0s autopkgtest [13:05:47]: starting date and time: 2025-02-19 13:05:47+0000 0s autopkgtest [13:05:47]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:05:47]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.z0trak0p/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-2.secgroup --name adt-plucky-s390x-tombo-20250219-130547-juju-7f2275-prod-proposed-migration-environment-20-2777983d-1f01-4d8e-92af-c6db160edaf3 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -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/ 115s autopkgtest [13:07:42]: testbed dpkg architecture: s390x 115s autopkgtest [13:07:42]: testbed apt version: 2.9.30 116s autopkgtest [13:07:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 116s autopkgtest [13:07:43]: testbed release detected to be: None 117s autopkgtest [13:07:44]: updating testbed package index (apt update) 117s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 117s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 117s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 117s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 117s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 117s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 117s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 117s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [744 kB] 118s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [104 kB] 118s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x Packages [760 B] 118s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [653 kB] 118s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [4900 B] 118s Fetched 1711 kB in 1s (1810 kB/s) 118s Reading package lists... 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Calculating upgrade... 119s The following packages were automatically installed and are no longer required: 119s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 119s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 119s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 119s linux-tools-6.11.0-8-generic 119s Use 'sudo apt autoremove' to remove them. 119s The following packages will be upgraded: 119s iproute2 libgpgme11t64 liblsof0 libp11-kit0 lsof sysvinit-utils 119s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Need to get 1982 kB of archives. 119s After this operation, 22.5 kB of additional disk space will be used. 119s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x sysvinit-utils s390x 3.14-1ubuntu1 [36.0 kB] 120s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x iproute2 s390x 6.13.0-1ubuntu1 [1174 kB] 120s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libp11-kit0 s390x 0.25.5-2ubuntu3 [316 kB] 120s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x lsof s390x 4.99.4+dfsg-1 [243 kB] 120s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x liblsof0 s390x 4.99.4+dfsg-1 [58.5 kB] 120s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.24.2-1ubuntu1 [154 kB] 120s Preconfiguring packages ... 120s Fetched 1982 kB in 1s (2994 kB/s) 120s (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 ... 81030 files and directories currently installed.) 120s Preparing to unpack .../sysvinit-utils_3.14-1ubuntu1_s390x.deb ... 120s Unpacking sysvinit-utils (3.14-1ubuntu1) over (3.08-6ubuntu3) ... 120s Setting up sysvinit-utils (3.14-1ubuntu1) ... 120s (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 ... 81030 files and directories currently installed.) 120s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_s390x.deb ... 121s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 121s Preparing to unpack .../libp11-kit0_0.25.5-2ubuntu3_s390x.deb ... 121s Unpacking libp11-kit0:s390x (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 121s Preparing to unpack .../lsof_4.99.4+dfsg-1_s390x.deb ... 121s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 121s Preparing to unpack .../liblsof0_4.99.4+dfsg-1_s390x.deb ... 121s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 121s Preparing to unpack .../libgpgme11t64_1.24.2-1ubuntu1_s390x.deb ... 121s Unpacking libgpgme11t64:s390x (1.24.2-1ubuntu1) over (1.24.1-4ubuntu1) ... 121s Setting up liblsof0 (4.99.4+dfsg-1) ... 121s Setting up iproute2 (6.13.0-1ubuntu1) ... 121s Setting up libp11-kit0:s390x (0.25.5-2ubuntu3) ... 121s Setting up lsof (4.99.4+dfsg-1) ... 121s Setting up libgpgme11t64:s390x (1.24.2-1ubuntu1) ... 121s Processing triggers for man-db (2.13.0-1) ... 121s Processing triggers for libc-bin (2.40-4ubuntu1) ... 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s The following packages will be REMOVED: 122s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 122s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 122s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 122s linux-tools-6.11.0-8-generic* 122s 0 upgraded, 0 newly installed, 9 to remove and 0 not upgraded. 122s After this operation, 167 MB disk space will be freed. 122s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81031 files and directories currently installed.) 