0s autopkgtest [12:47:56]: starting date and time: 2025-02-19 12:47:56+0000 0s autopkgtest [12:47:56]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [12:47:56]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.c32e9enf/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sphinx --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@lcy02-8.secgroup --name adt-plucky-amd64-tombo-20250219-124756-juju-7f2275-prod-proposed-migration-environment-20-981f2ce4-eb51-455c-8fdf-57b078bf9d21 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 47s autopkgtest [12:48:43]: testbed dpkg architecture: amd64 47s autopkgtest [12:48:43]: testbed apt version: 2.9.29 47s autopkgtest [12:48:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 47s autopkgtest [12:48:43]: testbed release detected to be: None 48s autopkgtest [12:48:44]: updating testbed package index (apt update) 48s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 48s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 48s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 48s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 48s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 48s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 48s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 48s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 48s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [101 kB] 48s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [81.8 kB] 48s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 48s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 48s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [697 kB] 48s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [265 kB] 48s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [11.5 kB] 48s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3128 B] 48s Fetched 2124 kB in 0s (5769 kB/s) 49s Reading package lists... 49s Reading package lists... 49s Building dependency tree... 49s Reading state information... 50s Calculating upgrade... 50s The following NEW packages will be installed: 50s libapt-pkg7.0 50s The following packages will be upgraded: 50s apt apt-utils iproute2 liblsof0 libp11-kit0 lsof rsyslog 50s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 50s Need to get 5234 kB of archives. 50s After this operation, 4074 kB of additional disk space will be used. 50s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.30 [1131 kB] 50s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.30 [1434 kB] 50s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.30 [222 kB] 50s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 51s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libp11-kit0 amd64 0.25.5-2ubuntu3 [311 kB] 51s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu1 [555 kB] 51s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 lsof amd64 4.99.4+dfsg-1 [245 kB] 51s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsof0 amd64 4.99.4+dfsg-1 [59.6 kB] 51s Preconfiguring packages ... 51s Fetched 5234 kB in 1s (8912 kB/s) 51s Selecting previously unselected package libapt-pkg7.0:amd64. 51s (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 ... 108925 files and directories currently installed.) 51s Preparing to unpack .../libapt-pkg7.0_2.9.30_amd64.deb ... 51s Unpacking libapt-pkg7.0:amd64 (2.9.30) ... 51s Setting up libapt-pkg7.0:amd64 (2.9.30) ... 51s (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 ... 108974 files and directories currently installed.) 51s Preparing to unpack .../archives/apt_2.9.30_amd64.deb ... 51s Unpacking apt (2.9.30) over (2.9.29) ... 52s Setting up apt (2.9.30) ... 52s (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 ... 108974 files and directories currently installed.) 52s Preparing to unpack .../0-apt-utils_2.9.30_amd64.deb ... 52s Unpacking apt-utils (2.9.30) over (2.9.29) ... 52s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_amd64.deb ... 52s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 53s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_amd64.deb ... 53s Unpacking libp11-kit0:amd64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 53s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_amd64.deb ... 53s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 53s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_amd64.deb ... 53s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 53s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_amd64.deb ... 53s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 53s Setting up apt-utils (2.9.30) ... 53s Setting up liblsof0 (4.99.4+dfsg-1) ... 53s Setting up iproute2 (6.13.0-1ubuntu1) ... 53s Setting up rsyslog (8.2412.0-2ubuntu1) ... 53s info: The user `syslog' is already a member of `adm'. 54s Setting up libp11-kit0:amd64 (0.25.5-2ubuntu3) ... 54s Setting up lsof (4.99.4+dfsg-1) ... 54s Processing triggers for man-db (2.13.0-1) ... 56s Processing triggers for libc-bin (2.40-4ubuntu1) ... 57s Reading package lists... 57s Building dependency tree... 57s Reading state information... 57s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s autopkgtest [12:48:53]: upgrading testbed (apt dist-upgrade and autopurge) 57s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 58s Starting 2 pkgProblemResolver with broken count: 0 58s Done 59s Entering ResolveByKeep 59s 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Starting pkgProblemResolver with broken count: 0 60s Starting 2 pkgProblemResolver with broken count: 0 60s Done 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s autopkgtest [12:48:56]: rebooting testbed after setup commands that affected boot 81s autopkgtest [12:49:17]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 81s autopkgtest [12:49:17]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 83s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (dsc) [2291 B] 83s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (tar) [22.3 MB] 83s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (diff) [9600 B] 84s gpgv: Signature made Wed Jan 29 22:42:44 2025 UTC 84s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 84s gpgv: Can't check signature: No public key 84s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7build1.dsc: no acceptable signature found 84s autopkgtest [12:49:20]: testing package tombo version 1.5.1-7build1 84s autopkgtest [12:49:20]: build not needed 85s autopkgtest [12:49:21]: test run-unit-test: preparing testbed 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s Starting pkgProblemResolver with broken count: 0 85s Starting 2 pkgProblemResolver with broken count: 0 85s Done 86s The following NEW packages will be installed: 86s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 86s libhdf5-310 libhdf5-hl-310 libjs-jquery libjs-mathjax libjs-sphinxdoc 86s libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 python3-decorator 86s python3-h5py python3-h5py-serial python3-mappy python3-numpy 86s python3-packaging python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 86s tombo-doc 86s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 86s Need to get 70.6 MB of archives. 86s After this operation, 277 MB of additional disk space will be used. 86s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-lato all 2.015-1 [2781 kB] 86s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 86s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 86s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 86s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 86s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250213-1ubuntu1 [920 kB] 86s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 86s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-310 amd64 1.14.5+repack-3 [1519 kB] 86s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [62.6 kB] 86s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 86s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 86s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 86s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 86s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 86s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 86s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 86s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [5319 kB] 86s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.12.1-1 [1677 kB] 86s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.12.1-1 [7970 B] 86s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mappy amd64 2.27+dfsg-1build1 [203 kB] 86s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 86s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tqdm all 4.67.1-2 [92.5 kB] 86s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 86s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu1 [22.3 MB] 86s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 tombo amd64 1.5.1-7build1 [531 kB] 86s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 87s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 tombo-doc all 1.5.1-7build1 [21.7 MB] 87s Fetched 70.6 MB in 1s (96.0 MB/s) 87s Selecting previously unselected package fonts-lato. 87s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108975 files and directories currently installed.) 87s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 87s Unpacking fonts-lato (2.015-1) ... 87s Selecting previously unselected package fonts-font-awesome. 88s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 88s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 88s Selecting previously unselected package fonts-mathjax. 88s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 88s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 88s Selecting previously unselected package libaec0:amd64. 88s Preparing to unpack .../03-libaec0_1.1.3-1_amd64.deb ... 88s Unpacking libaec0:amd64 (1.1.3-1) ... 88s Selecting previously unselected package libblas3:amd64. 88s Preparing to unpack .../04-libblas3_3.12.1-2_amd64.deb ... 88s Unpacking libblas3:amd64 (3.12.1-2) ... 88s Selecting previously unselected package libgfortran5:amd64. 88s Preparing to unpack .../05-libgfortran5_15-20250213-1ubuntu1_amd64.deb ... 88s Unpacking libgfortran5:amd64 (15-20250213-1ubuntu1) ... 88s Selecting previously unselected package libsz2:amd64. 88s Preparing to unpack .../06-libsz2_1.1.3-1_amd64.deb ... 88s Unpacking libsz2:amd64 (1.1.3-1) ... 88s Selecting previously unselected package libhdf5-310:amd64. 88s Preparing to unpack .../07-libhdf5-310_1.14.5+repack-3_amd64.deb ... 88s Unpacking libhdf5-310:amd64 (1.14.5+repack-3) ... 88s Selecting previously unselected package libhdf5-hl-310:amd64. 88s Preparing to unpack .../08-libhdf5-hl-310_1.14.5+repack-3_amd64.deb ... 88s Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 88s Selecting previously unselected package libjs-jquery. 88s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 88s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 88s Selecting previously unselected package libjs-underscore. 