0s autopkgtest [12:44:12]: starting date and time: 2025-02-19 12:44:12+0000 0s autopkgtest [12:44:12]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [12:44:12]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.043r9czk/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-2@bos03-arm64-26.secgroup --name adt-plucky-arm64-tombo-20250219-124412-juju-7f2275-prod-proposed-migration-environment-2-6d5cc333-7d7a-4ec6-9919-0aa78295ba70 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 154s autopkgtest [12:46:46]: testbed dpkg architecture: arm64 154s autopkgtest [12:46:46]: testbed apt version: 2.9.29 154s autopkgtest [12:46:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 154s autopkgtest [12:46:46]: testbed release detected to be: None 156s autopkgtest [12:46:48]: updating testbed package index (apt update) 156s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 156s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 156s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 156s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 157s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 157s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 157s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 157s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 157s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [93.3 kB] 157s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 157s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [686 kB] 157s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [11.2 kB] 157s Fetched 1752 kB in 1s (1898 kB/s) 158s Reading package lists... 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 160s Calculating upgrade... 160s The following NEW packages will be installed: 160s libapt-pkg7.0 160s The following packages will be upgraded: 160s apt apt-utils iproute2 liblsof0 libp11-kit0 lsof rsyslog 160s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 160s Need to get 4842 kB of archives. 160s After this operation, 3409 kB of additional disk space will be used. 160s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libapt-pkg7.0 arm64 2.9.30 [1023 kB] 161s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 apt arm64 2.9.30 [1364 kB] 161s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 apt-utils arm64 2.9.30 [207 kB] 161s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 iproute2 arm64 6.13.0-1ubuntu1 [1158 kB] 161s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libp11-kit0 arm64 0.25.5-2ubuntu3 [280 kB] 161s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 rsyslog arm64 8.2412.0-2ubuntu1 [521 kB] 161s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 lsof arm64 4.99.4+dfsg-1 [236 kB] 161s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsof0 arm64 4.99.4+dfsg-1 [53.9 kB] 162s Preconfiguring packages ... 162s Fetched 4842 kB in 1s (5761 kB/s) 162s Selecting previously unselected package libapt-pkg7.0:arm64. 162s (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 ... 116620 files and directories currently installed.) 162s Preparing to unpack .../libapt-pkg7.0_2.9.30_arm64.deb ... 162s Unpacking libapt-pkg7.0:arm64 (2.9.30) ... 163s Setting up libapt-pkg7.0:arm64 (2.9.30) ... 163s (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 ... 116669 files and directories currently installed.) 163s Preparing to unpack .../archives/apt_2.9.30_arm64.deb ... 163s Unpacking apt (2.9.30) over (2.9.29) ... 163s Setting up apt (2.9.30) ... 164s (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 ... 116669 files and directories currently installed.) 164s Preparing to unpack .../0-apt-utils_2.9.30_arm64.deb ... 164s Unpacking apt-utils (2.9.30) over (2.9.29) ... 164s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_arm64.deb ... 164s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 165s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_arm64.deb ... 165s Unpacking libp11-kit0:arm64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 165s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_arm64.deb ... 165s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 165s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_arm64.deb ... 165s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 165s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_arm64.deb ... 165s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 166s Setting up apt-utils (2.9.30) ... 166s Setting up liblsof0 (4.99.4+dfsg-1) ... 166s Setting up iproute2 (6.13.0-1ubuntu1) ... 166s Setting up rsyslog (8.2412.0-2ubuntu1) ... 166s info: The user `syslog' is already a member of `adm'. 168s Setting up libp11-kit0:arm64 (0.25.5-2ubuntu3) ... 168s Setting up lsof (4.99.4+dfsg-1) ... 168s Processing triggers for man-db (2.13.0-1) ... 170s Processing triggers for libc-bin (2.40-4ubuntu1) ... 172s Reading package lists... 172s Building dependency tree... 172s Reading state information... 173s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 173s autopkgtest [12:47:05]: upgrading testbed (apt dist-upgrade and autopurge) 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 174s Starting 2 pkgProblemResolver with broken count: 0 174s Done 175s Entering ResolveByKeep 175s 176s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 176s Reading package lists... 176s Building dependency tree... 176s Reading state information... 177s Starting pkgProblemResolver with broken count: 0 177s Starting 2 pkgProblemResolver with broken count: 0 177s Done 178s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 178s autopkgtest [12:47:10]: rebooting testbed after setup commands that affected boot 200s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 208s autopkgtest [12:47:40]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 211s autopkgtest [12:47:43]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 215s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (dsc) [2291 B] 215s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (tar) [22.3 MB] 215s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (diff) [9600 B] 215s gpgv: Signature made Wed Jan 29 22:42:44 2025 UTC 215s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 215s gpgv: Can't check signature: No public key 215s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7build1.dsc: no acceptable signature found 215s autopkgtest [12:47:47]: testing package tombo version 1.5.1-7build1 216s autopkgtest [12:47:48]: build not needed 218s autopkgtest [12:47:50]: test run-unit-test: preparing testbed 218s Reading package lists... 218s Building dependency tree... 218s Reading state information... 219s Starting pkgProblemResolver with broken count: 0 219s Starting 2 pkgProblemResolver with broken count: 0 219s Done 220s The following NEW packages will be installed: 220s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 220s libhdf5-310 libhdf5-hl-310 libjs-jquery libjs-mathjax libjs-sphinxdoc 220s libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 python3-decorator 220s python3-h5py python3-h5py-serial python3-mappy python3-numpy 220s python3-packaging python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 220s tombo-doc 220s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 220s Need to get 64.7 MB of archives. 220s After this operation, 247 MB of additional disk space will be used. 220s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB] 220s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 220s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 221s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 221s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 221s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250213-1ubuntu1 [443 kB] 221s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 221s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 221s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 221s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 221s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 221s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 221s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 221s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 221s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 221s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 221s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [4148 kB] 221s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.12.1-1 [1453 kB] 221s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.12.1-1 [7970 B] 221s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mappy arm64 2.27+dfsg-1build1 [193 kB] 221s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 221s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.1-2 [92.5 kB] 221s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 221s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu1 [19.5 MB] 221s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 tombo arm64 1.5.1-7build1 [510 kB] 221s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 222s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 tombo-doc all 1.5.1-7build1 [21.7 MB] 223s Fetched 64.7 MB in 3s (22.8 MB/s) 223s Selecting previously unselected package fonts-lato. 223s (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 ... 116670 files and directories currently installed.) 223s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 223s Unpacking fonts-lato (2.015-1) ... 224s Selecting previously unselected package fonts-font-awesome. 224s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 224s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 224s Selecting previously unselected package fonts-mathjax. 224s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 224s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 224s Selecting previously unselected package libaec0:arm64. 224s Preparing to unpack .../03-libaec0_1.1.3-1_arm64.deb ... 224s Unpacking libaec0:arm64 (1.1.3-1) ... 224s Selecting previously unselected package libblas3:arm64. 224s Preparing to unpack .../04-libblas3_3.12.1-2_arm64.deb ... 224s Unpacking libblas3:arm64 (3.12.1-2) ... 224s Selecting previously unselected package libgfortran5:arm64. 224s Preparing to unpack .../05-libgfortran5_15-20250213-1ubuntu1_arm64.deb ... 224s Unpacking libgfortran5:arm64 (15-20250213-1ubuntu1) ... 224s Selecting previously unselected package libsz2:arm64. 224s Preparing to unpack .../06-libsz2_1.1.3-1_arm64.deb ... 224s Unpacking libsz2:arm64 (1.1.3-1) ... 224s Selecting previously unselected package libhdf5-310:arm64. 224s Preparing to unpack .../07-libhdf5-310_1.14.5+repack-3_arm64.deb ... 224s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 224s Selecting previously unselected package libhdf5-hl-310:arm64. 224s Preparing to unpack .../08-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... 224s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 224s Selecting previously unselected package libjs-jquery. 224s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 224s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 224s Selecting previously unselected package libjs-underscore. 224s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 224s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 224s Selecting previously unselected package libjs-sphinxdoc. 224s Preparing to unpack .../11-libjs-sphinxdoc_8.1.3-5_all.deb ... 