122s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 122s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 122s Removing libpython3.12t64:s390x (3.12.9-1) ... 122s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 122s Removing libnsl2:s390x (1.3.0-3build3) ... 122s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 122s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 123s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 123s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 124s Processing triggers for libc-bin (2.40-4ubuntu1) ... 124s (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 ... 55931 files and directories currently installed.) 124s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 124s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 124s autopkgtest [13:07:51]: upgrading testbed (apt dist-upgrade and autopurge) 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 124s Starting 2 pkgProblemResolver with broken count: 0 124s Done 125s Entering ResolveByKeep 125s 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s Starting pkgProblemResolver with broken count: 0 126s Starting 2 pkgProblemResolver with broken count: 0 126s Done 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s autopkgtest [13:07:53]: rebooting testbed after setup commands that affected boot 145s autopkgtest [13:08:12]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP Tue Feb 4 15:05:57 UTC 2025 147s autopkgtest [13:08:14]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 151s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (dsc) [2291 B] 151s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (tar) [22.3 MB] 151s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (diff) [9600 B] 151s gpgv: Signature made Wed Jan 29 22:42:44 2025 UTC 151s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 151s gpgv: Can't check signature: No public key 151s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7build1.dsc: no acceptable signature found 152s autopkgtest [13:08:19]: testing package tombo version 1.5.1-7build1 152s autopkgtest [13:08:19]: build not needed 153s autopkgtest [13:08:20]: test run-unit-test: preparing testbed 153s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Starting pkgProblemResolver with broken count: 0 154s Starting 2 pkgProblemResolver with broken count: 0 154s Done 154s The following NEW packages will be installed: 154s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 154s libhdf5-310 libhdf5-hl-310 libjs-jquery libjs-mathjax libjs-sphinxdoc 154s libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 python3-decorator 154s python3-h5py python3-h5py-serial python3-mappy python3-numpy 154s python3-packaging python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 154s tombo-doc 154s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 154s Need to get 68.2 MB of archives. 154s After this operation, 258 MB of additional disk space will be used. 154s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-lato all 2.015-1 [2781 kB] 155s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 155s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 155s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 155s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 155s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250213-1ubuntu1 [620 kB] 155s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 155s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-310 s390x 1.14.5+repack-3 [1477 kB] 155s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-310 s390x 1.14.5+repack-3 [61.0 kB] 155s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 155s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 155s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 155s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 155s Get:14 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 155s Get:15 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B] 155s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 155s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-13 [4601 kB] 156s Get:18 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py-serial s390x 3.12.1-1 [1669 kB] 156s Get:19 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py all 3.12.1-1 [7970 B] 156s Get:20 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mappy s390x 2.27+dfsg-1build1 [237 kB] 156s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.2-1 [51.5 kB] 156s Get:22 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-tqdm all 4.67.1-2 [92.5 kB] 156s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 156s Get:24 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.14.1-4ubuntu1 [21.2 MB] 157s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x tombo s390x 1.5.1-7build1 [533 kB] 157s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 157s Get:27 http://ftpmaster.internal/ubuntu plucky/universe s390x tombo-doc all 1.5.1-7build1 [21.7 MB] 158s Fetched 68.2 MB in 4s (17.0 MB/s) 158s Selecting previously unselected package fonts-lato. 158s (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 ... 55929 files and directories currently installed.) 