome-fasta GENOME_FASTA] 307s [--statistics-per-block STATISTICS_PER_BLOCK] 307s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 307s [--pdf-filename PDF_FILENAME] [--quiet] 307s [--help] 307s 307s Required Argument: 307s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 307s Binary files containing per-read statistics from 307s statistical testing. 307s 307s Ground Truth Arguments (provide bed files or motifs): 307s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 307s Modification description and bed format files 307s containing single base locations of ground truth 307s modified sites. Bed files should contain 6 fields 307s including strand. Format descriptions as 307s "mod_name:locs.bed". Example: "CpG 307s bisulfite":bisulfite_locs.bed 307s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 307s Bed format files containing single base locations of 307s ground truth unmodified sites. Bed files should 307s contain 6 fields including strand. 307s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 307s Ground truth, motif centered, modified base 307s descriptions for computing ROC and PR curves. Each 307s statistics file is associated with a set of motif 307s descriptions. Format descriptions as: 307s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 307s mod_pos indicates the alternate-base within the motif 307s (1-based index). Example: CCWGG:2:"dcm 307s 5mC"::GATC:2:"dam 6mA" would assess the performance of 307s a single Tombo statistics file for identification of 307s E. coli dam and dcm methylation. 307s --genome-fasta GENOME_FASTA 307s FASTA file used to re-squiggle. For faster sequence 307s access. 307s 307s Down-sampling Arguments: 307s --statistics-per-block STATISTICS_PER_BLOCK 307s Number of randomly selected per-read, per-base 307s statistics to extract from each genomic block for 307s plotting. Default: 100000 307s --total-statistics-limit TOTAL_STATISTICS_LIMIT 307s Total per-read statistics to be extracted for 307s plotting. Avoids memory overflow for large runs. 307s Default: 5000000 307s 307s Output Arguments: 307s --pdf-filename PDF_FILENAME 307s PDF filename to store plot(s). Default: 307s tombo_results.per_reads_roc.pdf 307s 307s Miscellaneous Arguments: 307s --quiet, -q Don't print status information. 307s --help, -h Print this help message and exit 307s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 307s [--upstream-bases {0,1,2,3,4}] 307s [--downstream-bases {0,1,2,3,4}] [--read-mean] 307s [--num-kmer-threshold NUM_KMER_THRESHOLD] 307s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 307s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 307s [--corrected-group CORRECTED_GROUP] 307s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 307s [--quiet] [--help] 307s 307s Required Argument: 307s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 307s Directories containing fast5 files. 307s 307s Data Processing Arguments: 307s --upstream-bases {0,1,2,3,4} 307s Upstream bases in k-mer. Default: 1 307s --downstream-bases {0,1,2,3,4} 307s Downstream bases in k-mer. Default: 2 307s --read-mean Plot k-mer means across whole reads as opposed to 307s individual k-mer event levels. 307s --num-kmer-threshold NUM_KMER_THRESHOLD 307s Observations of each k-mer required to include a read 307s in read level averages. Default: 1 307s 307s Plotting Region Arguments: 307s --num-reads NUM_READS 307s Number of reads to plot. Default: 100 307s 307s Output Arguments: 307s --pdf-filename PDF_FILENAME 307s PDF filename to store plot(s). Default: 307s tombo_results.kmer_distribution.pdf 307s --r-data-filename R_DATA_FILENAME 307s Filename to save R data structure. Default: Don't save 307s --dont-plot Don't plot result. Useful to produce only R data file. 307s 307s FAST5 Data Arguments: 307s --corrected-group CORRECTED_GROUP 307s FAST5 group created by resquiggle command. Default: 307s RawGenomeCorrected_000 307s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 307s FAST5 subgroup(s) (under /Analyses/[--basecall- 307s group]/) containing basecalls and created within 307s [--corrected-group] containing re-squiggle results. 307s Default: ['BaseCalled_template'] 307s 307s Miscellaneous Arguments: 307s --quiet, -q Don't print status information. 307s --help, -h Print this help message and exit 307s usage: tombo plot cluster_most_significant 307s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 307s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 307s --statistics-filename STATISTICS_FILENAME 307s [--genome-fasta GENOME_FASTA] 307s [--processes PROCESSES] 307s [--num-regions NUM_REGIONS] 307s [--num-bases NUM_BASES] 307s [--slide-span SLIDE_SPAN] 307s [--pdf-filename PDF_FILENAME] 307s [--r-data-filename R_DATA_FILENAME] 307s [--corrected-group CORRECTED_GROUP] 307s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 307s [--quiet] [--help] 307s 307s Required Arguments: 307s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 307s Directories containing fast5 files. 