224s Unpacking libjs-sphinxdoc (8.1.3-5) ... 224s Selecting previously unselected package liblapack3:arm64. 224s Preparing to unpack .../12-liblapack3_3.12.1-2_arm64.deb ... 224s Unpacking liblapack3:arm64 (3.12.1-2) ... 225s Selecting previously unselected package liblbfgsb0:arm64. 225s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 225s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 225s Selecting previously unselected package liblzf1:arm64. 225s Preparing to unpack .../14-liblzf1_3.6-4_arm64.deb ... 225s Unpacking liblzf1:arm64 (3.6-4) ... 225s Selecting previously unselected package python3-decorator. 225s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 225s Unpacking python3-decorator (5.1.1-5) ... 225s Selecting previously unselected package python3-numpy. 225s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-13_arm64.deb ... 225s Unpacking python3-numpy (1:1.26.4+ds-13) ... 225s Selecting previously unselected package python3-h5py-serial. 225s Preparing to unpack .../17-python3-h5py-serial_3.12.1-1_arm64.deb ... 225s Unpacking python3-h5py-serial (3.12.1-1) ... 225s Selecting previously unselected package python3-h5py. 225s Preparing to unpack .../18-python3-h5py_3.12.1-1_all.deb ... 225s Unpacking python3-h5py (3.12.1-1) ... 225s Selecting previously unselected package python3-mappy. 225s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1build1_arm64.deb ... 225s Unpacking python3-mappy (2.27+dfsg-1build1) ... 225s Selecting previously unselected package python3-packaging. 225s Preparing to unpack .../20-python3-packaging_24.2-1_all.deb ... 225s Unpacking python3-packaging (24.2-1) ... 225s Selecting previously unselected package python3-tqdm. 225s Preparing to unpack .../21-python3-tqdm_4.67.1-2_all.deb ... 225s Unpacking python3-tqdm (4.67.1-2) ... 225s Selecting previously unselected package sphinx-rtd-theme-common. 225s Preparing to unpack .../22-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 225s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 225s Selecting previously unselected package python3-scipy. 225s Preparing to unpack .../23-python3-scipy_1.14.1-4ubuntu1_arm64.deb ... 225s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 226s Selecting previously unselected package tombo. 226s Preparing to unpack .../24-tombo_1.5.1-7build1_arm64.deb ... 226s Unpacking tombo (1.5.1-7build1) ... 226s Selecting previously unselected package libjs-mathjax. 226s Preparing to unpack .../25-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 226s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 227s Selecting previously unselected package tombo-doc. 227s Preparing to unpack .../26-tombo-doc_1.5.1-7build1_all.deb ... 227s Unpacking tombo-doc (1.5.1-7build1) ... 227s Setting up fonts-lato (2.015-1) ... 227s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 227s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 227s Setting up python3-tqdm (4.67.1-2) ... 227s Setting up python3-mappy (2.27+dfsg-1build1) ... 227s Setting up libaec0:arm64 (1.1.3-1) ... 227s Setting up python3-decorator (5.1.1-5) ... 227s Setting up libblas3:arm64 (3.12.1-2) ... 227s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 227s Setting up python3-packaging (24.2-1) ... 228s Setting up liblzf1:arm64 (3.6-4) ... 228s Setting up libgfortran5:arm64 (15-20250213-1ubuntu1) ... 228s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 228s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 228s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 228s Setting up libsz2:arm64 (1.1.3-1) ... 228s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 228s Setting up liblapack3:arm64 (3.12.1-2) ... 228s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 228s Setting up python3-numpy (1:1.26.4+ds-13) ... 230s Setting up libjs-sphinxdoc (8.1.3-5) ... 230s Setting up tombo-doc (1.5.1-7build1) ... 230s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... 230s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 230s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 230s Setting up python3-scipy (1.14.1-4ubuntu1) ... 233s Setting up python3-h5py-serial (3.12.1-1) ... 234s Setting up python3-h5py (3.12.1-1) ... 234s Setting up tombo (1.5.1-7build1) ... 234s Processing triggers for man-db (2.13.0-1) ... 235s Processing triggers for libc-bin (2.40-4ubuntu1) ... 236s autopkgtest [12:48:08]: test run-unit-test: [----------------------- 237s ********* Testing help commands ********** 237s usage: tombo [-h] [-v] 237s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} ... 237s 237s ********** Tombo ********* 237s 237s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 237s 237s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 237s 237s Tombo command groups (additional help available within each command group): 237s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 237s preprocess Pre-process nanopore reads for Tombo processing. 237s filter Apply filter to Tombo index file for specified criterion. 237s detect_modifications Perform statistical testing to detect non-standard nucleotides. 237s text_output Output Tombo results in text files. 237s build_model Create canonical and alternative base Tombo models. 237s plot Save plots to visualize raw nanopore signal or testing results. 237s 237s options: 237s -h, --help show this help message and exit 237s -v, --version show Tombo version and exit. 237s usage: tombo resquiggle [--dna] [--rna] 237s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 237s [--q-score Q_SCORE] 237s [--signal-matching-score SIGNAL_MATCHING_SCORE] 237s [--processes PROCESSES] 237s [--corrected-group CORRECTED_GROUP] 237s [--basecall-group BASECALL_GROUP] 237s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 237s [--overwrite] 237s [--failed-reads-filename FAILED_READS_FILENAME] 237s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 237s [--print-advanced-arguments] [--quiet] [--help] 237s fast5s_basedir reference 237s 237s Required Arguments: 237s fast5s_basedir Directory containing fast5 files. All files ending in 237s "fast5" found recursively within this base directory 237s will be processed. 237s reference Reference genome/transcriptome FASTA file or minimap2 237s index (with "map-ont" preset) for mapping. 237s 237s Model Parameters: 237s --dna Explicitly select canonical DNA model. Default: 237s Automatically determine from FAST5s 237s --rna Explicitly select canonical RNA model. Default: 237s Automatically determine from FAST5s 237s 237s Read Filtering Argument: 237s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 237s Filter reads based on observations per base percentile 237s thresholds. Format thresholds as "percentile:thresh 237s [pctl2:thresh2 ...]". For example to filter reads with 237s 99th pctl > 200 obs/base or max > 5k obs/base use 237s "99:200 100:5000". 237s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 237s Default: 0.000000 237s --signal-matching-score SIGNAL_MATCHING_SCORE 237s Observed to expected signal matching score (higher 237s score indicates poor matching). Sample type defaults: 237s RNA : 2 || DNA : 1.1 237s 237s Multiprocessing Arguments: 237s --processes PROCESSES 237s Number of processes. Default: 1 237s 237s FAST5 Data Arguments: 237s --corrected-group CORRECTED_GROUP 237s FAST5 group created by resquiggle command. Default: 237s RawGenomeCorrected_000 237s --basecall-group BASECALL_GROUP 237s FAST5 group obtain original basecalls (under Analyses 237s group). Default: Basecall_1D_000 237s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 237s FAST5 subgroup(s) (under /Analyses/[--basecall- 237s group]/) containing basecalls and created within 237s [--corrected-group] containing re-squiggle results. 237s Default: ['BaseCalled_template'] 237s --overwrite Overwrite previous corrected group in FAST5 files. 237s Note: only effects --corrected-group or --new- 237s corrected-group. 237s 237s Input/Output Arguments: 237s --failed-reads-filename FAILED_READS_FILENAME 237s Output failed read filenames with assoicated error. 237s Default: Do not store failed reads. 237s --num-most-common-errors NUM_MOST_COMMON_ERRORS 237s Dynamically show this many most common errors so far 237s through run. Default: 0; Just show progress 237s 237s Advanced Arguments: 237s --print-advanced-arguments 237s Print advanced re-squiggle arguments and exit. 237s 237s Miscellaneous Arguments: 237s --quiet, -q Don't print status information. 237s --help, -h Print this help message and exit 237s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 237s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 237s [--basecall-group BASECALL_GROUP] 237s [--basecall-subgroup BASECALL_SUBGROUP] 237s [--overwrite] 237s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 237s [--processes PROCESSES] 237s [--quiet] [--help] 237s 237s Required Arguments: 237s --fast5-basedir FAST5_BASEDIR 237s Directory containing fast5 files. 237s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 237s FASTQ filenames containing basecalls to be added to 237s raw FAST5 files. 237s 237s FAST5 Data Arguments: 237s --basecall-group BASECALL_GROUP 237s FAST5 group obtain original basecalls (under Analyses 237s group). Default: Basecall_1D_000 237s --basecall-subgroup BASECALL_SUBGROUP 237s FAST5 subgroup (under /Analyses/[--basecall-group]/) 237s under which to store basecalls from FASTQs. Default: 237s BaseCalled_template 237s --overwrite Overwrite previous corrected group in FAST5 files. 237s Note: only effects --corrected-group or --new- 237s corrected-group. 237s 237s Sequencing Summary Argument: 237s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 237s Sequencing summary filenames produced by albacore. 237s These can make annotation of raw FAST5 files with 237s FASTQ sequence much faster. 237s 237s Multiprocessing Argument: 237s --processes PROCESSES 237s Number of processes. Default: 1 237s 237s Miscellaneous Arguments: 237s --quiet, -q Don't print status information. 237s --help, -h Print this help message and exit 237s usage: tombo filter clear_filters 237s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 237s [--corrected-group CORRECTED_GROUP] 237s [--quiet] [--help] 237s 237s Required Argument: 237s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 237s Directories containing fast5 files. 237s 237s FAST5 Data Argument: 237s --corrected-group CORRECTED_GROUP 237s FAST5 group created by resquiggle command. Default: 237s RawGenomeCorrected_000 237s 237s Miscellaneous Arguments: 237s --quiet, -q Don't print status information. 237s --help, -h Print this help message and exit 237s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 237s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 237s [--corrected-group CORRECTED_GROUP] [--quiet] 237s [--help] 237s 237s Required Argument: 237s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 237s Directories containing fast5 files. 237s 237s Read Filtering Argument: 237s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 237s Filter reads based on observations per base percentile 237s thresholds. Format thresholds as "percentile:thresh 237s [pctl2:thresh2 ...]". For example to filter reads with 237s 99th pctl > 200 obs/base or max > 5k obs/base use 237s "99:200 100:5000". 