158s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 158s Unpacking fonts-lato (2.015-1) ... 159s Selecting previously unselected package fonts-font-awesome. 159s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 159s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 159s Selecting previously unselected package fonts-mathjax. 159s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 159s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 159s Selecting previously unselected package libaec0:s390x. 159s Preparing to unpack .../03-libaec0_1.1.3-1_s390x.deb ... 159s Unpacking libaec0:s390x (1.1.3-1) ... 159s Selecting previously unselected package libblas3:s390x. 159s Preparing to unpack .../04-libblas3_3.12.1-2_s390x.deb ... 159s Unpacking libblas3:s390x (3.12.1-2) ... 159s Selecting previously unselected package libgfortran5:s390x. 159s Preparing to unpack .../05-libgfortran5_15-20250213-1ubuntu1_s390x.deb ... 159s Unpacking libgfortran5:s390x (15-20250213-1ubuntu1) ... 159s Selecting previously unselected package libsz2:s390x. 159s Preparing to unpack .../06-libsz2_1.1.3-1_s390x.deb ... 159s Unpacking libsz2:s390x (1.1.3-1) ... 159s Selecting previously unselected package libhdf5-310:s390x. 159s Preparing to unpack .../07-libhdf5-310_1.14.5+repack-3_s390x.deb ... 159s Unpacking libhdf5-310:s390x (1.14.5+repack-3) ... 159s Selecting previously unselected package libhdf5-hl-310:s390x. 159s Preparing to unpack .../08-libhdf5-hl-310_1.14.5+repack-3_s390x.deb ... 159s Unpacking libhdf5-hl-310:s390x (1.14.5+repack-3) ... 159s Selecting previously unselected package libjs-jquery. 159s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 159s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 159s Selecting previously unselected package libjs-underscore. 159s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 159s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 159s Selecting previously unselected package libjs-sphinxdoc. 159s Preparing to unpack .../11-libjs-sphinxdoc_8.1.3-5_all.deb ... 159s Unpacking libjs-sphinxdoc (8.1.3-5) ... 159s Selecting previously unselected package liblapack3:s390x. 159s Preparing to unpack .../12-liblapack3_3.12.1-2_s390x.deb ... 159s Unpacking liblapack3:s390x (3.12.1-2) ... 159s Selecting previously unselected package liblbfgsb0:s390x. 159s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 159s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 159s Selecting previously unselected package liblzf1:s390x. 159s Preparing to unpack .../14-liblzf1_3.6-4_s390x.deb ... 159s Unpacking liblzf1:s390x (3.6-4) ... 159s Selecting previously unselected package python3-decorator. 159s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 159s Unpacking python3-decorator (5.1.1-5) ... 159s Selecting previously unselected package python3-numpy. 159s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-13_s390x.deb ... 159s Unpacking python3-numpy (1:1.26.4+ds-13) ... 159s Selecting previously unselected package python3-h5py-serial. 159s Preparing to unpack .../17-python3-h5py-serial_3.12.1-1_s390x.deb ... 159s Unpacking python3-h5py-serial (3.12.1-1) ... 159s Selecting previously unselected package python3-h5py. 159s Preparing to unpack .../18-python3-h5py_3.12.1-1_all.deb ... 159s Unpacking python3-h5py (3.12.1-1) ... 159s Selecting previously unselected package python3-mappy. 159s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1build1_s390x.deb ... 159s Unpacking python3-mappy (2.27+dfsg-1build1) ... 159s Selecting previously unselected package python3-packaging. 159s Preparing to unpack .../20-python3-packaging_24.2-1_all.deb ... 159s Unpacking python3-packaging (24.2-1) ... 159s Selecting previously unselected package python3-tqdm. 159s Preparing to unpack .../21-python3-tqdm_4.67.1-2_all.deb ... 159s Unpacking python3-tqdm (4.67.1-2) ... 159s Selecting previously unselected package sphinx-rtd-theme-common. 159s Preparing to unpack .../22-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 159s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 159s Selecting previously unselected package python3-scipy. 159s Preparing to unpack .../23-python3-scipy_1.14.1-4ubuntu1_s390x.deb ... 159s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 160s Selecting previously unselected package tombo. 160s Preparing to unpack .../24-tombo_1.5.1-7build1_s390x.deb ... 160s Unpacking tombo (1.5.1-7build1) ... 160s Selecting previously unselected package libjs-mathjax. 160s Preparing to unpack .../25-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 160s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 160s Selecting previously unselected package tombo-doc. 160s Preparing to unpack .../26-tombo-doc_1.5.1-7build1_all.deb ... 160s Unpacking tombo-doc (1.5.1-7build1) ... 160s Setting up fonts-lato (2.015-1) ... 160s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 160s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 160s Setting up python3-tqdm (4.67.1-2) ... 161s Setting up python3-mappy (2.27+dfsg-1build1) ... 161s Setting up libaec0:s390x (1.1.3-1) ... 