307s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 307s Set of directories containing fast5 files for control 307s reads, containing only canonical nucleotides. 307s --statistics-filename STATISTICS_FILENAME 307s File to save/load genomic base anchored statistics. 307s 307s FASTA Sequence Argument: 307s --genome-fasta GENOME_FASTA 307s FASTA file used to re-squiggle. For faster sequence 307s access. 307s 307s Multiprocessing Argument: 307s --processes PROCESSES 307s Number of processes. Default: 1 307s 307s Plotting Region Arguments: 307s --num-regions NUM_REGIONS 307s Number of regions to plot. Default: 10 307s --num-bases NUM_BASES 307s Number of bases to plot/output. Default: 21 307s --slide-span SLIDE_SPAN 307s Number of bases offset over which to search when 307s computing distances for signal cluster plotting. 307s Default: 0 (exact position) 307s 307s Output Arguments: 307s --pdf-filename PDF_FILENAME 307s PDF filename to store plot(s). Default: 307s tombo_results.signal_clusters.pdf 307s --r-data-filename R_DATA_FILENAME 307s Filename to save R data structure. Default: Don't save 307s 307s FAST5 Data Arguments: 307s --corrected-group CORRECTED_GROUP 307s FAST5 group created by resquiggle command. Default: 307s RawGenomeCorrected_000 307s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 307s FAST5 subgroup(s) (under /Analyses/[--basecall- 307s group]/) containing basecalls and created within 307s [--corrected-group] containing re-squiggle results. 307s Default: ['BaseCalled_template'] 307s 307s Miscellaneous Arguments: 307s --quiet, -q Don't print status information. 307s --help, -h Print this help message and exit 307s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 307s 307s Required Arguments: 307s fast5s_basedir Directory containing fast5 files. All files ending in 307s "fast5" found recursively within this base directory will be 307s processed. 307s 307s Miscellaneous Arguments: 307s --quiet, -q Don't print status information. 307s --help, -h Print this help message and exit 307s usage: tombo build_model event_resquiggle 307s [--minimap2-executable MINIMAP2_EXECUTABLE] 307s [--minimap2-index MINIMAP2_INDEX] 307s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 307s [--graphmap-executable GRAPHMAP_EXECUTABLE] 307s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 307s [--normalization-type {median,pA,pA_raw,none}] 307s [--pore-model-filename PORE_MODEL_FILENAME] 307s [--outlier-threshold OUTLIER_THRESHOLD] 307s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 307s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 307s [--timeout TIMEOUT] 307s [--cpts-limit CPTS_LIMIT] 307s [--skip-index] [--overwrite] 307s [--failed-reads-filename FAILED_READS_FILENAME] 307s [--include-event-stdev] 307s [--corrected-group CORRECTED_GROUP] 307s [--basecall-group BASECALL_GROUP] 307s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 307s [--processes PROCESSES] 307s [--align-processes ALIGN_PROCESSES] 307s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 307s [--resquiggle-processes RESQUIGGLE_PROCESSES] 307s [--quiet] [--help] 307s fast5s_basedir reference_fasta 307s 307s Required Arguments: 307s fast5s_basedir Directory containing fast5 files. All files ending in 307s "fast5" found recursively within this base directory 307s will be processed. 307s reference_fasta Reference genome/transcriptome FASTA file for mapping. 307s 307s Mapper Arguments (One mapper is required): 307s --minimap2-executable MINIMAP2_EXECUTABLE 307s Path to minimap2 executable. 307s --minimap2-index MINIMAP2_INDEX 307s Path to minimap2 index (with map-ont preset) file 307s corresponding to the [genome_fasta] provided. 307s --bwa-mem-executable BWA_MEM_EXECUTABLE 307s Path to bwa-mem executable. 307s --graphmap-executable GRAPHMAP_EXECUTABLE 307s Path to graphmap executable. 307s --alignment-batch-size ALIGNMENT_BATCH_SIZE 307s Number of reads included in each alignment call. Note: 307s A new system mapping call is made for each batch 307s (including loading of the genome), so it is advised to 307s use larger values for larger genomes. Default: 1000 307s 307s Signal Processing Arguments: 307s --normalization-type {median,pA,pA_raw,none} 307s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 307s as in the ONT events (using offset, range and 307s digitization), "pA": k-mer-based correction for pA 307s drift as in nanopolish (requires [--pore-model- 307s filename]), "median": median and MAD from raw signal. 307s Default: median 307s --pore-model-filename PORE_MODEL_FILENAME 307s File containing kmer model parameters (level_mean and 307s level_stdv) used in order to compute kmer-based 307s corrected pA values. E.g. https://github.com/jts/nanop 307s olish/blob/master/etc/r9- 307s models/template_median68pA.5mers.model 307s --outlier-threshold OUTLIER_THRESHOLD 307s Windosrize the signal at this number of scale values. 