88s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 88s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 88s Selecting previously unselected package libjs-sphinxdoc. 88s Preparing to unpack .../11-libjs-sphinxdoc_8.1.3-5_all.deb ... 88s Unpacking libjs-sphinxdoc (8.1.3-5) ... 88s Selecting previously unselected package liblapack3:amd64. 88s Preparing to unpack .../12-liblapack3_3.12.1-2_amd64.deb ... 88s Unpacking liblapack3:amd64 (3.12.1-2) ... 88s Selecting previously unselected package liblbfgsb0:amd64. 88s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 88s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 88s Selecting previously unselected package liblzf1:amd64. 88s Preparing to unpack .../14-liblzf1_3.6-4_amd64.deb ... 88s Unpacking liblzf1:amd64 (3.6-4) ... 88s Selecting previously unselected package python3-decorator. 88s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 88s Unpacking python3-decorator (5.1.1-5) ... 88s Selecting previously unselected package python3-numpy. 88s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-13_amd64.deb ... 88s Unpacking python3-numpy (1:1.26.4+ds-13) ... 88s Selecting previously unselected package python3-h5py-serial. 88s Preparing to unpack .../17-python3-h5py-serial_3.12.1-1_amd64.deb ... 88s Unpacking python3-h5py-serial (3.12.1-1) ... 89s Selecting previously unselected package python3-h5py. 89s Preparing to unpack .../18-python3-h5py_3.12.1-1_all.deb ... 89s Unpacking python3-h5py (3.12.1-1) ... 89s Selecting previously unselected package python3-mappy. 89s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1build1_amd64.deb ... 89s Unpacking python3-mappy (2.27+dfsg-1build1) ... 89s Selecting previously unselected package python3-packaging. 89s Preparing to unpack .../20-python3-packaging_24.2-1_all.deb ... 89s Unpacking python3-packaging (24.2-1) ... 89s Selecting previously unselected package python3-tqdm. 89s Preparing to unpack .../21-python3-tqdm_4.67.1-2_all.deb ... 89s Unpacking python3-tqdm (4.67.1-2) ... 89s Selecting previously unselected package sphinx-rtd-theme-common. 89s Preparing to unpack .../22-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 89s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 89s Selecting previously unselected package python3-scipy. 89s Preparing to unpack .../23-python3-scipy_1.14.1-4ubuntu1_amd64.deb ... 89s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 89s Selecting previously unselected package tombo. 89s Preparing to unpack .../24-tombo_1.5.1-7build1_amd64.deb ... 89s Unpacking tombo (1.5.1-7build1) ... 89s Selecting previously unselected package libjs-mathjax. 89s Preparing to unpack .../25-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 89s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 90s Selecting previously unselected package tombo-doc. 90s Preparing to unpack .../26-tombo-doc_1.5.1-7build1_all.deb ... 90s Unpacking tombo-doc (1.5.1-7build1) ... 90s Setting up fonts-lato (2.015-1) ... 90s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 90s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 90s Setting up python3-tqdm (4.67.1-2) ... 91s Setting up python3-mappy (2.27+dfsg-1build1) ... 91s Setting up libaec0:amd64 (1.1.3-1) ... 91s Setting up python3-decorator (5.1.1-5) ... 91s Setting up libblas3:amd64 (3.12.1-2) ... 91s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 91s Setting up python3-packaging (24.2-1) ... 91s Setting up liblzf1:amd64 (3.6-4) ... 91s Setting up libgfortran5:amd64 (15-20250213-1ubuntu1) ... 91s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 91s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 91s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 91s Setting up libsz2:amd64 (1.1.3-1) ... 91s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 91s Setting up liblapack3:amd64 (3.12.1-2) ... 91s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 91s Setting up python3-numpy (1:1.26.4+ds-13) ... 92s Setting up libjs-sphinxdoc (8.1.3-5) ... 92s Setting up tombo-doc (1.5.1-7build1) ... 92s Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... 92s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 92s Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 92s Setting up python3-scipy (1.14.1-4ubuntu1) ... 95s Setting up python3-h5py-serial (3.12.1-1) ... 95s Setting up python3-h5py (3.12.1-1) ... 96s Setting up tombo (1.5.1-7build1) ... 96s Processing triggers for man-db (2.13.0-1) ... 96s Processing triggers for libc-bin (2.40-4ubuntu1) ... 97s autopkgtest [12:49:33]: test run-unit-test: [----------------------- 97s ********* Testing help commands ********** 97s usage: tombo [-h] [-v] 97s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} ... 97s 97s ********** Tombo ********* 97s 97s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 97s 97s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 97s 97s Tombo command groups (additional help available within each command group): 97s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 97s preprocess Pre-process nanopore reads for Tombo processing. 97s filter Apply filter to Tombo index file for specified criterion. 97s detect_modifications Perform statistical testing to detect non-standard nucleotides. 97s text_output Output Tombo results in text files. 97s build_model Create canonical and alternative base Tombo models. 97s plot Save plots to visualize raw nanopore signal or testing results. 97s 97s options: 97s -h, --help show this help message and exit 97s -v, --version show Tombo version and exit. 97s usage: tombo resquiggle [--dna] [--rna] 97s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 97s [--q-score Q_SCORE] 97s [--signal-matching-score SIGNAL_MATCHING_SCORE] 97s [--processes PROCESSES] 97s [--corrected-group CORRECTED_GROUP] 97s [--basecall-group BASECALL_GROUP] 97s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 97s [--overwrite] 97s [--failed-reads-filename FAILED_READS_FILENAME] 97s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 97s [--print-advanced-arguments] [--quiet] [--help] 97s fast5s_basedir reference 97s 97s Required Arguments: 97s fast5s_basedir Directory containing fast5 files. All files ending in 97s "fast5" found recursively within this base directory 97s will be processed. 97s reference Reference genome/transcriptome FASTA file or minimap2 97s index (with "map-ont" preset) for mapping. 97s 97s Model Parameters: 97s --dna Explicitly select canonical DNA model. Default: 97s Automatically determine from FAST5s 97s --rna Explicitly select canonical RNA model. Default: 97s Automatically determine from FAST5s 97s 97s Read Filtering Argument: 97s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 97s Filter reads based on observations per base percentile 97s thresholds. Format thresholds as "percentile:thresh 97s [pctl2:thresh2 ...]". For example to filter reads with 97s 99th pctl > 200 obs/base or max > 5k obs/base use 97s "99:200 100:5000". 97s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 97s Default: 0.000000 97s --signal-matching-score SIGNAL_MATCHING_SCORE 97s Observed to expected signal matching score (higher 97s score indicates poor matching). Sample type defaults: 97s RNA : 2 || DNA : 1.1 97s 97s Multiprocessing Arguments: 97s --processes PROCESSES 97s Number of processes. Default: 1 97s 97s FAST5 Data Arguments: 97s --corrected-group CORRECTED_GROUP 97s FAST5 group created by resquiggle command. Default: 97s RawGenomeCorrected_000 97s --basecall-group BASECALL_GROUP 97s FAST5 group obtain original basecalls (under Analyses 97s group). Default: Basecall_1D_000 97s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 97s FAST5 subgroup(s) (under /Analyses/[--basecall- 97s group]/) containing basecalls and created within 97s [--corrected-group] containing re-squiggle results. 97s Default: ['BaseCalled_template'] 97s --overwrite Overwrite previous corrected group in FAST5 files. 97s Note: only effects --corrected-group or --new- 97s corrected-group. 97s 97s Input/Output Arguments: 97s --failed-reads-filename FAILED_READS_FILENAME 97s Output failed read filenames with assoicated error. 97s Default: Do not store failed reads. 97s --num-most-common-errors NUM_MOST_COMMON_ERRORS 97s Dynamically show this many most common errors so far 97s through run. Default: 0; Just show progress 97s 97s Advanced Arguments: 97s --print-advanced-arguments 97s Print advanced re-squiggle arguments and exit. 97s 97s Miscellaneous Arguments: 97s --quiet, -q Don't print status information. 97s --help, -h Print this help message and exit 97s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 97s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 97s [--basecall-group BASECALL_GROUP] 97s [--basecall-subgroup BASECALL_SUBGROUP] 97s [--overwrite] 97s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 97s [--processes PROCESSES] 97s [--quiet] [--help] 97s 97s Required Arguments: 97s --fast5-basedir FAST5_BASEDIR 97s Directory containing fast5 files. 97s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 97s FASTQ filenames containing basecalls to be added to 97s raw FAST5 files. 97s 97s FAST5 Data Arguments: 97s --basecall-group BASECALL_GROUP 97s FAST5 group obtain original basecalls (under Analyses 97s group). Default: Basecall_1D_000 97s --basecall-subgroup BASECALL_SUBGROUP 97s FAST5 subgroup (under /Analyses/[--basecall-group]/) 97s under which to store basecalls from FASTQs. Default: 97s BaseCalled_template 97s --overwrite Overwrite previous corrected group in FAST5 files. 97s Note: only effects --corrected-group or --new- 97s corrected-group. 97s 97s Sequencing Summary Argument: 97s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 97s Sequencing summary filenames produced by albacore. 97s These can make annotation of raw FAST5 files with 97s FASTQ sequence much faster. 97s 97s Multiprocessing Argument: 97s --processes PROCESSES 97s Number of processes. Default: 1 97s 97s Miscellaneous Arguments: 97s --quiet, -q Don't print status information. 97s --help, -h Print this help message and exit 98s usage: tombo filter clear_filters 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s [--corrected-group CORRECTED_GROUP] 98s [--quiet] [--help] 98s 98s Required Argument: 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s Directories containing fast5 files. 98s 98s FAST5 Data Argument: 98s --corrected-group CORRECTED_GROUP 98s FAST5 group created by resquiggle command. Default: 98s RawGenomeCorrected_000 98s 98s Miscellaneous Arguments: 98s --quiet, -q Don't print status information. 98s --help, -h Print this help message and exit 98s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 98s [--corrected-group CORRECTED_GROUP] [--quiet] 98s [--help] 98s 98s Required Argument: 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s Directories containing fast5 files. 98s 98s Read Filtering Argument: 98s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 98s Filter reads based on observations per base percentile 98s thresholds. Format thresholds as "percentile:thresh 98s [pctl2:thresh2 ...]". For example to filter reads with 98s 99th pctl > 200 obs/base or max > 5k obs/base use 98s "99:200 100:5000". 