237s 237s FAST5 Data Argument: 237s --corrected-group CORRECTED_GROUP 237s FAST5 group created by resquiggle command. Default: 237s RawGenomeCorrected_000 237s 237s Miscellaneous Arguments: 237s --quiet, -q Don't print status information. 237s --help, -h Print this help message and exit 237s usage: tombo filter level_coverage 237s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 237s [--percent-to-filter PERCENT_TO_FILTER] 237s [--corrected-group CORRECTED_GROUP] 237s [--quiet] [--help] 237s 237s Required Arguments: 237s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 237s Directories containing fast5 files. 237s 237s Read Filtering Argument: 237s --percent-to-filter PERCENT_TO_FILTER 237s Percentage of all reads to filter. Reads are randomly 237s selected weighted according to the approximate 237s coverage at the mapped genomic location. This can be 237s useful in modeling and testing. Default: 10.000000 237s 237s FAST5 Data Arguments: 237s --corrected-group CORRECTED_GROUP 237s FAST5 group created by resquiggle command. Default: 237s RawGenomeCorrected_000 237s 237s Miscellaneous Arguments: 237s --quiet, -q Don't print status information. 237s --help, -h Print this help message and exit 237s usage: tombo filter q_score 237s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 237s [--q-score Q_SCORE] 237s [--corrected-group CORRECTED_GROUP] 237s [--basecall-group BASECALL_GROUP] [--quiet] 237s [--help] 237s 237s Required Arguments: 237s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 237s Directories containing fast5 files. 237s 237s Read Filtering Argument: 237s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 237s Default: 7.000000 237s 237s FAST5 Data Arguments: 237s --corrected-group CORRECTED_GROUP 237s FAST5 group created by resquiggle command. Default: 237s RawGenomeCorrected_000 237s --basecall-group BASECALL_GROUP 237s FAST5 group obtain original basecalls (under Analyses 237s group). Default: Basecall_1D_000 237s 237s Miscellaneous Arguments: 237s --quiet, -q Don't print status information. 237s --help, -h Print this help message and exit 238s usage: tombo filter raw_signal_matching 238s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 238s --signal-matching-score SIGNAL_MATCHING_SCORE 238s [--corrected-group CORRECTED_GROUP] 238s [--quiet] [--help] 238s 238s Required Arguments: 238s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 238s Directories containing fast5 files. 238s --signal-matching-score SIGNAL_MATCHING_SCORE 238s Observed to expected signal matching score (higher 238s score indicates poor matching). Sample type defaults: 238s RNA : 2 || DNA : 1.1 238s 238s FAST5 Data Arguments: 238s --corrected-group CORRECTED_GROUP 238s FAST5 group created by resquiggle command. Default: 238s RawGenomeCorrected_000 238s 238s Miscellaneous Arguments: 238s --quiet, -q Don't print status information. 238s --help, -h Print this help message and exit 238s usage: tombo filter genome_locations 238s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 238s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 238s [--include-partial-overlap] 238s [--corrected-group CORRECTED_GROUP] 238s [--quiet] [--help] 238s 238s Required Arguments: 238s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 238s Directories containing fast5 files. 238s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 238s Filter out reads not falling completely within include 238s regions. Omit start and end coordinates to include an 238s entire chromosome/sequence record. Format regions as 238s "chrm[:start-end] [chrm2[:start2-end2] ...]". 238s 238s Filter Argument: 238s --include-partial-overlap 238s Include reads that partially overlap the specified 238s region. Default: Only include reads completely 238s contained in a specified region 238s 238s FAST5 Data Argument: 238s --corrected-group CORRECTED_GROUP 238s FAST5 group created by resquiggle command. Default: 238s RawGenomeCorrected_000 238s 238s Miscellaneous Arguments: 238s --quiet, -q Don't print status information. 238s --help, -h Print this help message and exit 238s usage: tombo detect_modifications de_novo 238s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 238s --statistics-file-basename STATISTICS_FILE_BASENAME 238s [--dna] [--rna] 238s [--fishers-method-context FISHERS_METHOD_CONTEXT] 238s [--minimum-test-reads MINIMUM_TEST_READS] 238s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 238s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 238s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 238s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 238s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 238s [--processes PROCESSES] 238s [--corrected-group CORRECTED_GROUP] 238s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 238s [--quiet] [--help] 238s 238s Required Argument: 238s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 238s Directories containing fast5 files. 238s --statistics-file-basename STATISTICS_FILE_BASENAME 238s File base name to save base by base statistics from 238s testing. Filenames will be [--statistics-file- 238s basename].[--alternate-bases]?.tombo.stats 238s 238s Comparison Model Arguments: 238s --dna Explicitly select canonical DNA model. Default: 238s Automatically determine from FAST5s 238s --rna Explicitly select canonical RNA model. Default: 238s Automatically determine from FAST5s 238s 238s Significance Test Arguments: 238s --fishers-method-context FISHERS_METHOD_CONTEXT 238s Number of context bases up and downstream over which 238s to compute Fisher's method combined p-values. Note: 238s Not applicable for alternative model likelihood ratio 238s tests. Default: 1. 238s --minimum-test-reads MINIMUM_TEST_READS 238s Number of reads required at a position to perform 238s significance testing or contribute to model 238s estimation. Default: 1 238s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 238s P-value threshold when computing fraction of 238s significant reads at each genomic position. If two 238s values are provided, statistics between these values 238s are not considered. Default thresholds: DNA:0.15-0.5 , 238s RNA:0.05-0.4 238s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 238s Dampen fraction modified estimates for low coverage 238s sites. Two parameters are unmodified and modified 238s pseudo read counts. This is equivalent to a beta prior 238s on the fraction estimate. Set to "0 0" to disable 238s dampened fraction estimation. Default: [2, 0] 238s 238s Output Argument: 238s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 238s Base for binary files containing per-read statistics 238s from statistical testing. Filenames will be [--per- 238s read-statistics-basename].[--alternate- 238s bases]?.tombo.per_read_stats 238s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 238s Number of the most significant sites to store for 238s faster access. If a longer list of most significant 238s sites is required the list must be re-computed from 238s all batches. Very large values can increase RAM usage. 238s Default: 100000 238s 238s Multiprocessing Arguments: 238s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 238s Size of regions over which to multiprocesses statistic 238s computation. For very deep samples a smaller value is 238s recommmended in order to control memory consumption. 238s Default: 10000 238s --processes PROCESSES 238s Number of processes. Default: 1 238s 238s FAST5 Data Arguments: 238s --corrected-group CORRECTED_GROUP 238s FAST5 group created by resquiggle command. Default: 238s RawGenomeCorrected_000 238s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 238s FAST5 subgroup(s) (under /Analyses/[--basecall- 238s group]/) containing basecalls and created within 238s [--corrected-group] containing re-squiggle results. 238s Default: ['BaseCalled_template'] 238s 238s Miscellaneous Arguments: 238s --quiet, -q Don't print status information. 238s --help, -h Print this help message and exit 238s usage: tombo detect_modifications alternative_model 238s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 238s [--statistics-file-basename STATISTICS_FILE_BASENAME] 238s [--alternate-bases {dam,5mC,6mA,CpG,dcm} [{dam,5mC,6mA,CpG,dcm} ...]] 238s [--print-available-models] 238s [--dna] [--rna] 238s [--minimum-test-reads MINIMUM_TEST_READS] 238s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 238s [--standard-log-likelihood-ratio] 238s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 238s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 238s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 238s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 238s [--processes PROCESSES] 238s [--corrected-group CORRECTED_GROUP] 238s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 238s [--quiet] [--help] 238s 238s Required Argument: 238s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 238s Directories containing fast5 files. 238s --statistics-file-basename STATISTICS_FILE_BASENAME 238s File base name to save base by base statistics from 238s testing. Filenames will be [--statistics-file- 238s basename].[--alternate-bases]?.tombo.stats 238s --alternate-bases {dam,5mC,6mA,CpG,dcm} [{dam,5mC,6mA,CpG,dcm} ...] 238s Default non-standard base model for testing (not 238s required if user created --alternate-model-filenames 238s is provided). 238s 238s Comparison Arguments: 238s --print-available-models 238s Print available alternative models and exit. 238s --dna Explicitly select canonical DNA model. Default: 238s Automatically determine from FAST5s 238s --rna Explicitly select canonical RNA model. Default: 238s Automatically determine from FAST5s 238s 238s Significance Test Arguments: 238s --minimum-test-reads MINIMUM_TEST_READS 238s Number of reads required at a position to perform 238s significance testing or contribute to model 238s estimation. Default: 1 238s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 238s Log likelihood ratio threshold when computing fraction 238s of significant reads at each genomic position. If two 238s values are provided, statistics between these values 238s are not considered. Default thresholds: DNA:-1.5-2.5 , 238s RNA:-2.5-2.5 238s --standard-log-likelihood-ratio 238s Use a standard log likelihood ratio (LLR) statistic. 238s Default is to use an outlier-robust LLR-like 238s statistic. Detail in full online documentation. 238s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 238s Dampen fraction modified estimates for low coverage 238s sites. Two parameters are unmodified and modified 238s pseudo read counts. This is equivalent to a beta prior 238s on the fraction estimate. Set to "0 0" to disable 238s dampened fraction estimation. Default: [2, 0] 238s 238s Output Argument: 238s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 238s Base for binary files containing per-read statistics 238s from statistical testing. Filenames will be [--per- 238s read-statistics-basename].[--alternate- 238s bases]?.tombo.per_read_stats 238s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 238s Number of the most significant sites to store for 238s faster access. If a longer list of most significant 238s sites is required the list must be re-computed from 238s all batches. Very large values can increase RAM usage. 