307s Negative value disables outlier clipping. Default: 307s 5.000000 307s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 307s Specify the 2 parameters for segmentation 1) running 307s neighboring windows width 2) minimum raw observations 307s per genomic base. Sample type defaults: RNA : 12 6 || 307s DNA : 5 3 307s 307s Read Filtering Arguments: 307s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 307s Filter reads based on observations per base percentile 307s thresholds. Format thresholds as "percentile:thresh 307s [pctl2:thresh2 ...]". For example to filter reads with 307s 99th pctl > 200 obs/base or max > 5k obs/base use 307s "99:200 100:5000". 307s --timeout TIMEOUT Timeout in seconds for processing a single read. 307s Default: No timeout. 307s --cpts-limit CPTS_LIMIT 307s Maximum number of changepoints to find within a single 307s indel group. Default: No limit. 307s 307s Input/Output Arguments: 307s --skip-index Skip creation of tombo index. This drastically slows 307s downstream tombo commands. Default stores tombo index 307s named ".[--fast5-basedir].[--corrected- 307s group].tombo.index" to be loaded automatically for 307s downstream commands. 307s --overwrite Overwrite previous corrected group in FAST5 files. 307s Note: only effects --corrected-group or --new- 307s corrected-group. 307s --failed-reads-filename FAILED_READS_FILENAME 307s Output failed read filenames with assoicated error. 307s Default: Do not store failed reads. 307s --include-event-stdev 307s Include corrected event standard deviation in output 307s FAST5 data. 307s 307s FAST5 Data Arguments: 307s --corrected-group CORRECTED_GROUP 307s FAST5 group created by resquiggle command. Default: 307s RawGenomeCorrected_000 307s --basecall-group BASECALL_GROUP 307s FAST5 group obtain original basecalls (under Analyses 307s group). Default: Basecall_1D_000 307s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 307s FAST5 subgroup(s) (under /Analyses/[--basecall- 307s group]/) containing basecalls and created within 307s [--corrected-group] containing re-squiggle results. 307s Default: ['BaseCalled_template'] 307s 307s Multiprocessing Arguments: 307s --processes PROCESSES 307s Number of processes. Default: 2 307s --align-processes ALIGN_PROCESSES 307s Number of processes to use for parsing and aligning 307s original basecalls. Each process will independently 307s load the genome into memory, so use caution with 307s larger genomes (e.g. human). Default: 1 307s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 307s Number of threads to use for aligner system call. 307s Default: [--processes] / (2 * [--align-processes)] 307s --resquiggle-processes RESQUIGGLE_PROCESSES 307s Number of processes to use for resquiggle algorithm. 307s Default: [--processes] / 2 307s 307s Miscellaneous Arguments: 307s --quiet, -q Don't print status information. 307s --help, -h Print this help message and exit 307s usage: tombo build_model estimate_reference 307s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 307s --tombo-model-filename TOMBO_MODEL_FILENAME 307s [--estimate-mean] 307s [--kmer-specific-sd] 307s [--upstream-bases {0,1,2,3,4}] 307s [--downstream-bases {0,1,2,3,4}] 307s [--minimum-test-reads MINIMUM_TEST_READS] 307s [--coverage-threshold COVERAGE_THRESHOLD] 307s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 307s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 307s [--processes PROCESSES] 307s [--corrected-group CORRECTED_GROUP] 307s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 307s [--quiet] [--help] 307s 307s Required Arguments: 307s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 307s Directories containing fast5 files. 307s --tombo-model-filename TOMBO_MODEL_FILENAME 307s Filename to save Tombo model. 307s 307s Modeling Arguments: 307s --estimate-mean Use the mean instead of median for model level 307s estimation. Note: This can cause poor fits due to 307s outliers 307s --kmer-specific-sd Estimate standard deviation for each k-mers 307s individually. 307s --upstream-bases {0,1,2,3,4} 307s Upstream bases in k-mer. Default: 1 307s --downstream-bases {0,1,2,3,4} 307s Downstream bases in k-mer. Default: 2 307s 307s Filtering Arguments: 307s --minimum-test-reads MINIMUM_TEST_READS 307s Number of reads required at a position to perform 307s significance testing or contribute to model 307s estimation. Default: 10 307s --coverage-threshold COVERAGE_THRESHOLD 307s Maximum mean coverage per region when estimating k-mer 307s model (limits compute time for deep samples). Default: 307s 100 307s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 307s Number of each k-mer observations required in order to 307s produce a reference (genomic locations for standard 307s reference and per-read for alternative reference). 307s Default: 5 307s 307s Multiprocessing Arguments: 307s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 307s Size of regions over which to multiprocesses statistic 307s computation. For very deep samples a smaller value is 307s recommmended in order to control memory consumption. 