98s 98s FAST5 Data Argument: 98s --corrected-group CORRECTED_GROUP 98s FAST5 group created by resquiggle command. Default: 98s RawGenomeCorrected_000 98s 98s Miscellaneous Arguments: 98s --quiet, -q Don't print status information. 98s --help, -h Print this help message and exit 98s usage: tombo filter level_coverage 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s [--percent-to-filter PERCENT_TO_FILTER] 98s [--corrected-group CORRECTED_GROUP] 98s [--quiet] [--help] 98s 98s Required Arguments: 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s Directories containing fast5 files. 98s 98s Read Filtering Argument: 98s --percent-to-filter PERCENT_TO_FILTER 98s Percentage of all reads to filter. Reads are randomly 98s selected weighted according to the approximate 98s coverage at the mapped genomic location. This can be 98s useful in modeling and testing. Default: 10.000000 98s 98s FAST5 Data Arguments: 98s --corrected-group CORRECTED_GROUP 98s FAST5 group created by resquiggle command. Default: 98s RawGenomeCorrected_000 98s 98s Miscellaneous Arguments: 98s --quiet, -q Don't print status information. 98s --help, -h Print this help message and exit 98s usage: tombo filter q_score 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s [--q-score Q_SCORE] 98s [--corrected-group CORRECTED_GROUP] 98s [--basecall-group BASECALL_GROUP] [--quiet] 98s [--help] 98s 98s Required Arguments: 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s Directories containing fast5 files. 98s 98s Read Filtering Argument: 98s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 98s Default: 7.000000 98s 98s FAST5 Data Arguments: 98s --corrected-group CORRECTED_GROUP 98s FAST5 group created by resquiggle command. Default: 98s RawGenomeCorrected_000 98s --basecall-group BASECALL_GROUP 98s FAST5 group obtain original basecalls (under Analyses 98s group). Default: Basecall_1D_000 98s 98s Miscellaneous Arguments: 98s --quiet, -q Don't print status information. 98s --help, -h Print this help message and exit 98s usage: tombo filter raw_signal_matching 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s --signal-matching-score SIGNAL_MATCHING_SCORE 98s [--corrected-group CORRECTED_GROUP] 98s [--quiet] [--help] 98s 98s Required Arguments: 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s Directories containing fast5 files. 98s --signal-matching-score SIGNAL_MATCHING_SCORE 98s Observed to expected signal matching score (higher 98s score indicates poor matching). Sample type defaults: 98s RNA : 2 || DNA : 1.1 98s 98s FAST5 Data Arguments: 98s --corrected-group CORRECTED_GROUP 98s FAST5 group created by resquiggle command. Default: 98s RawGenomeCorrected_000 98s 98s Miscellaneous Arguments: 98s --quiet, -q Don't print status information. 98s --help, -h Print this help message and exit 98s usage: tombo filter genome_locations 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 98s [--include-partial-overlap] 98s [--corrected-group CORRECTED_GROUP] 98s [--quiet] [--help] 98s 98s Required Arguments: 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s Directories containing fast5 files. 98s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 98s Filter out reads not falling completely within include 98s regions. Omit start and end coordinates to include an 98s entire chromosome/sequence record. Format regions as 98s "chrm[:start-end] [chrm2[:start2-end2] ...]". 98s 98s Filter Argument: 98s --include-partial-overlap 98s Include reads that partially overlap the specified 98s region. Default: Only include reads completely 98s contained in a specified region 98s 98s FAST5 Data Argument: 98s --corrected-group CORRECTED_GROUP 98s FAST5 group created by resquiggle command. Default: 98s RawGenomeCorrected_000 98s 98s Miscellaneous Arguments: 98s --quiet, -q Don't print status information. 98s --help, -h Print this help message and exit 98s usage: tombo detect_modifications de_novo 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s --statistics-file-basename STATISTICS_FILE_BASENAME 98s [--dna] [--rna] 98s [--fishers-method-context FISHERS_METHOD_CONTEXT] 98s [--minimum-test-reads MINIMUM_TEST_READS] 98s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 98s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 98s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 98s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 98s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 98s [--processes PROCESSES] 98s [--corrected-group CORRECTED_GROUP] 98s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 98s [--quiet] [--help] 98s 98s Required Argument: 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s Directories containing fast5 files. 98s --statistics-file-basename STATISTICS_FILE_BASENAME 98s File base name to save base by base statistics from 98s testing. Filenames will be [--statistics-file- 98s basename].[--alternate-bases]?.tombo.stats 98s 98s Comparison Model Arguments: 98s --dna Explicitly select canonical DNA model. Default: 98s Automatically determine from FAST5s 98s --rna Explicitly select canonical RNA model. Default: 98s Automatically determine from FAST5s 98s 98s Significance Test Arguments: 98s --fishers-method-context FISHERS_METHOD_CONTEXT 98s Number of context bases up and downstream over which 98s to compute Fisher's method combined p-values. Note: 98s Not applicable for alternative model likelihood ratio 98s tests. Default: 1. 98s --minimum-test-reads MINIMUM_TEST_READS 98s Number of reads required at a position to perform 98s significance testing or contribute to model 98s estimation. Default: 1 98s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 98s P-value threshold when computing fraction of 98s significant reads at each genomic position. If two 98s values are provided, statistics between these values 98s are not considered. Default thresholds: DNA:0.15-0.5 , 98s RNA:0.05-0.4 98s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 98s Dampen fraction modified estimates for low coverage 98s sites. Two parameters are unmodified and modified 98s pseudo read counts. This is equivalent to a beta prior 98s on the fraction estimate. Set to "0 0" to disable 98s dampened fraction estimation. Default: [2, 0] 98s 98s Output Argument: 98s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 98s Base for binary files containing per-read statistics 98s from statistical testing. Filenames will be [--per- 98s read-statistics-basename].[--alternate- 98s bases]?.tombo.per_read_stats 98s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 98s Number of the most significant sites to store for 98s faster access. If a longer list of most significant 98s sites is required the list must be re-computed from 98s all batches. Very large values can increase RAM usage. 98s Default: 100000 98s 98s Multiprocessing Arguments: 98s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 98s Size of regions over which to multiprocesses statistic 98s computation. For very deep samples a smaller value is 98s recommmended in order to control memory consumption. 98s Default: 10000 98s --processes PROCESSES 98s Number of processes. Default: 1 98s 98s FAST5 Data Arguments: 98s --corrected-group CORRECTED_GROUP 98s FAST5 group created by resquiggle command. Default: 98s RawGenomeCorrected_000 98s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 98s FAST5 subgroup(s) (under /Analyses/[--basecall- 98s group]/) containing basecalls and created within 98s [--corrected-group] containing re-squiggle results. 98s Default: ['BaseCalled_template'] 98s 98s Miscellaneous Arguments: 98s --quiet, -q Don't print status information. 98s --help, -h Print this help message and exit 98s usage: tombo detect_modifications alternative_model 98s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 98s [--statistics-file-basename STATISTICS_FILE_BASENAME] 98s [--alternate-bases {CpG,dcm,dam,6mA,5mC} [{CpG,dcm,dam,6mA,5mC} ...]] 98s [--print-available-models] 98s [--dna] [--rna] 98s [--minimum-test-reads MINIMUM_TEST_READS] 98s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 98s [--standard-log-likelihood-ratio] 98s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 98s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 98s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 98s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 98s [--processes PROCESSES] 98s [--corrected-group CORRECTED_GROUP] 98s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 98s [--quiet] [--help] 98s 98s Required Argument: 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s Directories containing fast5 files. 98s --statistics-file-basename STATISTICS_FILE_BASENAME 98s File base name to save base by base statistics from 98s testing. Filenames will be [--statistics-file- 98s basename].[--alternate-bases]?.tombo.stats 98s --alternate-bases {CpG,dcm,dam,6mA,5mC} [{CpG,dcm,dam,6mA,5mC} ...] 98s Default non-standard base model for testing (not 98s required if user created --alternate-model-filenames 98s is provided). 98s 98s Comparison Arguments: 98s --print-available-models 98s Print available alternative models and exit. 98s --dna Explicitly select canonical DNA model. Default: 98s Automatically determine from FAST5s 98s --rna Explicitly select canonical RNA model. Default: 98s Automatically determine from FAST5s 98s 98s Significance Test Arguments: 98s --minimum-test-reads MINIMUM_TEST_READS 98s Number of reads required at a position to perform 98s significance testing or contribute to model 98s estimation. Default: 1 98s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 98s Log likelihood ratio threshold when computing fraction 98s of significant reads at each genomic position. If two 98s values are provided, statistics between these values 98s are not considered. Default thresholds: DNA:-1.5-2.5 , 98s RNA:-2.5-2.5 98s --standard-log-likelihood-ratio 98s Use a standard log likelihood ratio (LLR) statistic. 98s Default is to use an outlier-robust LLR-like 98s statistic. Detail in full online documentation. 98s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 98s Dampen fraction modified estimates for low coverage 98s sites. Two parameters are unmodified and modified 98s pseudo read counts. This is equivalent to a beta prior 98s on the fraction estimate. Set to "0 0" to disable 98s dampened fraction estimation. Default: [2, 0] 98s 98s Output Argument: 98s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 98s Base for binary files containing per-read statistics 98s from statistical testing. Filenames will be [--per- 98s read-statistics-basename].[--alternate- 98s bases]?.tombo.per_read_stats 98s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 98s Number of the most significant sites to store for 98s faster access. If a longer list of most significant 98s sites is required the list must be re-computed from 98s all batches. Very large values can increase RAM usage. 98s Default: 100000 98s 98s Multiprocessing Arguments: 98s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 98s Size of regions over which to multiprocesses statistic 98s computation. For very deep samples a smaller value is 98s recommmended in order to control memory consumption. 