161s Setting up python3-decorator (5.1.1-5) ... 161s Setting up libblas3:s390x (3.12.1-2) ... 161s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 161s Setting up python3-packaging (24.2-1) ... 161s Setting up liblzf1:s390x (3.6-4) ... 161s Setting up libgfortran5:s390x (15-20250213-1ubuntu1) ... 161s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 161s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 161s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 161s Setting up libsz2:s390x (1.1.3-1) ... 161s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 161s Setting up liblapack3:s390x (3.12.1-2) ... 161s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 161s Setting up python3-numpy (1:1.26.4+ds-13) ... 162s Setting up libjs-sphinxdoc (8.1.3-5) ... 162s Setting up tombo-doc (1.5.1-7build1) ... 162s Setting up libhdf5-310:s390x (1.14.5+repack-3) ... 162s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 162s Setting up libhdf5-hl-310:s390x (1.14.5+repack-3) ... 162s Setting up python3-scipy (1.14.1-4ubuntu1) ... 165s Setting up python3-h5py-serial (3.12.1-1) ... 165s Setting up python3-h5py (3.12.1-1) ... 165s Setting up tombo (1.5.1-7build1) ... 166s Processing triggers for man-db (2.13.0-1) ... 166s Processing triggers for libc-bin (2.40-4ubuntu1) ... 167s autopkgtest [13:08:34]: test run-unit-test: [----------------------- 167s ********* Testing help commands ********** 167s usage: tombo [-h] [-v] 167s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} ... 167s 167s ********** Tombo ********* 167s 167s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 167s 167s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 167s 167s Tombo command groups (additional help available within each command group): 167s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 167s preprocess Pre-process nanopore reads for Tombo processing. 167s filter Apply filter to Tombo index file for specified criterion. 167s detect_modifications Perform statistical testing to detect non-standard nucleotides. 167s text_output Output Tombo results in text files. 167s build_model Create canonical and alternative base Tombo models. 167s plot Save plots to visualize raw nanopore signal or testing results. 167s 167s options: 167s -h, --help show this help message and exit 167s -v, --version show Tombo version and exit. 168s usage: tombo resquiggle [--dna] [--rna] 168s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 168s [--q-score Q_SCORE] 168s [--signal-matching-score SIGNAL_MATCHING_SCORE] 168s [--processes PROCESSES] 168s [--corrected-group CORRECTED_GROUP] 168s [--basecall-group BASECALL_GROUP] 168s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 168s [--overwrite] 168s [--failed-reads-filename FAILED_READS_FILENAME] 168s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 168s [--print-advanced-arguments] [--quiet] [--help] 168s fast5s_basedir reference 168s 168s Required Arguments: 168s fast5s_basedir Directory containing fast5 files. All files ending in 168s "fast5" found recursively within this base directory 168s will be processed. 168s reference Reference genome/transcriptome FASTA file or minimap2 168s index (with "map-ont" preset) for mapping. 168s 168s Model Parameters: 168s --dna Explicitly select canonical DNA model. Default: 168s Automatically determine from FAST5s 168s --rna Explicitly select canonical RNA model. Default: 168s Automatically determine from FAST5s 168s 168s Read Filtering Argument: 168s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 168s Filter reads based on observations per base percentile 168s thresholds. Format thresholds as "percentile:thresh 168s [pctl2:thresh2 ...]". For example to filter reads with 168s 99th pctl > 200 obs/base or max > 5k obs/base use 168s "99:200 100:5000". 168s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 168s Default: 0.000000 168s --signal-matching-score SIGNAL_MATCHING_SCORE 168s Observed to expected signal matching score (higher 168s score indicates poor matching). Sample type defaults: 168s RNA : 2 || DNA : 1.1 168s 168s Multiprocessing Arguments: 168s --processes PROCESSES 168s Number of processes. Default: 1 168s 168s FAST5 Data Arguments: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s --basecall-group BASECALL_GROUP 168s FAST5 group obtain original basecalls (under Analyses 168s group). Default: Basecall_1D_000 168s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 168s FAST5 subgroup(s) (under /Analyses/[--basecall- 168s group]/) containing basecalls and created within 168s [--corrected-group] containing re-squiggle results. 168s Default: ['BaseCalled_template'] 168s --overwrite Overwrite previous corrected group in FAST5 files. 168s Note: only effects --corrected-group or --new- 168s corrected-group. 168s 168s Input/Output Arguments: 168s --failed-reads-filename FAILED_READS_FILENAME 168s Output failed read filenames with assoicated error. 168s Default: Do not store failed reads. 