307s Default: 10000 307s --processes PROCESSES 307s Number of processes. Default: 1 307s 307s FAST5 Data Arguments: 307s --corrected-group CORRECTED_GROUP 307s FAST5 group created by resquiggle command. Default: 307s RawGenomeCorrected_000 307s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 307s FAST5 subgroup(s) (under /Analyses/[--basecall- 307s group]/) containing basecalls and created within 307s [--corrected-group] containing re-squiggle results. 307s Default: ['BaseCalled_template'] 307s 307s Miscellaneous Arguments: 307s --quiet, -q Don't print status information. 307s --help, -h Print this help message and exit 307s usage: tombo build_model estimate_alt_reference 307s --alternate-model-filename ALTERNATE_MODEL_FILENAME 307s --alternate-model-name ALTERNATE_MODEL_NAME 307s --alternate-model-base {A,C,G,T} 307s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 307s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 307s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 307s [--control-density-filename CONTROL_DENSITY_FILENAME] 307s [--dna] [--rna] 307s [--tombo-model-filename TOMBO_MODEL_FILENAME] 307s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 307s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 307s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 307s [--save-density-basename SAVE_DENSITY_BASENAME] 307s [--processes PROCESSES] 307s [--corrected-group CORRECTED_GROUP] 307s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 307s [--quiet] [--help] 307s 307s Required Arguments: 307s --alternate-model-filename ALTERNATE_MODEL_FILENAME 307s Tombo model for alternative likelihood ratio 307s significance testing. 307s --alternate-model-name ALTERNATE_MODEL_NAME 307s A short name to associate with this alternate model 307s (e.g. 5mC, 6mA, etc.). This text will be included in 307s output filenames when this model is used for testing. 307s --alternate-model-base {A,C,G,T} 307s Non-standard base is an alternative to this base. 307s 307s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 307s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 307s Directories containing fast5 files. 307s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 307s Set of directories containing fast5 files for control 307s reads, containing only canonical nucleotides. 307s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 307s File containing k-mer level kernel density estimates 307s for the alternative sample saved using --save-density- 307s basename. 307s --control-density-filename CONTROL_DENSITY_FILENAME 307s File containing k-mer level kernel density estimates 307s for the control sample saved using --save-density- 307s basename. 307s 307s Standard Model Arguments: 307s --dna Explicitly select canonical DNA model. Default: 307s Automatically determine from FAST5s 307s --rna Explicitly select canonical RNA model. Default: 307s Automatically determine from FAST5s 307s --tombo-model-filename TOMBO_MODEL_FILENAME 307s Tombo model filename. If no file is provided, the 307s default DNA or RNA Tombo model will be used. 307s 307s Model Fitting Arguments: 307s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 307s When esitmating the alternative base incorporation 307s rate, this percent of k-mers are assumed to have 307s significantly shifted signal so the alternative 307s distribution minimally overlaps the standard base 307s distribution. Default: 5.000000 307s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 307s Bandwidth applied when performing Gaussian kernal 307s density esitmation on standard and alternative base 307s signal distributions. Default: 0.050000 307s 307s Filtering Argument: 307s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 307s Number of each k-mer observations required in order to 307s produce a reference (genomic locations for standard 307s reference and per-read for alternative reference). 307s Default: 1000 307s 307s Output Argument: 307s --save-density-basename SAVE_DENSITY_BASENAME 307s Basename to save alternative model estimation density 307s estimation information. See scripts/debug_est_alt.R 307s for info use example. Default: Don't save. 307s 307s Multiprocessing Arguments: 307s --processes PROCESSES 307s Number of processes. Default: 1 307s 307s FAST5 Data Arguments: 307s --corrected-group CORRECTED_GROUP 307s FAST5 group created by resquiggle command. Default: 307s RawGenomeCorrected_000 307s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 307s FAST5 subgroup(s) (under /Analyses/[--basecall- 307s group]/) containing basecalls and created within 307s [--corrected-group] containing re-squiggle results. 307s Default: ['BaseCalled_template'] 307s 307s Miscellaneous Arguments: 307s --quiet, -q Don't print status information. 307s --help, -h Print this help message and exit 307s This test only tests the help system 307s There is an extensive test in 307s 307s tombo/tests/shell_tests.sh 307s 307s but this requires to download larger data 307s sets which is not done for the moment. 308s autopkgtest [18:10:30]: test run-unit-test: -----------------------] 313s run-unit-test PASS 313s autopkgtest [18:10:35]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 317s autopkgtest [18:10:39]: @@@@@@@@@@@@@@@@@@@@ summary 317s run-unit-test PASS