98s Default: 10000 98s --processes PROCESSES 98s Number of processes. Default: 1 98s 98s FAST5 Data Arguments: 98s --corrected-group CORRECTED_GROUP 98s FAST5 group created by resquiggle command. Default: 98s RawGenomeCorrected_000 98s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 98s FAST5 subgroup(s) (under /Analyses/[--basecall- 98s group]/) containing basecalls and created within 98s [--corrected-group] containing re-squiggle results. 98s Default: ['BaseCalled_template'] 98s 98s Miscellaneous Arguments: 98s --quiet, -q Don't print status information. 98s --help, -h Print this help message and exit 98s usage: tombo detect_modifications model_sample_compare 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s --statistics-file-basename STATISTICS_FILE_BASENAME 98s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 98s [--sample-only-estimates] 98s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 98s [--dna] [--rna] 98s [--fishers-method-context FISHERS_METHOD_CONTEXT] 98s [--minimum-test-reads MINIMUM_TEST_READS] 98s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 98s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 98s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 98s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 98s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 98s [--processes PROCESSES] 98s [--corrected-group CORRECTED_GROUP] 98s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 98s [--quiet] [--help] 98s 98s Required Argument: 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s Directories containing fast5 files. 98s --statistics-file-basename STATISTICS_FILE_BASENAME 98s File base name to save base by base statistics from 98s testing. Filenames will be [--statistics-file- 98s basename].[--alternate-bases]?.tombo.stats 98s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 98s Set of directories containing fast5 files for control 98s reads, containing only canonical nucleotides. 98s 98s Model Prior Arguments: 98s --sample-only-estimates 98s Only use canonical sample to estimate expected signal 98s level and spread. Default: Use canonical model to 98s improve estimtates (esp. for low coverage regions) 98s using baysian posterior estimates. 98s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 98s Prior weights (one each for mean and spread) applied 98s to canonical base model for estimating posterior model 98s parameters for sample comparison. Default: [5, 40] 98s --dna Explicitly select canonical DNA model. Default: 98s Automatically determine from FAST5s 98s --rna Explicitly select canonical RNA model. Default: 98s Automatically determine from FAST5s 98s 98s Significance Test Arguments: 98s --fishers-method-context FISHERS_METHOD_CONTEXT 98s Number of context bases up and downstream over which 98s to compute Fisher's method combined p-values. Note: 98s Not applicable for alternative model likelihood ratio 98s tests. Default: 1. 98s --minimum-test-reads MINIMUM_TEST_READS 98s Number of reads required at a position to perform 98s significance testing or contribute to model 98s estimation. Default: 1 98s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 98s P-value threshold when computing fraction of 98s significant reads at each genomic position. If two 98s values are provided, statistics between these values 98s are not considered. Default thresholds: DNA:0.15-0.5 , 98s RNA:0.05-0.4 98s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 98s Dampen fraction modified estimates for low coverage 98s sites. Two parameters are unmodified and modified 98s pseudo read counts. This is equivalent to a beta prior 98s on the fraction estimate. Set to "0 0" to disable 98s dampened fraction estimation. Default: [2, 0] 98s 98s Output Argument: 98s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 98s Base for binary files containing per-read statistics 98s from statistical testing. Filenames will be [--per- 98s read-statistics-basename].[--alternate- 98s bases]?.tombo.per_read_stats 98s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 98s Number of the most significant sites to store for 98s faster access. If a longer list of most significant 98s sites is required the list must be re-computed from 98s all batches. Very large values can increase RAM usage. 98s Default: 100000 98s 98s Multiprocessing Arguments: 98s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 98s Size of regions over which to multiprocesses statistic 98s computation. For very deep samples a smaller value is 98s recommmended in order to control memory consumption. 98s Default: 10000 98s --processes PROCESSES 98s Number of processes. Default: 1 98s 98s FAST5 Data Arguments: 98s --corrected-group CORRECTED_GROUP 98s FAST5 group created by resquiggle command. Default: 98s RawGenomeCorrected_000 98s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 98s FAST5 subgroup(s) (under /Analyses/[--basecall- 98s group]/) containing basecalls and created within 98s [--corrected-group] containing re-squiggle results. 98s Default: ['BaseCalled_template'] 98s 98s Miscellaneous Arguments: 98s --quiet, -q Don't print status information. 98s --help, -h Print this help message and exit 98s usage: tombo detect_modifications level_sample_compare 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s --statistics-file-basename STATISTICS_FILE_BASENAME 98s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 98s [--fishers-method-context FISHERS_METHOD_CONTEXT] 98s [--minimum-test-reads MINIMUM_TEST_READS] 98s [--statistic-type {ks,u,t}] 98s [--store-p-value] 98s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 98s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 98s [--processes PROCESSES] 98s [--corrected-group CORRECTED_GROUP] 98s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 98s [--quiet] [--help] 98s 98s Required Argument: 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s Directories containing fast5 files. 98s --statistics-file-basename STATISTICS_FILE_BASENAME 98s File base name to save base by base statistics from 98s testing. Filenames will be [--statistics-file- 98s basename].[--alternate-bases]?.tombo.stats 98s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 98s Set of directories containing fast5 files for 98s alternate set of reads. 98s 98s Significance Test Arguments: 98s --fishers-method-context FISHERS_METHOD_CONTEXT 98s Number of context bases up and downstream over which 98s to compute Fisher's method combined p-values. Note: 98s Not applicable for alternative model likelihood ratio 98s tests. Default: 1. 98s --minimum-test-reads MINIMUM_TEST_READS 98s Number of reads required at a position to perform 98s significance testing or contribute to model 98s estimation. Default: 50 98s --statistic-type {ks,u,t} 98s Type of statistical test to apply. Default: "ks" 98s --store-p-value Store p-value instead of effect-size statistic. 98s Statistics are D-statistic (KS-test), deviation from 98s even common language effect size (u-test), and Cohen's 98s D (t-test). 98s 98s Output Argument: 98s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 98s Number of the most significant sites to store for 98s faster access. If a longer list of most significant 98s sites is required the list must be re-computed from 98s all batches. Very large values can increase RAM usage. 98s Default: 100000 98s 98s Multiprocessing Arguments: 98s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 98s Size of regions over which to multiprocesses statistic 98s computation. For very deep samples a smaller value is 98s recommmended in order to control memory consumption. 98s Default: 10000 98s --processes PROCESSES 98s Number of processes. Default: 1 98s 98s FAST5 Data Arguments: 98s --corrected-group CORRECTED_GROUP 98s FAST5 group created by resquiggle command. Default: 98s RawGenomeCorrected_000 98s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 98s FAST5 subgroup(s) (under /Analyses/[--basecall- 98s group]/) containing basecalls and created within 98s [--corrected-group] containing re-squiggle results. 98s Default: ['BaseCalled_template'] 98s 98s Miscellaneous Arguments: 98s --quiet, -q Don't print status information. 98s --help, -h Print this help message and exit 98s usage: tombo detect_modifications aggregate_per_read_stats 98s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 98s --statistics-filename STATISTICS_FILENAME 98s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 98s [--minimum-test-reads MINIMUM_TEST_READS] 98s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 98s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 98s [--processes PROCESSES] 98s [--corrected-group CORRECTED_GROUP] 98s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 98s [--quiet] [--help] 98s 98s Required Argument: 98s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 98s Binary file containing per-read statistics from 98s statistical testing. 98s --statistics-filename STATISTICS_FILENAME 98s File to save/load genomic base anchored statistics. 98s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 98s P-value or log likelihood ratio threshold when 98s computing fraction of significant reads at each 98s genomic position. If two values are provided, 98s statistics between these values are not considered. 98s 98s Significance Test Arguments: 98s --minimum-test-reads MINIMUM_TEST_READS 98s Number of reads required at a position to perform 98s significance testing or contribute to model 98s estimation. Default: 1 98s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 98s Dampen fraction modified estimates for low coverage 98s sites. Two parameters are unmodified and modified 98s pseudo read counts. This is equivalent to a beta prior 98s on the fraction estimate. Set to "0 0" to disable 98s dampened fraction estimation. Default: [2, 0] 98s 98s Output Argument: 98s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 98s Number of the most significant sites to store for 98s faster access. If a longer list of most significant 98s sites is required the list must be re-computed from 98s all batches. Very large values can increase RAM usage. 98s Default: 100000 98s 98s Multiprocessing Arguments: 98s --processes PROCESSES 98s Number of processes. Default: 1 98s 98s FAST5 Data Arguments: 98s --corrected-group CORRECTED_GROUP 98s FAST5 group created by resquiggle command. Default: 98s RawGenomeCorrected_000 98s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 98s FAST5 subgroup(s) (under /Analyses/[--basecall- 98s group]/) containing basecalls and created within 98s [--corrected-group] containing re-squiggle results. 98s Default: ['BaseCalled_template'] 98s 98s Miscellaneous Arguments: 98s --quiet, -q Don't print status information. 