238s Default: 100000 238s 238s Multiprocessing Arguments: 238s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 238s Size of regions over which to multiprocesses statistic 238s computation. For very deep samples a smaller value is 238s recommmended in order to control memory consumption. 238s Default: 10000 238s --processes PROCESSES 238s Number of processes. Default: 1 238s 238s FAST5 Data Arguments: 238s --corrected-group CORRECTED_GROUP 238s FAST5 group created by resquiggle command. Default: 238s RawGenomeCorrected_000 238s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 238s FAST5 subgroup(s) (under /Analyses/[--basecall- 238s group]/) containing basecalls and created within 238s [--corrected-group] containing re-squiggle results. 238s Default: ['BaseCalled_template'] 238s 238s Miscellaneous Arguments: 238s --quiet, -q Don't print status information. 238s --help, -h Print this help message and exit 238s usage: tombo detect_modifications model_sample_compare 238s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 238s --statistics-file-basename STATISTICS_FILE_BASENAME 238s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 238s [--sample-only-estimates] 238s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 238s [--dna] [--rna] 238s [--fishers-method-context FISHERS_METHOD_CONTEXT] 238s [--minimum-test-reads MINIMUM_TEST_READS] 238s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 238s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 238s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 238s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 238s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 238s [--processes PROCESSES] 238s [--corrected-group CORRECTED_GROUP] 238s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 238s [--quiet] [--help] 238s 238s Required Argument: 238s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 238s Directories containing fast5 files. 238s --statistics-file-basename STATISTICS_FILE_BASENAME 238s File base name to save base by base statistics from 238s testing. Filenames will be [--statistics-file- 238s basename].[--alternate-bases]?.tombo.stats 238s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 238s Set of directories containing fast5 files for control 238s reads, containing only canonical nucleotides. 238s 238s Model Prior Arguments: 238s --sample-only-estimates 238s Only use canonical sample to estimate expected signal 238s level and spread. Default: Use canonical model to 238s improve estimtates (esp. for low coverage regions) 238s using baysian posterior estimates. 238s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 238s Prior weights (one each for mean and spread) applied 238s to canonical base model for estimating posterior model 238s parameters for sample comparison. Default: [5, 40] 238s --dna Explicitly select canonical DNA model. Default: 238s Automatically determine from FAST5s 238s --rna Explicitly select canonical RNA model. Default: 238s Automatically determine from FAST5s 238s 238s Significance Test Arguments: 238s --fishers-method-context FISHERS_METHOD_CONTEXT 238s Number of context bases up and downstream over which 238s to compute Fisher's method combined p-values. Note: 238s Not applicable for alternative model likelihood ratio 238s tests. Default: 1. 238s --minimum-test-reads MINIMUM_TEST_READS 238s Number of reads required at a position to perform 238s significance testing or contribute to model 238s estimation. Default: 1 238s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 238s P-value threshold when computing fraction of 238s significant reads at each genomic position. If two 238s values are provided, statistics between these values 238s are not considered. Default thresholds: DNA:0.15-0.5 , 238s RNA:0.05-0.4 238s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 238s Dampen fraction modified estimates for low coverage 238s sites. Two parameters are unmodified and modified 238s pseudo read counts. This is equivalent to a beta prior 238s on the fraction estimate. Set to "0 0" to disable 238s dampened fraction estimation. Default: [2, 0] 238s 238s Output Argument: 238s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 238s Base for binary files containing per-read statistics 238s from statistical testing. Filenames will be [--per- 238s read-statistics-basename].[--alternate- 238s bases]?.tombo.per_read_stats 238s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 238s Number of the most significant sites to store for 238s faster access. If a longer list of most significant 238s sites is required the list must be re-computed from 238s all batches. Very large values can increase RAM usage. 238s Default: 100000 238s 238s Multiprocessing Arguments: 238s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 238s Size of regions over which to multiprocesses statistic 238s computation. For very deep samples a smaller value is 238s recommmended in order to control memory consumption. 238s Default: 10000 238s --processes PROCESSES 238s Number of processes. Default: 1 238s 238s FAST5 Data Arguments: 238s --corrected-group CORRECTED_GROUP 238s FAST5 group created by resquiggle command. Default: 238s RawGenomeCorrected_000 238s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 238s FAST5 subgroup(s) (under /Analyses/[--basecall- 238s group]/) containing basecalls and created within 238s [--corrected-group] containing re-squiggle results. 238s Default: ['BaseCalled_template'] 238s 238s Miscellaneous Arguments: 238s --quiet, -q Don't print status information. 238s --help, -h Print this help message and exit 238s usage: tombo detect_modifications level_sample_compare 238s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 238s --statistics-file-basename STATISTICS_FILE_BASENAME 238s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 238s [--fishers-method-context FISHERS_METHOD_CONTEXT] 238s [--minimum-test-reads MINIMUM_TEST_READS] 238s [--statistic-type {ks,u,t}] 238s [--store-p-value] 238s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 238s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 238s [--processes PROCESSES] 238s [--corrected-group CORRECTED_GROUP] 238s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 238s [--quiet] [--help] 238s 238s Required Argument: 238s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 238s Directories containing fast5 files. 238s --statistics-file-basename STATISTICS_FILE_BASENAME 238s File base name to save base by base statistics from 238s testing. Filenames will be [--statistics-file- 238s basename].[--alternate-bases]?.tombo.stats 238s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 238s Set of directories containing fast5 files for 238s alternate set of reads. 238s 238s Significance Test Arguments: 238s --fishers-method-context FISHERS_METHOD_CONTEXT 238s Number of context bases up and downstream over which 238s to compute Fisher's method combined p-values. Note: 238s Not applicable for alternative model likelihood ratio 238s tests. Default: 1. 238s --minimum-test-reads MINIMUM_TEST_READS 238s Number of reads required at a position to perform 238s significance testing or contribute to model 238s estimation. Default: 50 238s --statistic-type {ks,u,t} 238s Type of statistical test to apply. Default: "ks" 238s --store-p-value Store p-value instead of effect-size statistic. 238s Statistics are D-statistic (KS-test), deviation from 238s even common language effect size (u-test), and Cohen's 238s D (t-test). 238s 238s Output Argument: 238s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 238s Number of the most significant sites to store for 238s faster access. If a longer list of most significant 238s sites is required the list must be re-computed from 238s all batches. Very large values can increase RAM usage. 238s Default: 100000 238s 238s Multiprocessing Arguments: 238s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 238s Size of regions over which to multiprocesses statistic 238s computation. For very deep samples a smaller value is 238s recommmended in order to control memory consumption. 238s Default: 10000 238s --processes PROCESSES 238s Number of processes. Default: 1 238s 238s FAST5 Data Arguments: 238s --corrected-group CORRECTED_GROUP 238s FAST5 group created by resquiggle command. Default: 238s RawGenomeCorrected_000 238s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 238s FAST5 subgroup(s) (under /Analyses/[--basecall- 238s group]/) containing basecalls and created within 238s [--corrected-group] containing re-squiggle results. 238s Default: ['BaseCalled_template'] 238s 238s Miscellaneous Arguments: 238s --quiet, -q Don't print status information. 238s --help, -h Print this help message and exit 238s usage: tombo detect_modifications aggregate_per_read_stats 238s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 238s --statistics-filename STATISTICS_FILENAME 238s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 238s [--minimum-test-reads MINIMUM_TEST_READS] 238s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 238s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 238s [--processes PROCESSES] 238s [--corrected-group CORRECTED_GROUP] 238s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 238s [--quiet] [--help] 238s 238s Required Argument: 238s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 238s Binary file containing per-read statistics from 238s statistical testing. 238s --statistics-filename STATISTICS_FILENAME 238s File to save/load genomic base anchored statistics. 238s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 238s P-value or log likelihood ratio threshold when 238s computing fraction of significant reads at each 238s genomic position. If two values are provided, 238s statistics between these values are not considered. 238s 238s Significance Test Arguments: 238s --minimum-test-reads MINIMUM_TEST_READS 238s Number of reads required at a position to perform 238s significance testing or contribute to model 238s estimation. Default: 1 238s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 238s Dampen fraction modified estimates for low coverage 238s sites. Two parameters are unmodified and modified 238s pseudo read counts. This is equivalent to a beta prior 238s on the fraction estimate. Set to "0 0" to disable 238s dampened fraction estimation. Default: [2, 0] 238s 238s Output Argument: 238s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 238s Number of the most significant sites to store for 238s faster access. If a longer list of most significant 238s sites is required the list must be re-computed from 238s all batches. Very large values can increase RAM usage. 238s Default: 100000 238s 238s Multiprocessing Arguments: 238s --processes PROCESSES 238s Number of processes. Default: 1 238s 238s FAST5 Data Arguments: 238s --corrected-group CORRECTED_GROUP 238s FAST5 group created by resquiggle command. Default: 238s RawGenomeCorrected_000 238s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 238s FAST5 subgroup(s) (under /Analyses/[--basecall- 238s group]/) containing basecalls and created within 238s [--corrected-group] containing re-squiggle results. 238s Default: ['BaseCalled_template'] 238s 238s Miscellaneous Arguments: 238s --quiet, -q Don't print status information. 