168s --num-most-common-errors NUM_MOST_COMMON_ERRORS 168s Dynamically show this many most common errors so far 168s through run. Default: 0; Just show progress 168s 168s Advanced Arguments: 168s --print-advanced-arguments 168s Print advanced re-squiggle arguments and exit. 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 168s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 168s [--basecall-group BASECALL_GROUP] 168s [--basecall-subgroup BASECALL_SUBGROUP] 168s [--overwrite] 168s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 168s [--processes PROCESSES] 168s [--quiet] [--help] 168s 168s Required Arguments: 168s --fast5-basedir FAST5_BASEDIR 168s Directory containing fast5 files. 168s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 168s FASTQ filenames containing basecalls to be added to 168s raw FAST5 files. 168s 168s FAST5 Data Arguments: 168s --basecall-group BASECALL_GROUP 168s FAST5 group obtain original basecalls (under Analyses 168s group). Default: Basecall_1D_000 168s --basecall-subgroup BASECALL_SUBGROUP 168s FAST5 subgroup (under /Analyses/[--basecall-group]/) 168s under which to store basecalls from FASTQs. Default: 168s BaseCalled_template 168s --overwrite Overwrite previous corrected group in FAST5 files. 168s Note: only effects --corrected-group or --new- 168s corrected-group. 168s 168s Sequencing Summary Argument: 168s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 168s Sequencing summary filenames produced by albacore. 168s These can make annotation of raw FAST5 files with 168s FASTQ sequence much faster. 168s 168s Multiprocessing Argument: 168s --processes PROCESSES 168s Number of processes. Default: 1 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo filter clear_filters 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s [--corrected-group CORRECTED_GROUP] 168s [--quiet] [--help] 168s 168s Required Argument: 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s Directories containing fast5 files. 168s 168s FAST5 Data Argument: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 168s [--corrected-group CORRECTED_GROUP] [--quiet] 168s [--help] 168s 168s Required Argument: 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s Directories containing fast5 files. 168s 168s Read Filtering Argument: 168s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 168s Filter reads based on observations per base percentile 168s thresholds. Format thresholds as "percentile:thresh 168s [pctl2:thresh2 ...]". For example to filter reads with 168s 99th pctl > 200 obs/base or max > 5k obs/base use 168s "99:200 100:5000". 168s 168s FAST5 Data Argument: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo filter level_coverage 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s [--percent-to-filter PERCENT_TO_FILTER] 168s [--corrected-group CORRECTED_GROUP] 168s [--quiet] [--help] 168s 168s Required Arguments: 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s Directories containing fast5 files. 168s 168s Read Filtering Argument: 168s --percent-to-filter PERCENT_TO_FILTER 168s Percentage of all reads to filter. Reads are randomly 168s selected weighted according to the approximate 168s coverage at the mapped genomic location. This can be 168s useful in modeling and testing. Default: 10.000000 168s 168s FAST5 Data Arguments: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo filter q_score 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s [--q-score Q_SCORE] 168s [--corrected-group CORRECTED_GROUP] 168s [--basecall-group BASECALL_GROUP] [--quiet] 168s [--help] 168s 168s Required Arguments: 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s Directories containing fast5 files. 168s 168s Read Filtering Argument: 168s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 168s Default: 7.000000 168s 168s FAST5 Data Arguments: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s --basecall-group BASECALL_GROUP 168s FAST5 group obtain original basecalls (under Analyses 168s group). Default: Basecall_1D_000 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo filter raw_signal_matching 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s --signal-matching-score SIGNAL_MATCHING_SCORE 168s [--corrected-group CORRECTED_GROUP] 168s [--quiet] [--help] 168s 168s Required Arguments: 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s Directories containing fast5 files. 168s --signal-matching-score SIGNAL_MATCHING_SCORE 168s Observed to expected signal matching score (higher 168s score indicates poor matching). Sample type defaults: 168s RNA : 2 || DNA : 1.1 168s 168s FAST5 Data Arguments: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo filter genome_locations 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 168s [--include-partial-overlap] 168s [--corrected-group CORRECTED_GROUP] 168s [--quiet] [--help] 168s 168s Required Arguments: 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s Directories containing fast5 files. 168s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 168s Filter out reads not falling completely within include 168s regions. Omit start and end coordinates to include an 168s entire chromosome/sequence record. Format regions as 168s "chrm[:start-end] [chrm2[:start2-end2] ...]". 