98s --help, -h Print this help message and exit 98s usage: tombo text_output browser_files 98s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 98s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 98s [--statistics-filename STATISTICS_FILENAME] 98s [--genome-fasta GENOME_FASTA] 98s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 98s [--browser-file-basename BROWSER_FILE_BASENAME] 98s [--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} ...]] 98s [--corrected-group CORRECTED_GROUP] 98s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 98s [--quiet] [--help] 98s 98s Data Arguments: 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s Directories containing fast5 files. 98s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 98s Set of directories containing fast5 files for control 98s reads, containing only canonical nucleotides. 98s --statistics-filename STATISTICS_FILENAME 98s File to save/load genomic base anchored statistics. 98s 98s Statistic Motif Filter Arguments: 98s --genome-fasta GENOME_FASTA 98s FASTA file used to re-squiggle. For faster sequence 98s access. 98s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 98s Ground truth, motif centered, modified base 98s descriptions for output filtering. Format descriptions 98s as: "motif:mod_pos:name". The mod_pos indicates the 98s modified base within the motif (1-based index). 98s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 98s output for identification of E. coli dam and dcm 98s methylation. 98s 98s Output Arguments: 98s --browser-file-basename BROWSER_FILE_BASENAME 98s Basename for output browser files. Two files (plus and 98s minus strand) will be produced for each --file-types 98s supplied. Filenames formatted as "[browser-file- 98s basename].[file- 98s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 98s Default: tombo_results 98s --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} ...] 98s Data types of genome browser files to produce. 98s Produced coverage files are in bedGraph format, while 98s all other file types will be in wiggle format 98s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 98s Default: "coverage" 98s 98s FAST5 Data Arguments: 98s --corrected-group CORRECTED_GROUP 98s FAST5 group created by resquiggle command. Default: 98s RawGenomeCorrected_000 98s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 98s FAST5 subgroup(s) (under /Analyses/[--basecall- 98s group]/) containing basecalls and created within 98s [--corrected-group] containing re-squiggle results. 98s Default: ['BaseCalled_template'] 98s 98s Miscellaneous Arguments: 98s --quiet, -q Don't print status information. 98s --help, -h Print this help message and exit 98s usage: tombo text_output signif_sequence_context 98s --statistics-filename STATISTICS_FILENAME 98s [--genome-fasta GENOME_FASTA] 98s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 98s [--num-regions NUM_REGIONS] 98s [--num-bases NUM_BASES] 98s [--sequences-filename SEQUENCES_FILENAME] 98s [--corrected-group CORRECTED_GROUP] 98s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 98s [--quiet] [--help] 98s 98s Required Argument: 98s --statistics-filename STATISTICS_FILENAME 98s File to save/load genomic base anchored statistics. 98s 98s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 98s --genome-fasta GENOME_FASTA 98s FASTA file used to re-squiggle. For faster sequence 98s access. 98s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 98s Directories containing fast5 files. 98s 98s Region Selection Arguments: 98s --num-regions NUM_REGIONS 98s Number of regions to plot. Default: 100 98s --num-bases NUM_BASES 98s Number of bases to plot/output. Default: 15 98s 98s Output Arguments: 98s --sequences-filename SEQUENCES_FILENAME 98s File for sequences from selected regions. Sequences 98s will be stored in FASTA format. Default: 98s tombo_results.significant_regions.fasta. 98s 98s FAST5 Data Arguments: 98s --corrected-group CORRECTED_GROUP 98s FAST5 group created by resquiggle command. Default: 98s RawGenomeCorrected_000 98s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 98s FAST5 subgroup(s) (under /Analyses/[--basecall- 98s group]/) containing basecalls and created within 98s [--corrected-group] containing re-squiggle results. 98s Default: ['BaseCalled_template'] 98s 98s Miscellaneous Arguments: 98s --quiet, -q Don't print status information. 98s --help, -h Print this help message and exit 99s usage: tombo plot max_coverage 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 99s [--plot-standard-model] 99s [--plot-alternate-model {dcm,6mA,5mC,CpG,dam}] 99s [--overplot-threshold OVERPLOT_THRESHOLD] 99s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 99s [--num-regions NUM_REGIONS] 99s [--num-bases NUM_BASES] 99s [--pdf-filename PDF_FILENAME] 99s [--corrected-group CORRECTED_GROUP] 99s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 99s [--quiet] [--help] 99s 99s Required Argument: 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s Directories containing fast5 files. 99s 99s Comparison Arguments: 99s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 99s Set of directories containing fast5 files for control 99s reads, containing only canonical nucleotides. 99s --plot-standard-model 99s Add default standard model distribution to the plot. 99s --plot-alternate-model {dcm,6mA,5mC,CpG,dam} 99s Add alternative model distribution to the plot. 99s 99s Overplotting Arguments: 99s --overplot-threshold OVERPLOT_THRESHOLD 99s Coverage level to trigger alternative plot type 99s instead of raw signal. Default: 50 99s --overplot-type {Downsample,Boxplot,Quantile,Density} 99s Plot type for regions with higher coverage. Default: 99s Downsample 99s 99s Plotting Region Arguments: 99s --num-regions NUM_REGIONS 99s Number of regions to plot. Default: 10 99s --num-bases NUM_BASES 99s Number of bases to plot/output. Default: 21 99s 99s Output Argument: 99s --pdf-filename PDF_FILENAME 99s PDF filename to store plot(s). Default: 99s tombo_results.max_coverage.pdf 99s 99s FAST5 Data Arguments: 99s --corrected-group CORRECTED_GROUP 99s FAST5 group created by resquiggle command. Default: 99s RawGenomeCorrected_000 99s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 99s FAST5 subgroup(s) (under /Analyses/[--basecall- 99s group]/) containing basecalls and created within 99s [--corrected-group] containing re-squiggle results. 99s Default: ['BaseCalled_template'] 99s 99s Miscellaneous Arguments: 99s --quiet, -q Don't print status information. 99s --help, -h Print this help message and exit 99s usage: tombo plot genome_locations 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 99s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 99s [--plot-standard-model] 99s [--plot-alternate-model {6mA,5mC,dcm,CpG,dam}] 99s [--overplot-threshold OVERPLOT_THRESHOLD] 99s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 99s [--num-bases NUM_BASES] 99s [--pdf-filename PDF_FILENAME] 99s [--corrected-group CORRECTED_GROUP] 99s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 99s [--quiet] [--help] 99s 99s Required Arguments: 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s Directories containing fast5 files. 99s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 99s Genomic locations at which to plot signal. Format 99s locations as "chrm:position[:strand] 99s [chrm2:position2[:strand2] ...]" (strand not 99s applicable for all applications) 99s 99s Comparison Arguments: 99s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 99s Set of directories containing fast5 files for control 99s reads, containing only canonical nucleotides. 99s --plot-standard-model 99s Add default standard model distribution to the plot. 99s --plot-alternate-model {6mA,5mC,dcm,CpG,dam} 99s Add alternative model distribution to the plot. 99s 99s Overplotting Arguments: 99s --overplot-threshold OVERPLOT_THRESHOLD 99s Coverage level to trigger alternative plot type 99s instead of raw signal. Default: 50 99s --overplot-type {Downsample,Boxplot,Quantile,Density} 99s Plot type for regions with higher coverage. Default: 99s Downsample 99s 99s Plotting Region Argument: 99s --num-bases NUM_BASES 99s Number of bases to plot/output. Default: 21 99s 99s Output Argument: 99s --pdf-filename PDF_FILENAME 99s PDF filename to store plot(s). Default: 99s tombo_results.genome_locations.pdf 99s 99s FAST5 Data Arguments: 99s --corrected-group CORRECTED_GROUP 99s FAST5 group created by resquiggle command. Default: 99s RawGenomeCorrected_000 99s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 99s FAST5 subgroup(s) (under /Analyses/[--basecall- 99s group]/) containing basecalls and created within 99s [--corrected-group] containing re-squiggle results. 99s Default: ['BaseCalled_template'] 99s 99s Miscellaneous Arguments: 99s --quiet, -q Don't print status information. 99s --help, -h Print this help message and exit 99s usage: tombo plot motif_centered 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s --motif MOTIF --genome-fasta GENOME_FASTA 99s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 99s [--plot-standard-model] 99s [--plot-alternate-model {CpG,dcm,5mC,6mA,dam}] 99s [--overplot-threshold OVERPLOT_THRESHOLD] 99s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 99s [--num-regions NUM_REGIONS] 99s [--num-bases NUM_BASES] [--deepest-coverage] 99s [--pdf-filename PDF_FILENAME] 99s [--corrected-group CORRECTED_GROUP] 99s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 99s [--quiet] [--help] 99s 99s Required Arguments: 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s Directories containing fast5 files. 99s --motif MOTIF Motif of interest at which to plot signal and 99s statsitics. Supports IUPAC single letter codes (use T 99s for RNA). 99s --genome-fasta GENOME_FASTA 99s FASTA file used to re-squiggle. For faster sequence 99s access. 99s 99s Comparison Arguments: 99s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 99s Set of directories containing fast5 files for control 99s reads, containing only canonical nucleotides. 99s --plot-standard-model 99s Add default standard model distribution to the plot. 99s --plot-alternate-model {CpG,dcm,5mC,6mA,dam} 99s Add alternative model distribution to the plot. 99s 99s Overplotting Arguments: 99s --overplot-threshold OVERPLOT_THRESHOLD 99s Coverage level to trigger alternative plot type 99s instead of raw signal. Default: 50 99s --overplot-type {Downsample,Boxplot,Quantile,Density} 99s Plot type for regions with higher coverage. Default: 99s Downsample 99s 99s Plotting Region Arguments: 99s --num-regions NUM_REGIONS 99s Number of regions to plot. Default: 10 99s --num-bases NUM_BASES 99s Number of bases to plot/output. Default: 21 99s --deepest-coverage Plot the deepest coverage regions. 99s 99s Output Argument: 99s --pdf-filename PDF_FILENAME 99s PDF filename to store plot(s). Default: 99s tombo_results.motif_centered.pdf 99s 99s FAST5 Data Arguments: 99s --corrected-group CORRECTED_GROUP 99s FAST5 group created by resquiggle command. Default: 99s RawGenomeCorrected_000 99s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 99s FAST5 subgroup(s) (under /Analyses/[--basecall- 99s group]/) containing basecalls and created within 99s [--corrected-group] containing re-squiggle results. 