238s --help, -h Print this help message and exit 238s usage: tombo text_output browser_files 238s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 238s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 238s [--statistics-filename STATISTICS_FILENAME] 238s [--genome-fasta GENOME_FASTA] 238s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 238s [--browser-file-basename BROWSER_FILE_BASENAME] 238s [--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} ...]] 238s [--corrected-group CORRECTED_GROUP] 238s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 238s [--quiet] [--help] 238s 238s Data Arguments: 238s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 238s Directories containing fast5 files. 238s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 238s Set of directories containing fast5 files for control 238s reads, containing only canonical nucleotides. 238s --statistics-filename STATISTICS_FILENAME 238s File to save/load genomic base anchored statistics. 238s 238s Statistic Motif Filter Arguments: 238s --genome-fasta GENOME_FASTA 238s FASTA file used to re-squiggle. For faster sequence 238s access. 238s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 238s Ground truth, motif centered, modified base 238s descriptions for output filtering. Format descriptions 238s as: "motif:mod_pos:name". The mod_pos indicates the 238s modified base within the motif (1-based index). 238s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 238s output for identification of E. coli dam and dcm 238s methylation. 238s 238s Output Arguments: 238s --browser-file-basename BROWSER_FILE_BASENAME 238s Basename for output browser files. Two files (plus and 238s minus strand) will be produced for each --file-types 238s supplied. Filenames formatted as "[browser-file- 238s basename].[file- 238s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 238s Default: tombo_results 238s --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} ...] 238s Data types of genome browser files to produce. 238s Produced coverage files are in bedGraph format, while 238s all other file types will be in wiggle format 238s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 238s Default: "coverage" 238s 238s FAST5 Data Arguments: 238s --corrected-group CORRECTED_GROUP 238s FAST5 group created by resquiggle command. Default: 238s RawGenomeCorrected_000 238s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 238s FAST5 subgroup(s) (under /Analyses/[--basecall- 238s group]/) containing basecalls and created within 238s [--corrected-group] containing re-squiggle results. 238s Default: ['BaseCalled_template'] 238s 238s Miscellaneous Arguments: 238s --quiet, -q Don't print status information. 238s --help, -h Print this help message and exit 238s usage: tombo text_output signif_sequence_context 238s --statistics-filename STATISTICS_FILENAME 238s [--genome-fasta GENOME_FASTA] 238s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 238s [--num-regions NUM_REGIONS] 238s [--num-bases NUM_BASES] 238s [--sequences-filename SEQUENCES_FILENAME] 238s [--corrected-group CORRECTED_GROUP] 238s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 238s [--quiet] [--help] 238s 238s Required Argument: 238s --statistics-filename STATISTICS_FILENAME 238s File to save/load genomic base anchored statistics. 238s 238s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 238s --genome-fasta GENOME_FASTA 238s FASTA file used to re-squiggle. For faster sequence 238s access. 238s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 238s Directories containing fast5 files. 238s 238s Region Selection Arguments: 238s --num-regions NUM_REGIONS 238s Number of regions to plot. Default: 100 238s --num-bases NUM_BASES 238s Number of bases to plot/output. Default: 15 238s 238s Output Arguments: 238s --sequences-filename SEQUENCES_FILENAME 238s File for sequences from selected regions. Sequences 238s will be stored in FASTA format. Default: 238s tombo_results.significant_regions.fasta. 238s 238s FAST5 Data Arguments: 238s --corrected-group CORRECTED_GROUP 238s FAST5 group created by resquiggle command. Default: 238s RawGenomeCorrected_000 238s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 238s FAST5 subgroup(s) (under /Analyses/[--basecall- 238s group]/) containing basecalls and created within 238s [--corrected-group] containing re-squiggle results. 238s Default: ['BaseCalled_template'] 238s 238s Miscellaneous Arguments: 238s --quiet, -q Don't print status information. 238s --help, -h Print this help message and exit 239s usage: tombo plot max_coverage 239s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 239s [--plot-standard-model] 239s [--plot-alternate-model {dcm,dam,5mC,CpG,6mA}] 239s [--overplot-threshold OVERPLOT_THRESHOLD] 239s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 239s [--num-regions NUM_REGIONS] 239s [--num-bases NUM_BASES] 239s [--pdf-filename PDF_FILENAME] 239s [--corrected-group CORRECTED_GROUP] 239s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 239s [--quiet] [--help] 239s 239s Required Argument: 239s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s Directories containing fast5 files. 239s 239s Comparison Arguments: 239s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 239s Set of directories containing fast5 files for control 239s reads, containing only canonical nucleotides. 239s --plot-standard-model 239s Add default standard model distribution to the plot. 239s --plot-alternate-model {dcm,dam,5mC,CpG,6mA} 239s Add alternative model distribution to the plot. 239s 239s Overplotting Arguments: 239s --overplot-threshold OVERPLOT_THRESHOLD 239s Coverage level to trigger alternative plot type 239s instead of raw signal. Default: 50 239s --overplot-type {Downsample,Boxplot,Quantile,Density} 239s Plot type for regions with higher coverage. Default: 239s Downsample 239s 239s Plotting Region Arguments: 239s --num-regions NUM_REGIONS 239s Number of regions to plot. Default: 10 239s --num-bases NUM_BASES 239s Number of bases to plot/output. Default: 21 239s 239s Output Argument: 239s --pdf-filename PDF_FILENAME 239s PDF filename to store plot(s). Default: 239s tombo_results.max_coverage.pdf 239s 239s FAST5 Data Arguments: 239s --corrected-group CORRECTED_GROUP 239s FAST5 group created by resquiggle command. Default: 239s RawGenomeCorrected_000 239s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 239s FAST5 subgroup(s) (under /Analyses/[--basecall- 239s group]/) containing basecalls and created within 239s [--corrected-group] containing re-squiggle results. 239s Default: ['BaseCalled_template'] 239s 239s Miscellaneous Arguments: 239s --quiet, -q Don't print status information. 239s --help, -h Print this help message and exit 239s usage: tombo plot genome_locations 239s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 239s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 239s [--plot-standard-model] 239s [--plot-alternate-model {6mA,dcm,dam,5mC,CpG}] 239s [--overplot-threshold OVERPLOT_THRESHOLD] 239s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 239s [--num-bases NUM_BASES] 239s [--pdf-filename PDF_FILENAME] 239s [--corrected-group CORRECTED_GROUP] 239s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 239s [--quiet] [--help] 239s 239s Required Arguments: 239s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s Directories containing fast5 files. 239s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 239s Genomic locations at which to plot signal. Format 239s locations as "chrm:position[:strand] 239s [chrm2:position2[:strand2] ...]" (strand not 239s applicable for all applications) 239s 239s Comparison Arguments: 239s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 239s Set of directories containing fast5 files for control 239s reads, containing only canonical nucleotides. 239s --plot-standard-model 239s Add default standard model distribution to the plot. 239s --plot-alternate-model {6mA,dcm,dam,5mC,CpG} 239s Add alternative model distribution to the plot. 239s 239s Overplotting Arguments: 239s --overplot-threshold OVERPLOT_THRESHOLD 239s Coverage level to trigger alternative plot type 239s instead of raw signal. Default: 50 239s --overplot-type {Downsample,Boxplot,Quantile,Density} 239s Plot type for regions with higher coverage. Default: 239s Downsample 239s 239s Plotting Region Argument: 239s --num-bases NUM_BASES 239s Number of bases to plot/output. Default: 21 239s 239s Output Argument: 239s --pdf-filename PDF_FILENAME 239s PDF filename to store plot(s). Default: 239s tombo_results.genome_locations.pdf 239s 239s FAST5 Data Arguments: 239s --corrected-group CORRECTED_GROUP 239s FAST5 group created by resquiggle command. Default: 239s RawGenomeCorrected_000 239s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 239s FAST5 subgroup(s) (under /Analyses/[--basecall- 239s group]/) containing basecalls and created within 239s [--corrected-group] containing re-squiggle results. 239s Default: ['BaseCalled_template'] 239s 239s Miscellaneous Arguments: 239s --quiet, -q Don't print status information. 239s --help, -h Print this help message and exit 239s usage: tombo plot motif_centered 239s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s --motif MOTIF --genome-fasta GENOME_FASTA 239s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 239s [--plot-standard-model] 239s [--plot-alternate-model {CpG,5mC,6mA,dam,dcm}] 239s [--overplot-threshold OVERPLOT_THRESHOLD] 239s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 239s [--num-regions NUM_REGIONS] 239s [--num-bases NUM_BASES] [--deepest-coverage] 239s [--pdf-filename PDF_FILENAME] 239s [--corrected-group CORRECTED_GROUP] 239s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 239s [--quiet] [--help] 239s 239s Required Arguments: 239s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s Directories containing fast5 files. 239s --motif MOTIF Motif of interest at which to plot signal and 239s statsitics. Supports IUPAC single letter codes (use T 239s for RNA). 239s --genome-fasta GENOME_FASTA 239s FASTA file used to re-squiggle. For faster sequence 239s access. 239s 239s Comparison Arguments: 239s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 239s Set of directories containing fast5 files for control 239s reads, containing only canonical nucleotides. 239s --plot-standard-model 239s Add default standard model distribution to the plot. 239s --plot-alternate-model {CpG,5mC,6mA,dam,dcm} 239s Add alternative model distribution to the plot. 239s 239s Overplotting Arguments: 239s --overplot-threshold OVERPLOT_THRESHOLD 239s Coverage level to trigger alternative plot type 239s instead of raw signal. Default: 50 239s --overplot-type {Downsample,Boxplot,Quantile,Density} 239s Plot type for regions with higher coverage. Default: 239s Downsample 239s 239s Plotting Region Arguments: 239s --num-regions NUM_REGIONS 239s Number of regions to plot. Default: 10 239s --num-bases NUM_BASES 239s Number of bases to plot/output. Default: 21 239s --deepest-coverage Plot the deepest coverage regions. 239s 239s Output Argument: 239s --pdf-filename PDF_FILENAME 239s PDF filename to store plot(s). Default: 239s tombo_results.motif_centered.pdf 239s 239s FAST5 Data Arguments: 239s --corrected-group CORRECTED_GROUP 239s FAST5 group created by resquiggle command. Default: 239s RawGenomeCorrected_000 239s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 239s FAST5 subgroup(s) (under /Analyses/[--basecall- 239s group]/) containing basecalls and created within 239s [--corrected-group] containing re-squiggle results. 