168s 168s Filter Argument: 168s --include-partial-overlap 168s Include reads that partially overlap the specified 168s region. Default: Only include reads completely 168s contained in a specified region 168s 168s FAST5 Data Argument: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo detect_modifications de_novo 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s --statistics-file-basename STATISTICS_FILE_BASENAME 168s [--dna] [--rna] 168s [--fishers-method-context FISHERS_METHOD_CONTEXT] 168s [--minimum-test-reads MINIMUM_TEST_READS] 168s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 168s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 168s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 168s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 168s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 168s [--processes PROCESSES] 168s [--corrected-group CORRECTED_GROUP] 168s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 168s [--quiet] [--help] 168s 168s Required Argument: 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s Directories containing fast5 files. 168s --statistics-file-basename STATISTICS_FILE_BASENAME 168s File base name to save base by base statistics from 168s testing. Filenames will be [--statistics-file- 168s basename].[--alternate-bases]?.tombo.stats 168s 168s Comparison Model Arguments: 168s --dna Explicitly select canonical DNA model. Default: 168s Automatically determine from FAST5s 168s --rna Explicitly select canonical RNA model. Default: 168s Automatically determine from FAST5s 168s 168s Significance Test Arguments: 168s --fishers-method-context FISHERS_METHOD_CONTEXT 168s Number of context bases up and downstream over which 168s to compute Fisher's method combined p-values. Note: 168s Not applicable for alternative model likelihood ratio 168s tests. Default: 1. 168s --minimum-test-reads MINIMUM_TEST_READS 168s Number of reads required at a position to perform 168s significance testing or contribute to model 168s estimation. Default: 1 168s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 168s P-value threshold when computing fraction of 168s significant reads at each genomic position. If two 168s values are provided, statistics between these values 168s are not considered. Default thresholds: DNA:0.15-0.5 , 168s RNA:0.05-0.4 168s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 168s Dampen fraction modified estimates for low coverage 168s sites. Two parameters are unmodified and modified 168s pseudo read counts. This is equivalent to a beta prior 168s on the fraction estimate. Set to "0 0" to disable 168s dampened fraction estimation. Default: [2, 0] 168s 168s Output Argument: 168s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 168s Base for binary files containing per-read statistics 168s from statistical testing. Filenames will be [--per- 168s read-statistics-basename].[--alternate- 168s bases]?.tombo.per_read_stats 168s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 168s Number of the most significant sites to store for 168s faster access. If a longer list of most significant 168s sites is required the list must be re-computed from 168s all batches. Very large values can increase RAM usage. 168s Default: 100000 168s 168s Multiprocessing Arguments: 168s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 168s Size of regions over which to multiprocesses statistic 168s computation. For very deep samples a smaller value is 168s recommmended in order to control memory consumption. 168s Default: 10000 168s --processes PROCESSES 168s Number of processes. Default: 1 168s 168s FAST5 Data Arguments: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 168s FAST5 subgroup(s) (under /Analyses/[--basecall- 168s group]/) containing basecalls and created within 168s [--corrected-group] containing re-squiggle results. 168s Default: ['BaseCalled_template'] 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo detect_modifications alternative_model 168s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 168s [--statistics-file-basename STATISTICS_FILE_BASENAME] 168s [--alternate-bases {dam,6mA,dcm,CpG,5mC} [{dam,6mA,dcm,CpG,5mC} ...]] 168s [--print-available-models] 168s [--dna] [--rna] 168s [--minimum-test-reads MINIMUM_TEST_READS] 168s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 168s [--standard-log-likelihood-ratio] 168s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 168s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 168s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 168s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 168s [--processes PROCESSES] 168s [--corrected-group CORRECTED_GROUP] 168s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 168s [--quiet] [--help] 168s 168s Required Argument: 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s Directories containing fast5 files. 168s --statistics-file-basename STATISTICS_FILE_BASENAME 168s File base name to save base by base statistics from 168s testing. Filenames will be [--statistics-file- 168s basename].