99s Default: ['BaseCalled_template'] 99s 99s Miscellaneous Arguments: 99s --quiet, -q Don't print status information. 99s --help, -h Print this help message and exit 99s usage: tombo plot max_difference 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 99s [--overplot-threshold OVERPLOT_THRESHOLD] 99s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 99s [--num-regions NUM_REGIONS] 99s [--num-bases NUM_BASES] 99s [--pdf-filename PDF_FILENAME] 99s [--sequences-filename SEQUENCES_FILENAME] 99s [--corrected-group CORRECTED_GROUP] 99s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 99s [--quiet] [--help] 99s 99s Required Arguments: 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s Directories containing fast5 files. 99s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 99s Set of directories containing fast5 files for control 99s reads, containing only canonical nucleotides. 99s 99s Overplotting Arguments: 99s --overplot-threshold OVERPLOT_THRESHOLD 99s Coverage level to trigger alternative plot type 99s instead of raw signal. Default: 50 99s --overplot-type {Downsample,Boxplot,Quantile,Density} 99s Plot type for regions with higher coverage. Default: 99s Downsample 99s 99s Plotting Region Arguments: 99s --num-regions NUM_REGIONS 99s Number of regions to plot. Default: 10 99s --num-bases NUM_BASES 99s Number of bases to plot/output. Default: 21 99s 99s Output Arguments: 99s --pdf-filename PDF_FILENAME 99s PDF filename to store plot(s). Default: 99s tombo_results.max_difference.pdf 99s --sequences-filename SEQUENCES_FILENAME 99s File for sequences from selected regions. Sequences 99s will be stored in FASTA format. Default: None. 99s 99s FAST5 Data Arguments: 99s --corrected-group CORRECTED_GROUP 99s FAST5 group created by resquiggle command. Default: 99s RawGenomeCorrected_000 99s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 99s FAST5 subgroup(s) (under /Analyses/[--basecall- 99s group]/) containing basecalls and created within 99s [--corrected-group] containing re-squiggle results. 99s Default: ['BaseCalled_template'] 99s 99s Miscellaneous Arguments: 99s --quiet, -q Don't print status information. 99s --help, -h Print this help message and exit 99s usage: tombo plot most_significant 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s --statistics-filename STATISTICS_FILENAME 99s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 99s [--plot-standard-model] 99s [--plot-alternate-model {5mC,dcm,dam,CpG,6mA}] 99s [--overplot-threshold OVERPLOT_THRESHOLD] 99s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 99s [--num-regions NUM_REGIONS] 99s [--num-bases NUM_BASES] 99s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 99s [--pdf-filename PDF_FILENAME] 99s [--sequences-filename SEQUENCES_FILENAME] 99s [--corrected-group CORRECTED_GROUP] 99s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 99s [--quiet] [--help] 99s 99s Required Arguments: 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s Directories containing fast5 files. 99s --statistics-filename STATISTICS_FILENAME 99s File to save/load genomic base anchored statistics. 99s 99s Comparison Arguments: 99s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 99s Set of directories containing fast5 files for control 99s reads, containing only canonical nucleotides. 99s --plot-standard-model 99s Add default standard model distribution to the plot. 99s --plot-alternate-model {5mC,dcm,dam,CpG,6mA} 99s Add alternative model distribution to the plot. 99s 99s Overplotting Arguments: 99s --overplot-threshold OVERPLOT_THRESHOLD 99s Coverage level to trigger alternative plot type 99s instead of raw signal. Default: 50 99s --overplot-type {Downsample,Boxplot,Quantile,Density} 99s Plot type for regions with higher coverage. Default: 99s Downsample 99s 99s Plotting Region Arguments: 99s --num-regions NUM_REGIONS 99s Number of regions to plot. Default: 10 99s --num-bases NUM_BASES 99s Number of bases to plot/output. Default: 21 99s 99s Statistical Argument: 99s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 99s Dampen fraction modified estimates for low coverage 99s sites. Two parameters are unmodified and modified 99s pseudo read counts. This is equivalent to a beta prior 99s on the fraction estimate. Set to "0 0" to disable 99s dampened fraction estimation. Default: [2, 0] 99s 99s Output Arguments: 99s --pdf-filename PDF_FILENAME 99s PDF filename to store plot(s). Default: 99s tombo_results.significant_difference.pdf 99s --sequences-filename SEQUENCES_FILENAME 99s File for sequences from selected regions. Sequences 99s will be stored in FASTA format. Default: None. 99s 99s FAST5 Data Arguments: 99s --corrected-group CORRECTED_GROUP 99s FAST5 group created by resquiggle command. Default: 99s RawGenomeCorrected_000 99s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 99s FAST5 subgroup(s) (under /Analyses/[--basecall- 99s group]/) containing basecalls and created within 99s [--corrected-group] containing re-squiggle results. 99s Default: ['BaseCalled_template'] 99s 99s Miscellaneous Arguments: 99s --quiet, -q Don't print status information. 99s --help, -h Print this help message and exit 99s usage: tombo plot motif_with_stats 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s --motif MOTIF 99s --statistics-filename STATISTICS_FILENAME 99s --genome-fasta GENOME_FASTA 99s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 99s [--plot-standard-model] 99s [--plot-alternate-model {5mC,6mA,CpG,dam,dcm}] 99s [--overplot-threshold OVERPLOT_THRESHOLD] 99s [--num-regions NUM_REGIONS] 99s [--num-context NUM_CONTEXT] 99s [--num-statistics NUM_STATISTICS] 99s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 99s [--pdf-filename PDF_FILENAME] 99s [--corrected-group CORRECTED_GROUP] 99s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 99s [--quiet] [--help] 99s 99s Required Arguments: 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s Directories containing fast5 files. 99s --motif MOTIF Motif of interest at which to plot signal and 99s statsitics. Supports IUPAC single letter codes (use T 99s for RNA). 99s --statistics-filename STATISTICS_FILENAME 99s File to save/load genomic base anchored statistics. 99s --genome-fasta GENOME_FASTA 99s FASTA file used to re-squiggle. For faster sequence 99s access. 99s 99s Comparison Arguments: 99s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 99s Set of directories containing fast5 files for control 99s reads, containing only canonical nucleotides. 99s --plot-standard-model 99s Add default standard model distribution to the plot. 99s --plot-alternate-model {5mC,6mA,CpG,dam,dcm} 99s Add alternative model distribution to the plot. 99s 99s Overplotting Argument: 99s --overplot-threshold OVERPLOT_THRESHOLD 99s Coverage level to trigger alternative plot type 99s instead of raw signal. Default: 50 99s 99s Plotting Region Arguments: 99s --num-regions NUM_REGIONS 99s Number of regions to plot. Default: 3 99s --num-context NUM_CONTEXT 99s Number of context bases around motif. Default: 5 99s --num-statistics NUM_STATISTICS 99s Number of motif centered regions to include in 99s statistic distributions. Default: 200 99s 99s Statistical Argument: 99s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 99s Dampen fraction modified estimates for low coverage 99s sites. Two parameters are unmodified and modified 99s pseudo read counts. This is equivalent to a beta prior 99s on the fraction estimate. Set to "0 0" to disable 99s dampened fraction estimation. Default: [2, 0] 99s 99s Output Argument: 99s --pdf-filename PDF_FILENAME 99s PDF filename to store plot(s). Default: 99s tombo_results.motif_statistics.pdf 99s 99s FAST5 Data Arguments: 99s --corrected-group CORRECTED_GROUP 99s FAST5 group created by resquiggle command. Default: 99s RawGenomeCorrected_000 99s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 99s FAST5 subgroup(s) (under /Analyses/[--basecall- 99s group]/) containing basecalls and created within 99s [--corrected-group] containing re-squiggle results. 99s Default: ['BaseCalled_template'] 99s 99s Miscellaneous Arguments: 99s --quiet, -q Don't print status information. 99s --help, -h Print this help message and exit 99s usage: tombo plot per_read 99s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 99s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 99s [--genome-fasta GENOME_FASTA] 99s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 99s [--num-reads NUM_READS] [--num-bases NUM_BASES] 99s [--box-center] [--pdf-filename PDF_FILENAME] 99s [--corrected-group CORRECTED_GROUP] 99s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 99s [--quiet] [--help] 99s 99s Required Arguments: 99s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 99s Genomic locations at which to plot signal. Format 99s locations as "chrm:position[:strand] 99s [chrm2:position2[:strand2] ...]" (strand not 99s applicable for all applications) 99s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 99s Binary file containing per-read statistics from 99s statistical testing. 99s 99s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 99s --genome-fasta GENOME_FASTA 99s FASTA file used to re-squiggle. For faster sequence 99s access. 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s Directories containing fast5 files. 99s 99s Plotting Region Arguments: 99s --num-reads NUM_READS 99s Number of reads to plot. Default: 100 99s --num-bases NUM_BASES 99s Number of bases to plot/output. Default: 51 99s --box-center Plot a box around the central base. 99s 99s Output Argument: 99s --pdf-filename PDF_FILENAME 99s PDF filename to store plot(s). Default: 99s tombo_results.per_read_stats.pdf 99s 99s FAST5 Data Arguments: 99s --corrected-group CORRECTED_GROUP 99s FAST5 group created by resquiggle command. Default: 99s RawGenomeCorrected_000 99s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 99s FAST5 subgroup(s) (under /Analyses/[--basecall- 99s group]/) containing basecalls and created within 99s [--corrected-group] containing re-squiggle results. 99s Default: ['BaseCalled_template'] 99s 99s Miscellaneous Arguments: 99s --quiet, -q Don't print status information. 99s --help, -h Print this help message and exit 99s usage: tombo plot roc 99s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 99s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 99s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 99s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 99s [--genome-fasta GENOME_FASTA] 99s [--pdf-filename PDF_FILENAME] 99s [--statistics-per-block STATISTICS_PER_BLOCK] 99s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 99s [--quiet] [--help] 99s 99s Required Argument: 99s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 99s Files to load genomic base anchored statistics. 99s 99s Ground Truth Arguments (provide bed files or motifs): 99s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 99s Modification description and bed format files 99s containing single base locations of ground truth 99s modified sites. Bed files should contain 6 fields 99s including strand. Format descriptions as 99s "mod_name:locs.bed". Example: "CpG 99s bisulfite":bisulfite_locs.bed 99s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 99s Bed format files containing single base locations of 99s ground truth unmodified sites. Bed files should 99s contain 6 fields including strand. 