239s Default: ['BaseCalled_template'] 239s 239s Miscellaneous Arguments: 239s --quiet, -q Don't print status information. 239s --help, -h Print this help message and exit 239s usage: tombo plot max_difference 239s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 239s [--overplot-threshold OVERPLOT_THRESHOLD] 239s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 239s [--num-regions NUM_REGIONS] 239s [--num-bases NUM_BASES] 239s [--pdf-filename PDF_FILENAME] 239s [--sequences-filename SEQUENCES_FILENAME] 239s [--corrected-group CORRECTED_GROUP] 239s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 239s [--quiet] [--help] 239s 239s Required Arguments: 239s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s Directories containing fast5 files. 239s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 239s Set of directories containing fast5 files for control 239s reads, containing only canonical nucleotides. 239s 239s Overplotting Arguments: 239s --overplot-threshold OVERPLOT_THRESHOLD 239s Coverage level to trigger alternative plot type 239s instead of raw signal. Default: 50 239s --overplot-type {Downsample,Boxplot,Quantile,Density} 239s Plot type for regions with higher coverage. Default: 239s Downsample 239s 239s Plotting Region Arguments: 239s --num-regions NUM_REGIONS 239s Number of regions to plot. Default: 10 239s --num-bases NUM_BASES 239s Number of bases to plot/output. Default: 21 239s 239s Output Arguments: 239s --pdf-filename PDF_FILENAME 239s PDF filename to store plot(s). Default: 239s tombo_results.max_difference.pdf 239s --sequences-filename SEQUENCES_FILENAME 239s File for sequences from selected regions. Sequences 239s will be stored in FASTA format. Default: None. 239s 239s FAST5 Data Arguments: 239s --corrected-group CORRECTED_GROUP 239s FAST5 group created by resquiggle command. Default: 239s RawGenomeCorrected_000 239s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 239s FAST5 subgroup(s) (under /Analyses/[--basecall- 239s group]/) containing basecalls and created within 239s [--corrected-group] containing re-squiggle results. 239s Default: ['BaseCalled_template'] 239s 239s Miscellaneous Arguments: 239s --quiet, -q Don't print status information. 239s --help, -h Print this help message and exit 239s usage: tombo plot most_significant 239s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s --statistics-filename STATISTICS_FILENAME 239s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 239s [--plot-standard-model] 239s [--plot-alternate-model {CpG,dam,6mA,5mC,dcm}] 239s [--overplot-threshold OVERPLOT_THRESHOLD] 239s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 239s [--num-regions NUM_REGIONS] 239s [--num-bases NUM_BASES] 239s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 239s [--pdf-filename PDF_FILENAME] 239s [--sequences-filename SEQUENCES_FILENAME] 239s [--corrected-group CORRECTED_GROUP] 239s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 239s [--quiet] [--help] 239s 239s Required Arguments: 239s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s Directories containing fast5 files. 239s --statistics-filename STATISTICS_FILENAME 239s File to save/load genomic base anchored statistics. 239s 239s Comparison Arguments: 239s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 239s Set of directories containing fast5 files for control 239s reads, containing only canonical nucleotides. 239s --plot-standard-model 239s Add default standard model distribution to the plot. 239s --plot-alternate-model {CpG,dam,6mA,5mC,dcm} 239s Add alternative model distribution to the plot. 239s 239s Overplotting Arguments: 239s --overplot-threshold OVERPLOT_THRESHOLD 239s Coverage level to trigger alternative plot type 239s instead of raw signal. Default: 50 239s --overplot-type {Downsample,Boxplot,Quantile,Density} 239s Plot type for regions with higher coverage. Default: 239s Downsample 239s 239s Plotting Region Arguments: 239s --num-regions NUM_REGIONS 239s Number of regions to plot. Default: 10 239s --num-bases NUM_BASES 239s Number of bases to plot/output. Default: 21 239s 239s Statistical Argument: 239s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 239s Dampen fraction modified estimates for low coverage 239s sites. Two parameters are unmodified and modified 239s pseudo read counts. This is equivalent to a beta prior 239s on the fraction estimate. Set to "0 0" to disable 239s dampened fraction estimation. Default: [2, 0] 239s 239s Output Arguments: 239s --pdf-filename PDF_FILENAME 239s PDF filename to store plot(s). Default: 239s tombo_results.significant_difference.pdf 239s --sequences-filename SEQUENCES_FILENAME 239s File for sequences from selected regions. Sequences 239s will be stored in FASTA format. Default: None. 239s 239s FAST5 Data Arguments: 239s --corrected-group CORRECTED_GROUP 239s FAST5 group created by resquiggle command. Default: 239s RawGenomeCorrected_000 239s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 239s FAST5 subgroup(s) (under /Analyses/[--basecall- 239s group]/) containing basecalls and created within 239s [--corrected-group] containing re-squiggle results. 239s Default: ['BaseCalled_template'] 239s 239s Miscellaneous Arguments: 239s --quiet, -q Don't print status information. 239s --help, -h Print this help message and exit 239s usage: tombo plot motif_with_stats 239s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s --motif MOTIF 239s --statistics-filename STATISTICS_FILENAME 239s --genome-fasta GENOME_FASTA 239s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 239s [--plot-standard-model] 239s [--plot-alternate-model {dcm,5mC,6mA,dam,CpG}] 239s [--overplot-threshold OVERPLOT_THRESHOLD] 239s [--num-regions NUM_REGIONS] 239s [--num-context NUM_CONTEXT] 239s [--num-statistics NUM_STATISTICS] 239s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 239s [--pdf-filename PDF_FILENAME] 239s [--corrected-group CORRECTED_GROUP] 239s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 239s [--quiet] [--help] 239s 239s Required Arguments: 239s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s Directories containing fast5 files. 239s --motif MOTIF Motif of interest at which to plot signal and 239s statsitics. Supports IUPAC single letter codes (use T 239s for RNA). 239s --statistics-filename STATISTICS_FILENAME 239s File to save/load genomic base anchored statistics. 239s --genome-fasta GENOME_FASTA 239s FASTA file used to re-squiggle. For faster sequence 239s access. 239s 239s Comparison Arguments: 239s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 239s Set of directories containing fast5 files for control 239s reads, containing only canonical nucleotides. 239s --plot-standard-model 239s Add default standard model distribution to the plot. 239s --plot-alternate-model {dcm,5mC,6mA,dam,CpG} 239s Add alternative model distribution to the plot. 239s 239s Overplotting Argument: 239s --overplot-threshold OVERPLOT_THRESHOLD 239s Coverage level to trigger alternative plot type 239s instead of raw signal. Default: 50 239s 239s Plotting Region Arguments: 239s --num-regions NUM_REGIONS 239s Number of regions to plot. Default: 3 239s --num-context NUM_CONTEXT 239s Number of context bases around motif. Default: 5 239s --num-statistics NUM_STATISTICS 239s Number of motif centered regions to include in 239s statistic distributions. Default: 200 239s 239s Statistical Argument: 239s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 239s Dampen fraction modified estimates for low coverage 239s sites. Two parameters are unmodified and modified 239s pseudo read counts. This is equivalent to a beta prior 239s on the fraction estimate. Set to "0 0" to disable 239s dampened fraction estimation. Default: [2, 0] 239s 239s Output Argument: 239s --pdf-filename PDF_FILENAME 239s PDF filename to store plot(s). Default: 239s tombo_results.motif_statistics.pdf 239s 239s FAST5 Data Arguments: 239s --corrected-group CORRECTED_GROUP 239s FAST5 group created by resquiggle command. Default: 239s RawGenomeCorrected_000 239s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 239s FAST5 subgroup(s) (under /Analyses/[--basecall- 239s group]/) containing basecalls and created within 239s [--corrected-group] containing re-squiggle results. 239s Default: ['BaseCalled_template'] 239s 239s Miscellaneous Arguments: 239s --quiet, -q Don't print status information. 239s --help, -h Print this help message and exit 239s usage: tombo plot per_read 239s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 239s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 239s [--genome-fasta GENOME_FASTA] 239s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 239s [--num-reads NUM_READS] [--num-bases NUM_BASES] 239s [--box-center] [--pdf-filename PDF_FILENAME] 239s [--corrected-group CORRECTED_GROUP] 239s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 239s [--quiet] [--help] 239s 239s Required Arguments: 239s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 239s Genomic locations at which to plot signal. Format 239s locations as "chrm:position[:strand] 239s [chrm2:position2[:strand2] ...]" (strand not 239s applicable for all applications) 239s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 239s Binary file containing per-read statistics from 239s statistical testing. 239s 239s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 239s --genome-fasta GENOME_FASTA 239s FASTA file used to re-squiggle. For faster sequence 239s access. 239s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s Directories containing fast5 files. 239s 239s Plotting Region Arguments: 239s --num-reads NUM_READS 239s Number of reads to plot. Default: 100 239s --num-bases NUM_BASES 239s Number of bases to plot/output. Default: 51 239s --box-center Plot a box around the central base. 239s 239s Output Argument: 239s --pdf-filename PDF_FILENAME 239s PDF filename to store plot(s). Default: 239s tombo_results.per_read_stats.pdf 239s 239s FAST5 Data Arguments: 239s --corrected-group CORRECTED_GROUP 239s FAST5 group created by resquiggle command. Default: 239s RawGenomeCorrected_000 239s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 239s FAST5 subgroup(s) (under /Analyses/[--basecall- 239s group]/) containing basecalls and created within 239s [--corrected-group] containing re-squiggle results. 239s Default: ['BaseCalled_template'] 239s 239s Miscellaneous Arguments: 239s --quiet, -q Don't print status information. 239s --help, -h Print this help message and exit 239s usage: tombo plot roc 239s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 239s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 239s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 239s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 239s [--genome-fasta GENOME_FASTA] 239s [--pdf-filename PDF_FILENAME] 239s [--statistics-per-block STATISTICS_PER_BLOCK] 239s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 239s [--quiet] [--help] 239s 239s Required Argument: 239s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 239s Files to load genomic base anchored statistics. 