99s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 99s Ground truth, motif centered, modified base 99s descriptions for computing ROC and PR curves. Each 99s statistics file is associated with a set of motif 99s descriptions. Format descriptions as: 99s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 99s mod_pos indicates the alternate-base within the motif 99s (1-based index). Example: CCWGG:2:"dcm 99s 5mC"::GATC:2:"dam 6mA" would assess the performance of 99s a single Tombo statistics file for identification of 99s E. coli dam and dcm methylation. 99s --genome-fasta GENOME_FASTA 99s FASTA file used to re-squiggle. For faster sequence 99s access. 99s 99s Output Arguments: 99s --pdf-filename PDF_FILENAME 99s PDF filename to store plot(s). Default: 99s tombo_results.roc.pdf 99s 99s Down-sampling Arguments: 99s --statistics-per-block STATISTICS_PER_BLOCK 99s Number of randomly selected per-read, per-base 99s statistics to extract from each genomic block for 99s plotting. Default: Include all stats 99s --total-statistics-limit TOTAL_STATISTICS_LIMIT 99s Total per-read statistics to be extracted for 99s plotting. Avoids memory overflow for large runs. 99s Default: 5000000 99s 99s Miscellaneous Arguments: 99s --quiet, -q Don't print status information. 99s --help, -h Print this help message and exit 99s usage: tombo plot per_read_roc 99s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 99s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 99s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 99s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 99s [--genome-fasta GENOME_FASTA] 99s [--statistics-per-block STATISTICS_PER_BLOCK] 99s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 99s [--pdf-filename PDF_FILENAME] [--quiet] 99s [--help] 99s 99s Required Argument: 99s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 99s Binary files containing per-read statistics from 99s statistical testing. 99s 99s Ground Truth Arguments (provide bed files or motifs): 99s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 99s Modification description and bed format files 99s containing single base locations of ground truth 99s modified sites. Bed files should contain 6 fields 99s including strand. Format descriptions as 99s "mod_name:locs.bed". Example: "CpG 99s bisulfite":bisulfite_locs.bed 99s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 99s Bed format files containing single base locations of 99s ground truth unmodified sites. Bed files should 99s contain 6 fields including strand. 99s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 99s Ground truth, motif centered, modified base 99s descriptions for computing ROC and PR curves. Each 99s statistics file is associated with a set of motif 99s descriptions. Format descriptions as: 99s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 99s mod_pos indicates the alternate-base within the motif 99s (1-based index). Example: CCWGG:2:"dcm 99s 5mC"::GATC:2:"dam 6mA" would assess the performance of 99s a single Tombo statistics file for identification of 99s E. coli dam and dcm methylation. 99s --genome-fasta GENOME_FASTA 99s FASTA file used to re-squiggle. For faster sequence 99s access. 99s 99s Down-sampling Arguments: 99s --statistics-per-block STATISTICS_PER_BLOCK 99s Number of randomly selected per-read, per-base 99s statistics to extract from each genomic block for 99s plotting. Default: 100000 99s --total-statistics-limit TOTAL_STATISTICS_LIMIT 99s Total per-read statistics to be extracted for 99s plotting. Avoids memory overflow for large runs. 99s Default: 5000000 99s 99s Output Arguments: 99s --pdf-filename PDF_FILENAME 99s PDF filename to store plot(s). Default: 99s tombo_results.per_reads_roc.pdf 99s 99s Miscellaneous Arguments: 99s --quiet, -q Don't print status information. 99s --help, -h Print this help message and exit 99s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s [--upstream-bases {0,1,2,3,4}] 99s [--downstream-bases {0,1,2,3,4}] [--read-mean] 99s [--num-kmer-threshold NUM_KMER_THRESHOLD] 99s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 99s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 99s [--corrected-group CORRECTED_GROUP] 99s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 99s [--quiet] [--help] 99s 99s Required Argument: 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s Directories containing fast5 files. 99s 99s Data Processing Arguments: 99s --upstream-bases {0,1,2,3,4} 99s Upstream bases in k-mer. Default: 1 99s --downstream-bases {0,1,2,3,4} 99s Downstream bases in k-mer. Default: 2 99s --read-mean Plot k-mer means across whole reads as opposed to 99s individual k-mer event levels. 99s --num-kmer-threshold NUM_KMER_THRESHOLD 99s Observations of each k-mer required to include a read 99s in read level averages. Default: 1 99s 99s Plotting Region Arguments: 99s --num-reads NUM_READS 99s Number of reads to plot. Default: 100 99s 99s Output Arguments: 99s --pdf-filename PDF_FILENAME 99s PDF filename to store plot(s). Default: 99s tombo_results.kmer_distribution.pdf 99s --r-data-filename R_DATA_FILENAME 99s Filename to save R data structure. Default: Don't save 99s --dont-plot Don't plot result. Useful to produce only R data file. 99s 99s FAST5 Data Arguments: 99s --corrected-group CORRECTED_GROUP 99s FAST5 group created by resquiggle command. Default: 99s RawGenomeCorrected_000 99s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 99s FAST5 subgroup(s) (under /Analyses/[--basecall- 99s group]/) containing basecalls and created within 99s [--corrected-group] containing re-squiggle results. 99s Default: ['BaseCalled_template'] 99s 99s Miscellaneous Arguments: 99s --quiet, -q Don't print status information. 99s --help, -h Print this help message and exit 99s usage: tombo plot cluster_most_significant 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 99s --statistics-filename STATISTICS_FILENAME 99s [--genome-fasta GENOME_FASTA] 99s [--processes PROCESSES] 99s [--num-regions NUM_REGIONS] 99s [--num-bases NUM_BASES] 99s [--slide-span SLIDE_SPAN] 99s [--pdf-filename PDF_FILENAME] 99s [--r-data-filename R_DATA_FILENAME] 99s [--corrected-group CORRECTED_GROUP] 99s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 99s [--quiet] [--help] 99s 99s Required Arguments: 99s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 99s Directories containing fast5 files. 99s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 99s Set of directories containing fast5 files for control 99s reads, containing only canonical nucleotides. 99s --statistics-filename STATISTICS_FILENAME 99s File to save/load genomic base anchored statistics. 99s 99s FASTA Sequence Argument: 99s --genome-fasta GENOME_FASTA 99s FASTA file used to re-squiggle. For faster sequence 99s access. 99s 99s Multiprocessing Argument: 99s --processes PROCESSES 99s Number of processes. Default: 1 99s 99s Plotting Region Arguments: 99s --num-regions NUM_REGIONS 99s Number of regions to plot. Default: 10 99s --num-bases NUM_BASES 99s Number of bases to plot/output. Default: 21 99s --slide-span SLIDE_SPAN 99s Number of bases offset over which to search when 99s computing distances for signal cluster plotting. 99s Default: 0 (exact position) 99s 99s Output Arguments: 99s --pdf-filename PDF_FILENAME 99s PDF filename to store plot(s). Default: 99s tombo_results.signal_clusters.pdf 99s --r-data-filename R_DATA_FILENAME 99s Filename to save R data structure. Default: Don't save 99s 99s FAST5 Data Arguments: 99s --corrected-group CORRECTED_GROUP 99s FAST5 group created by resquiggle command. Default: 99s RawGenomeCorrected_000 99s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 99s FAST5 subgroup(s) (under /Analyses/[--basecall- 99s group]/) containing basecalls and created within 99s [--corrected-group] containing re-squiggle results. 99s Default: ['BaseCalled_template'] 99s 99s Miscellaneous Arguments: 99s --quiet, -q Don't print status information. 99s --help, -h Print this help message and exit 99s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 99s 99s Required Arguments: 99s fast5s_basedir Directory containing fast5 files. All files ending in 99s "fast5" found recursively within this base directory will be 99s processed. 99s 99s Miscellaneous Arguments: 99s --quiet, -q Don't print status information. 99s --help, -h Print this help message and exit 99s usage: tombo build_model event_resquiggle 99s [--minimap2-executable MINIMAP2_EXECUTABLE] 99s [--minimap2-index MINIMAP2_INDEX] 99s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 99s [--graphmap-executable GRAPHMAP_EXECUTABLE] 99s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 99s [--normalization-type {median,pA,pA_raw,none}] 99s [--pore-model-filename PORE_MODEL_FILENAME] 99s [--outlier-threshold OUTLIER_THRESHOLD] 99s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 99s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 99s [--timeout TIMEOUT] 99s [--cpts-limit CPTS_LIMIT] 99s [--skip-index] [--overwrite] 99s [--failed-reads-filename FAILED_READS_FILENAME] 99s [--include-event-stdev] 99s [--corrected-group CORRECTED_GROUP] 99s [--basecall-group BASECALL_GROUP] 99s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 99s [--processes PROCESSES] 99s [--align-processes ALIGN_PROCESSES] 99s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 99s [--resquiggle-processes RESQUIGGLE_PROCESSES] 99s [--quiet] [--help] 99s fast5s_basedir reference_fasta 99s 99s Required Arguments: 99s fast5s_basedir Directory containing fast5 files. All files ending in 99s "fast5" found recursively within this base directory 99s will be processed. 99s reference_fasta Reference genome/transcriptome FASTA file for mapping. 99s 99s Mapper Arguments (One mapper is required): 99s --minimap2-executable MINIMAP2_EXECUTABLE 99s Path to minimap2 executable. 99s --minimap2-index MINIMAP2_INDEX 99s Path to minimap2 index (with map-ont preset) file 99s corresponding to the [genome_fasta] provided. 99s --bwa-mem-executable BWA_MEM_EXECUTABLE 99s Path to bwa-mem executable. 99s --graphmap-executable GRAPHMAP_EXECUTABLE 99s Path to graphmap executable. 99s --alignment-batch-size ALIGNMENT_BATCH_SIZE 99s Number of reads included in each alignment call. Note: 99s A new system mapping call is made for each batch 99s (including loading of the genome), so it is advised to 99s use larger values for larger genomes. Default: 1000 99s 99s Signal Processing Arguments: 99s --normalization-type {median,pA,pA_raw,none} 99s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 99s as in the ONT events (using offset, range and 99s digitization), "pA": k-mer-based correction for pA 99s drift as in nanopolish (requires [--pore-model- 99s filename]), "median": median and MAD from raw signal. 99s Default: median 99s --pore-model-filename PORE_MODEL_FILENAME 99s File containing kmer model parameters (level_mean and 99s level_stdv) used in order to compute kmer-based 99s corrected pA values. E.g. https://github.com/jts/nanop 99s olish/blob/master/etc/r9- 99s models/template_median68pA.5mers.model 99s --outlier-threshold OUTLIER_THRESHOLD 99s Windosrize the signal at this number of scale values. 99s Negative value disables outlier clipping. Default: 99s 5.000000 99s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 99s Specify the 2 parameters for segmentation 1) running 99s neighboring windows width 2) minimum raw observations 99s per genomic base. Sample type defaults: RNA : 12 6 || 99s DNA : 5 3 99s 99s Read Filtering Arguments: 99s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 99s Filter reads based on observations per base percentile 99s thresholds. Format thresholds as "percentile:thresh 99s [pctl2:thresh2 ...]". For example to filter reads with 99s 99th pctl > 200 obs/base or max > 5k obs/base use 99s "99:200 100:5000". 99s --timeout TIMEOUT Timeout in seconds for processing a single read. 99s Default: No timeout. 99s --cpts-limit CPTS_LIMIT 99s Maximum number of changepoints to find within a single 99s indel group. Default: No limit. 99s 99s Input/Output Arguments: 99s --skip-index Skip creation of tombo index. This drastically slows 99s downstream tombo commands. Default stores tombo index 99s named ".[--fast5-basedir].[--corrected- 99s group].tombo.index" to be loaded automatically for 99s downstream commands. 99s --overwrite Overwrite previous corrected group in FAST5 files. 99s Note: only effects --corrected-group or --new- 99s corrected-group. 99s --failed-reads-filename FAILED_READS_FILENAME 99s Output failed read filenames with assoicated error. 99s Default: Do not store failed reads. 99s --include-event-stdev 99s Include corrected event standard deviation in output 99s FAST5 data. 99s 99s FAST5 Data Arguments: 99s --corrected-group CORRECTED_GROUP 99s FAST5 group created by resquiggle command. Default: 99s RawGenomeCorrected_000 99s --basecall-group BASECALL_GROUP 99s FAST5 group obtain original basecalls (under Analyses 99s group). Default: Basecall_1D_000 99s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 99s FAST5 subgroup(s) (under /Analyses/[--basecall- 99s group]/) containing basecalls and created within 99s [--corrected-group] containing re-squiggle results. 99s Default: ['BaseCalled_template'] 99s 99s Multiprocessing Arguments: 99s --processes PROCESSES 99s Number of processes. Default: 2 99s --align-processes ALIGN_PROCESSES 99s Number of processes to use for parsing and aligning 99s original basecalls. Each process will independently 99s load the genome into memory, so use caution with 99s larger genomes (e.g. human). Default: 1 99s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 99s Number of threads to use for aligner system call. 99s Default: [--processes] / (2 * [--align-processes)] 99s --resquiggle-processes RESQUIGGLE_PROCESSES 99s Number of processes to use for resquiggle algorithm. 99s Default: [--processes] / 2 99s 99s Miscellaneous Arguments: 99s --quiet, -q Don't print status information. 99s --help, -h Print this help message and exit 100s usage: tombo build_model estimate_reference 100s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 100s --tombo-model-filename TOMBO_MODEL_FILENAME 100s [--estimate-mean] 100s [--kmer-specific-sd] 100s [--upstream-bases {0,1,2,3,4}] 100s [--downstream-bases {0,1,2,3,4}] 100s [--minimum-test-reads MINIMUM_TEST_READS] 100s [--coverage-threshold COVERAGE_THRESHOLD] 100s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 100s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 100s [--processes PROCESSES] 100s [--corrected-group CORRECTED_GROUP] 100s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 100s [--quiet] [--help] 100s 100s Required Arguments: 100s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 100s Directories containing fast5 files. 100s --tombo-model-filename TOMBO_MODEL_FILENAME 100s Filename to save Tombo model. 100s 100s Modeling Arguments: 100s --estimate-mean Use the mean instead of median for model level 100s estimation. Note: This can cause poor fits due to 100s outliers 100s --kmer-specific-sd Estimate standard deviation for each k-mers 100s individually. 100s --upstream-bases {0,1,2,3,4} 100s Upstream bases in k-mer. Default: 1 100s --downstream-bases {0,1,2,3,4} 100s Downstream bases in k-mer. Default: 2 100s 100s Filtering Arguments: 100s --minimum-test-reads MINIMUM_TEST_READS 100s Number of reads required at a position to perform 100s significance testing or contribute to model 100s estimation. Default: 10 100s --coverage-threshold COVERAGE_THRESHOLD 100s Maximum mean coverage per region when estimating k-mer 100s model (limits compute time for deep samples). Default: 100s 100 100s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 100s Number of each k-mer observations required in order to 100s produce a reference (genomic locations for standard 100s reference and per-read for alternative reference). 100s Default: 5 100s 100s Multiprocessing Arguments: 100s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 100s Size of regions over which to multiprocesses statistic 100s computation. For very deep samples a smaller value is 100s recommmended in order to control memory consumption. 100s Default: 10000 100s --processes PROCESSES 100s Number of processes. Default: 1 100s 100s FAST5 Data Arguments: 100s --corrected-group CORRECTED_GROUP 100s FAST5 group created by resquiggle command. Default: 100s RawGenomeCorrected_000 100s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 100s FAST5 subgroup(s) (under /Analyses/[--basecall- 100s group]/) containing basecalls and created within 100s [--corrected-group] containing re-squiggle results. 100s Default: ['BaseCalled_template'] 100s 100s Miscellaneous Arguments: 100s --quiet, -q Don't print status information. 100s --help, -h Print this help message and exit 100s usage: tombo build_model estimate_alt_reference 100s --alternate-model-filename ALTERNATE_MODEL_FILENAME 100s --alternate-model-name ALTERNATE_MODEL_NAME 100s --alternate-model-base {A,C,G,T} 100s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 100s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 100s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 100s [--control-density-filename CONTROL_DENSITY_FILENAME] 100s [--dna] [--rna] 100s [--tombo-model-filename TOMBO_MODEL_FILENAME] 100s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 100s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 100s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 100s [--save-density-basename SAVE_DENSITY_BASENAME] 100s [--processes PROCESSES] 100s [--corrected-group CORRECTED_GROUP] 100s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 100s [--quiet] [--help] 100s 100s Required Arguments: 100s --alternate-model-filename ALTERNATE_MODEL_FILENAME 100s Tombo model for alternative likelihood ratio 100s significance testing. 100s --alternate-model-name ALTERNATE_MODEL_NAME 100s A short name to associate with this alternate model 100s (e.g. 5mC, 6mA, etc.). This text will be included in 100s output filenames when this model is used for testing. 100s --alternate-model-base {A,C,G,T} 100s Non-standard base is an alternative to this base. 100s 100s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 100s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 100s Directories containing fast5 files. 100s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 100s Set of directories containing fast5 files for control 100s reads, containing only canonical nucleotides. 100s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 100s File containing k-mer level kernel density estimates 100s for the alternative sample saved using --save-density- 100s basename. 100s --control-density-filename CONTROL_DENSITY_FILENAME 100s File containing k-mer level kernel density estimates 100s for the control sample saved using --save-density- 100s basename. 100s 100s Standard Model Arguments: 100s --dna Explicitly select canonical DNA model. Default: 100s Automatically determine from FAST5s 100s --rna Explicitly select canonical RNA model. Default: 100s Automatically determine from FAST5s 100s --tombo-model-filename TOMBO_MODEL_FILENAME 100s Tombo model filename. If no file is provided, the 100s default DNA or RNA Tombo model will be used. 100s 100s Model Fitting Arguments: 100s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 100s When esitmating the alternative base incorporation 100s rate, this percent of k-mers are assumed to have 100s significantly shifted signal so the alternative 100s distribution minimally overlaps the standard base 100s distribution. Default: 5.000000 100s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 100s Bandwidth applied when performing Gaussian kernal 100s density esitmation on standard and alternative base 100s signal distributions. Default: 0.050000 100s 100s Filtering Argument: 100s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 100s Number of each k-mer observations required in order to 100s produce a reference (genomic locations for standard 100s reference and per-read for alternative reference). 100s Default: 1000 100s 100s Output Argument: 100s --save-density-basename SAVE_DENSITY_BASENAME 100s Basename to save alternative model estimation density 100s estimation information. See scripts/debug_est_alt.R 100s for info use example. Default: Don't save. 100s 100s Multiprocessing Arguments: 100s --processes PROCESSES 100s Number of processes. Default: 1 100s 100s FAST5 Data Arguments: 100s --corrected-group CORRECTED_GROUP 100s FAST5 group created by resquiggle command. Default: 100s RawGenomeCorrected_000 100s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 100s FAST5 subgroup(s) (under /Analyses/[--basecall- 100s group]/) containing basecalls and created within 100s [--corrected-group] containing re-squiggle results. 100s Default: ['BaseCalled_template'] 100s 100s Miscellaneous Arguments: 100s --quiet, -q Don't print status information. 100s --help, -h Print this help message and exit 100s This test only tests the help system 100s There is an extensive test in 100s 100s tombo/tests/shell_tests.sh 100s 100s but this requires to download larger data 100s sets which is not done for the moment. 100s autopkgtest [12:49:36]: test run-unit-test: -----------------------] 100s run-unit-test PASS 100s autopkgtest [12:49:36]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 100s autopkgtest [12:49:36]: @@@@@@@@@@@@@@@@@@@@ summary 100s run-unit-test PASS 116s nova [W] Skipping flock for amd64 116s Creating nova instance adt-plucky-amd64-tombo-20250219-124756-juju-7f2275-prod-proposed-migration-environment-20-981f2ce4-eb51-455c-8fdf-57b078bf9d21 from image adt/ubuntu-plucky-amd64-server-20250218.img (UUID 0c5f6311-785d-4524-a0d8-db541aaf5c09)... 116s nova [W] Timed out waiting for ca42a7d3-8ac2-4860-a48d-1bdfb985852b to get deleted.