239s 239s Ground Truth Arguments (provide bed files or motifs): 239s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 239s Modification description and bed format files 239s containing single base locations of ground truth 239s modified sites. Bed files should contain 6 fields 239s including strand. Format descriptions as 239s "mod_name:locs.bed". Example: "CpG 239s bisulfite":bisulfite_locs.bed 239s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 239s Bed format files containing single base locations of 239s ground truth unmodified sites. Bed files should 239s contain 6 fields including strand. 239s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 239s Ground truth, motif centered, modified base 239s descriptions for computing ROC and PR curves. Each 239s statistics file is associated with a set of motif 239s descriptions. Format descriptions as: 239s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 239s mod_pos indicates the alternate-base within the motif 239s (1-based index). Example: CCWGG:2:"dcm 239s 5mC"::GATC:2:"dam 6mA" would assess the performance of 239s a single Tombo statistics file for identification of 239s E. coli dam and dcm methylation. 239s --genome-fasta GENOME_FASTA 239s FASTA file used to re-squiggle. For faster sequence 239s access. 239s 239s Output Arguments: 239s --pdf-filename PDF_FILENAME 239s PDF filename to store plot(s). Default: 239s tombo_results.roc.pdf 239s 239s Down-sampling Arguments: 239s --statistics-per-block STATISTICS_PER_BLOCK 239s Number of randomly selected per-read, per-base 239s statistics to extract from each genomic block for 239s plotting. Default: Include all stats 239s --total-statistics-limit TOTAL_STATISTICS_LIMIT 239s Total per-read statistics to be extracted for 239s plotting. Avoids memory overflow for large runs. 239s Default: 5000000 239s 239s Miscellaneous Arguments: 239s --quiet, -q Don't print status information. 239s --help, -h Print this help message and exit 239s usage: tombo plot per_read_roc 239s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 239s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 239s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 239s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 239s [--genome-fasta GENOME_FASTA] 239s [--statistics-per-block STATISTICS_PER_BLOCK] 239s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 239s [--pdf-filename PDF_FILENAME] [--quiet] 239s [--help] 239s 239s Required Argument: 239s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 239s Binary files containing per-read statistics from 239s statistical testing. 239s 239s Ground Truth Arguments (provide bed files or motifs): 239s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 239s Modification description and bed format files 239s containing single base locations of ground truth 239s modified sites. Bed files should contain 6 fields 239s including strand. Format descriptions as 239s "mod_name:locs.bed". Example: "CpG 239s bisulfite":bisulfite_locs.bed 239s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 239s Bed format files containing single base locations of 239s ground truth unmodified sites. Bed files should 239s contain 6 fields including strand. 239s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 239s Ground truth, motif centered, modified base 239s descriptions for computing ROC and PR curves. Each 239s statistics file is associated with a set of motif 239s descriptions. Format descriptions as: 239s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 239s mod_pos indicates the alternate-base within the motif 239s (1-based index). Example: CCWGG:2:"dcm 239s 5mC"::GATC:2:"dam 6mA" would assess the performance of 239s a single Tombo statistics file for identification of 239s E. coli dam and dcm methylation. 239s --genome-fasta GENOME_FASTA 239s FASTA file used to re-squiggle. For faster sequence 239s access. 239s 239s Down-sampling Arguments: 239s --statistics-per-block STATISTICS_PER_BLOCK 239s Number of randomly selected per-read, per-base 239s statistics to extract from each genomic block for 239s plotting. Default: 100000 239s --total-statistics-limit TOTAL_STATISTICS_LIMIT 239s Total per-read statistics to be extracted for 239s plotting. Avoids memory overflow for large runs. 239s Default: 5000000 239s 239s Output Arguments: 239s --pdf-filename PDF_FILENAME 239s PDF filename to store plot(s). Default: 239s tombo_results.per_reads_roc.pdf 239s 239s Miscellaneous Arguments: 239s --quiet, -q Don't print status information. 239s --help, -h Print this help message and exit 239s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s [--upstream-bases {0,1,2,3,4}] 239s [--downstream-bases {0,1,2,3,4}] [--read-mean] 239s [--num-kmer-threshold NUM_KMER_THRESHOLD] 239s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 239s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 239s [--corrected-group CORRECTED_GROUP] 239s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 239s [--quiet] [--help] 239s 239s Required Argument: 239s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 239s Directories containing fast5 files. 239s 239s Data Processing Arguments: 239s --upstream-bases {0,1,2,3,4} 239s Upstream bases in k-mer. Default: 1 239s --downstream-bases {0,1,2,3,4} 239s Downstream bases in k-mer. Default: 2 239s --read-mean Plot k-mer means across whole reads as opposed to 239s individual k-mer event levels. 239s --num-kmer-threshold NUM_KMER_THRESHOLD 239s Observations of each k-mer required to include a read 239s in read level averages. Default: 1 239s 239s Plotting Region Arguments: 239s --num-reads NUM_READS 239s Number of reads to plot. Default: 100 239s 239s Output Arguments: 239s --pdf-filename PDF_FILENAME 239s PDF filename to store plot(s). Default: 239s tombo_results.kmer_distribution.pdf 239s --r-data-filename R_DATA_FILENAME 239s Filename to save R data structure. Default: Don't save 239s --dont-plot Don't plot result. Useful to produce only R data file. 239s 239s FAST5 Data Arguments: 239s --corrected-group CORRECTED_GROUP 239s FAST5 group created by resquiggle command. Default: 239s RawGenomeCorrected_000 239s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 239s FAST5 subgroup(s) (under /Analyses/[--basecall- 239s group]/) containing basecalls and created within 239s [--corrected-group] containing re-squiggle results. 239s Default: ['BaseCalled_template'] 239s 239s Miscellaneous Arguments: 239s --quiet, -q Don't print status information. 239s --help, -h Print this help message and exit 240s usage: tombo plot cluster_most_significant 240s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 240s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 240s --statistics-filename STATISTICS_FILENAME 240s [--genome-fasta GENOME_FASTA] 240s [--processes PROCESSES] 240s [--num-regions NUM_REGIONS] 240s [--num-bases NUM_BASES] 240s [--slide-span SLIDE_SPAN] 240s [--pdf-filename PDF_FILENAME] 240s [--r-data-filename R_DATA_FILENAME] 240s [--corrected-group CORRECTED_GROUP] 240s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 240s [--quiet] [--help] 240s 240s Required Arguments: 240s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 240s Directories containing fast5 files. 240s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 240s Set of directories containing fast5 files for control 240s reads, containing only canonical nucleotides. 240s --statistics-filename STATISTICS_FILENAME 240s File to save/load genomic base anchored statistics. 240s 240s FASTA Sequence Argument: 240s --genome-fasta GENOME_FASTA 240s FASTA file used to re-squiggle. For faster sequence 240s access. 240s 240s Multiprocessing Argument: 240s --processes PROCESSES 240s Number of processes. Default: 1 240s 240s Plotting Region Arguments: 240s --num-regions NUM_REGIONS 240s Number of regions to plot. Default: 10 240s --num-bases NUM_BASES 240s Number of bases to plot/output. Default: 21 240s --slide-span SLIDE_SPAN 240s Number of bases offset over which to search when 240s computing distances for signal cluster plotting. 240s Default: 0 (exact position) 240s 240s Output Arguments: 240s --pdf-filename PDF_FILENAME 240s PDF filename to store plot(s). Default: 240s tombo_results.signal_clusters.pdf 240s --r-data-filename R_DATA_FILENAME 240s Filename to save R data structure. Default: Don't save 240s 240s FAST5 Data Arguments: 240s --corrected-group CORRECTED_GROUP 240s FAST5 group created by resquiggle command. Default: 240s RawGenomeCorrected_000 240s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 240s FAST5 subgroup(s) (under /Analyses/[--basecall- 240s group]/) containing basecalls and created within 240s [--corrected-group] containing re-squiggle results. 240s Default: ['BaseCalled_template'] 240s 240s Miscellaneous Arguments: 240s --quiet, -q Don't print status information. 240s --help, -h Print this help message and exit 240s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 240s 240s Required Arguments: 240s fast5s_basedir Directory containing fast5 files. All files ending in 240s "fast5" found recursively within this base directory will be 240s processed. 240s 240s Miscellaneous Arguments: 240s --quiet, -q Don't print status information. 240s --help, -h Print this help message and exit 240s usage: tombo build_model event_resquiggle 240s [--minimap2-executable MINIMAP2_EXECUTABLE] 240s [--minimap2-index MINIMAP2_INDEX] 240s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 240s [--graphmap-executable GRAPHMAP_EXECUTABLE] 240s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 240s [--normalization-type {median,pA,pA_raw,none}] 240s [--pore-model-filename PORE_MODEL_FILENAME] 240s [--outlier-threshold OUTLIER_THRESHOLD] 240s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 240s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 240s [--timeout TIMEOUT] 240s [--cpts-limit CPTS_LIMIT] 240s [--skip-index] [--overwrite] 240s [--failed-reads-filename FAILED_READS_FILENAME] 240s [--include-event-stdev] 240s [--corrected-group CORRECTED_GROUP] 240s [--basecall-group BASECALL_GROUP] 240s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 240s [--processes PROCESSES] 240s [--align-processes ALIGN_PROCESSES] 240s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 240s [--resquiggle-processes RESQUIGGLE_PROCESSES] 240s [--quiet] [--help] 240s fast5s_basedir reference_fasta 240s 240s Required Arguments: 240s fast5s_basedir Directory containing fast5 files. All files ending in 240s "fast5" found recursively within this base directory 240s will be processed. 240s reference_fasta Reference genome/transcriptome FASTA file for mapping. 240s 240s Mapper Arguments (One mapper is required): 240s --minimap2-executable MINIMAP2_EXECUTABLE 240s Path to minimap2 executable. 240s --minimap2-index MINIMAP2_INDEX 240s Path to minimap2 index (with map-ont preset) file 240s corresponding to the [genome_fasta] provided. 240s --bwa-mem-executable BWA_MEM_EXECUTABLE 240s Path to bwa-mem executable. 240s --graphmap-executable GRAPHMAP_EXECUTABLE 240s Path to graphmap executable. 240s --alignment-batch-size ALIGNMENT_BATCH_SIZE 240s Number of reads included in each alignment call. Note: 240s A new system mapping call is made for each batch 240s (including loading of the genome), so it is advised to 240s use larger values for larger genomes. Default: 1000 240s 240s Signal Processing Arguments: 240s --normalization-type {median,pA,pA_raw,none} 240s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 240s as in the ONT events (using offset, range and 240s digitization), "pA": k-mer-based correction for pA 240s drift as in nanopolish (requires [--pore-model- 240s filename]), "median": median and MAD from raw signal. 240s Default: median 240s --pore-model-filename PORE_MODEL_FILENAME 240s File containing kmer model parameters (level_mean and 240s level_stdv) used in order to compute kmer-based 240s corrected pA values. E.g. https://github.com/jts/nanop 240s olish/blob/master/etc/r9- 240s models/template_median68pA.5mers.model 240s --outlier-threshold OUTLIER_THRESHOLD 240s Windosrize the signal at this number of scale values. 240s Negative value disables outlier clipping. Default: 240s 5.000000 240s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 240s Specify the 2 parameters for segmentation 1) running 240s neighboring windows width 2) minimum raw observations 240s per genomic base. Sample type defaults: RNA : 12 6 || 240s DNA : 5 3 240s 240s Read Filtering Arguments: 240s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 240s Filter reads based on observations per base percentile 240s thresholds. Format thresholds as "percentile:thresh 240s [pctl2:thresh2 ...]". For example to filter reads with 240s 99th pctl > 200 obs/base or max > 5k obs/base use 240s "99:200 100:5000". 240s --timeout TIMEOUT Timeout in seconds for processing a single read. 240s Default: No timeout. 240s --cpts-limit CPTS_LIMIT 240s Maximum number of changepoints to find within a single 240s indel group. Default: No limit. 240s 240s Input/Output Arguments: 240s --skip-index Skip creation of tombo index. This drastically slows 240s downstream tombo commands. Default stores tombo index 240s named ".[--fast5-basedir].[--corrected- 240s group].tombo.index" to be loaded automatically for 240s downstream commands. 240s --overwrite Overwrite previous corrected group in FAST5 files. 240s Note: only effects --corrected-group or --new- 240s corrected-group. 240s --failed-reads-filename FAILED_READS_FILENAME 240s Output failed read filenames with assoicated error. 240s Default: Do not store failed reads. 240s --include-event-stdev 240s Include corrected event standard deviation in output 240s FAST5 data. 240s 240s FAST5 Data Arguments: 240s --corrected-group CORRECTED_GROUP 240s FAST5 group created by resquiggle command. Default: 240s RawGenomeCorrected_000 240s --basecall-group BASECALL_GROUP 240s FAST5 group obtain original basecalls (under Analyses 240s group). Default: Basecall_1D_000 240s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 240s FAST5 subgroup(s) (under /Analyses/[--basecall- 240s group]/) containing basecalls and created within 240s [--corrected-group] containing re-squiggle results. 240s Default: ['BaseCalled_template'] 240s 240s Multiprocessing Arguments: 240s --processes PROCESSES 240s Number of processes. Default: 2 240s --align-processes ALIGN_PROCESSES 240s Number of processes to use for parsing and aligning 240s original basecalls. Each process will independently 240s load the genome into memory, so use caution with 240s larger genomes (e.g. human). Default: 1 240s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 240s Number of threads to use for aligner system call. 240s Default: [--processes] / (2 * [--align-processes)] 240s --resquiggle-processes RESQUIGGLE_PROCESSES 240s Number of processes to use for resquiggle algorithm. 240s Default: [--processes] / 2 240s 240s Miscellaneous Arguments: 240s --quiet, -q Don't print status information. 240s --help, -h Print this help message and exit 240s usage: tombo build_model estimate_reference 240s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 240s --tombo-model-filename TOMBO_MODEL_FILENAME 240s [--estimate-mean] 240s [--kmer-specific-sd] 240s [--upstream-bases {0,1,2,3,4}] 240s [--downstream-bases {0,1,2,3,4}] 240s [--minimum-test-reads MINIMUM_TEST_READS] 240s [--coverage-threshold COVERAGE_THRESHOLD] 240s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 240s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 240s [--processes PROCESSES] 240s [--corrected-group CORRECTED_GROUP] 240s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 240s [--quiet] [--help] 240s 240s Required Arguments: 240s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 240s Directories containing fast5 files. 240s --tombo-model-filename TOMBO_MODEL_FILENAME 240s Filename to save Tombo model. 240s 240s Modeling Arguments: 240s --estimate-mean Use the mean instead of median for model level 240s estimation. Note: This can cause poor fits due to 240s outliers 240s --kmer-specific-sd Estimate standard deviation for each k-mers 240s individually. 240s --upstream-bases {0,1,2,3,4} 240s Upstream bases in k-mer. Default: 1 240s --downstream-bases {0,1,2,3,4} 240s Downstream bases in k-mer. Default: 2 240s 240s Filtering Arguments: 240s --minimum-test-reads MINIMUM_TEST_READS 240s Number of reads required at a position to perform 240s significance testing or contribute to model 240s estimation. Default: 10 240s --coverage-threshold COVERAGE_THRESHOLD 240s Maximum mean coverage per region when estimating k-mer 240s model (limits compute time for deep samples). Default: 240s 100 240s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 240s Number of each k-mer observations required in order to 240s produce a reference (genomic locations for standard 240s reference and per-read for alternative reference). 240s Default: 5 240s 240s Multiprocessing Arguments: 240s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 240s Size of regions over which to multiprocesses statistic 240s computation. For very deep samples a smaller value is 240s recommmended in order to control memory consumption. 240s Default: 10000 240s --processes PROCESSES 240s Number of processes. Default: 1 240s 240s FAST5 Data Arguments: 240s --corrected-group CORRECTED_GROUP 240s FAST5 group created by resquiggle command. Default: 240s RawGenomeCorrected_000 240s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 240s FAST5 subgroup(s) (under /Analyses/[--basecall- 240s group]/) containing basecalls and created within 240s [--corrected-group] containing re-squiggle results. 240s Default: ['BaseCalled_template'] 240s 240s Miscellaneous Arguments: 240s --quiet, -q Don't print status information. 240s --help, -h Print this help message and exit 240s usage: tombo build_model estimate_alt_reference 240s --alternate-model-filename ALTERNATE_MODEL_FILENAME 240s --alternate-model-name ALTERNATE_MODEL_NAME 240s --alternate-model-base {A,C,G,T} 240s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 240s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 240s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 240s [--control-density-filename CONTROL_DENSITY_FILENAME] 240s [--dna] [--rna] 240s [--tombo-model-filename TOMBO_MODEL_FILENAME] 240s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 240s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 240s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 240s [--save-density-basename SAVE_DENSITY_BASENAME] 240s [--processes PROCESSES] 240s [--corrected-group CORRECTED_GROUP] 240s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 240s [--quiet] [--help] 240s 240s Required Arguments: 240s --alternate-model-filename ALTERNATE_MODEL_FILENAME 240s Tombo model for alternative likelihood ratio 240s significance testing. 240s --alternate-model-name ALTERNATE_MODEL_NAME 240s A short name to associate with this alternate model 240s (e.g. 5mC, 6mA, etc.). This text will be included in 240s output filenames when this model is used for testing. 240s --alternate-model-base {A,C,G,T} 240s Non-standard base is an alternative to this base. 240s 240s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 240s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 240s Directories containing fast5 files. 240s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 240s Set of directories containing fast5 files for control 240s reads, containing only canonical nucleotides. 240s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 240s File containing k-mer level kernel density estimates 240s for the alternative sample saved using --save-density- 240s basename. 240s --control-density-filename CONTROL_DENSITY_FILENAME 240s File containing k-mer level kernel density estimates 240s for the control sample saved using --save-density- 240s basename. 240s 240s Standard Model Arguments: 240s --dna Explicitly select canonical DNA model. Default: 240s Automatically determine from FAST5s 240s --rna Explicitly select canonical RNA model. Default: 240s Automatically determine from FAST5s 240s --tombo-model-filename TOMBO_MODEL_FILENAME 240s Tombo model filename. If no file is provided, the 240s default DNA or RNA Tombo model will be used. 240s 240s Model Fitting Arguments: 240s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 240s When esitmating the alternative base incorporation 240s rate, this percent of k-mers are assumed to have 240s significantly shifted signal so the alternative 240s distribution minimally overlaps the standard base 240s distribution. Default: 5.000000 240s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 240s Bandwidth applied when performing Gaussian kernal 240s density esitmation on standard and alternative base 240s signal distributions. Default: 0.050000 240s 240s Filtering Argument: 240s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 240s Number of each k-mer observations required in order to 240s produce a reference (genomic locations for standard 240s reference and per-read for alternative reference). 240s Default: 1000 240s 240s Output Argument: 240s --save-density-basename SAVE_DENSITY_BASENAME 240s Basename to save alternative model estimation density 240s estimation information. See scripts/debug_est_alt.R 240s for info use example. Default: Don't save. 240s 240s Multiprocessing Arguments: 240s --processes PROCESSES 240s Number of processes. Default: 1 240s 240s FAST5 Data Arguments: 240s --corrected-group CORRECTED_GROUP 240s FAST5 group created by resquiggle command. Default: 240s RawGenomeCorrected_000 240s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 240s FAST5 subgroup(s) (under /Analyses/[--basecall- 240s group]/) containing basecalls and created within 240s [--corrected-group] containing re-squiggle results. 240s Default: ['BaseCalled_template'] 240s 240s Miscellaneous Arguments: 240s --quiet, -q Don't print status information. 240s --help, -h Print this help message and exit 240s This test only tests the help system 240s There is an extensive test in 240s 240s tombo/tests/shell_tests.sh 240s 240s but this requires to download larger data 240s sets which is not done for the moment. 240s autopkgtest [12:48:12]: test run-unit-test: -----------------------] 241s autopkgtest [12:48:13]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 241s run-unit-test PASS 242s autopkgtest [12:48:14]: @@@@@@@@@@@@@@@@@@@@ summary 242s run-unit-test PASS 248s nova [W] Using flock in prodstack6-arm64 248s Creating nova instance adt-plucky-arm64-tombo-20250219-124412-juju-7f2275-prod-proposed-migration-environment-2-6d5cc333-7d7a-4ec6-9919-0aa78295ba70 from image adt/ubuntu-plucky-arm64-server-20250219.img (UUID 02c92adb-9d9d-4b0e-b071-488d8ee6210f)... 248s nova [W] Timed out waiting for 9823b090-93d3-4eaa-8fb3-6d46d62156e2 to get deleted.