[--alternate-bases]?.tombo.stats 168s --alternate-bases {dam,6mA,dcm,CpG,5mC} [{dam,6mA,dcm,CpG,5mC} ...] 168s Default non-standard base model for testing (not 168s required if user created --alternate-model-filenames 168s is provided). 168s 168s Comparison Arguments: 168s --print-available-models 168s Print available alternative models and exit. 168s --dna Explicitly select canonical DNA model. Default: 168s Automatically determine from FAST5s 168s --rna Explicitly select canonical RNA model. Default: 168s Automatically determine from FAST5s 168s 168s Significance Test Arguments: 168s --minimum-test-reads MINIMUM_TEST_READS 168s Number of reads required at a position to perform 168s significance testing or contribute to model 168s estimation. Default: 1 168s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 168s Log likelihood ratio threshold when computing fraction 168s of significant reads at each genomic position. If two 168s values are provided, statistics between these values 168s are not considered. Default thresholds: DNA:-1.5-2.5 , 168s RNA:-2.5-2.5 168s --standard-log-likelihood-ratio 168s Use a standard log likelihood ratio (LLR) statistic. 168s Default is to use an outlier-robust LLR-like 168s statistic. Detail in full online documentation. 168s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 168s Dampen fraction modified estimates for low coverage 168s sites. Two parameters are unmodified and modified 168s pseudo read counts. This is equivalent to a beta prior 168s on the fraction estimate. Set to "0 0" to disable 168s dampened fraction estimation. Default: [2, 0] 168s 168s Output Argument: 168s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 168s Base for binary files containing per-read statistics 168s from statistical testing. Filenames will be [--per- 168s read-statistics-basename].[--alternate- 168s bases]?.tombo.per_read_stats 168s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 168s Number of the most significant sites to store for 168s faster access. If a longer list of most significant 168s sites is required the list must be re-computed from 168s all batches. Very large values can increase RAM usage. 168s Default: 100000 168s 168s Multiprocessing Arguments: 168s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 168s Size of regions over which to multiprocesses statistic 168s computation. For very deep samples a smaller value is 168s recommmended in order to control memory consumption. 168s Default: 10000 168s --processes PROCESSES 168s Number of processes. Default: 1 168s 168s FAST5 Data Arguments: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 168s FAST5 subgroup(s) (under /Analyses/[--basecall- 168s group]/) containing basecalls and created within 168s [--corrected-group] containing re-squiggle results. 168s Default: ['BaseCalled_template'] 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo detect_modifications model_sample_compare 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s --statistics-file-basename STATISTICS_FILE_BASENAME 168s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 168s [--sample-only-estimates] 168s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 168s [--dna] [--rna] 168s [--fishers-method-context FISHERS_METHOD_CONTEXT] 168s [--minimum-test-reads MINIMUM_TEST_READS] 168s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 168s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 168s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 168s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 168s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 168s [--processes PROCESSES] 168s [--corrected-group CORRECTED_GROUP] 168s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 168s [--quiet] [--help] 168s 168s Required Argument: 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s Directories containing fast5 files. 168s --statistics-file-basename STATISTICS_FILE_BASENAME 168s File base name to save base by base statistics from 168s testing. Filenames will be [--statistics-file- 168s basename].[--alternate-bases]?.tombo.stats 168s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 168s Set of directories containing fast5 files for control 168s reads, containing only canonical nucleotides. 168s 168s Model Prior Arguments: 168s --sample-only-estimates 168s Only use canonical sample to estimate expected signal 168s level and spread. Default: Use canonical model to 168s improve estimtates (esp. for low coverage regions) 168s using baysian posterior estimates. 168s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 168s Prior weights (one each for mean and spread) applied 168s to canonical base model for estimating posterior model 168s parameters for sample comparison. Default: [5, 40] 168s --dna Explicitly select canonical DNA model. Default: 168s Automatically determine from FAST5s 168s --rna Explicitly select canonical RNA model. Default: 168s Automatically determine from FAST5s 168s 168s Significance Test Arguments: 168s --fishers-method-context FISHERS_METHOD_CONTEXT 168s Number of context bases up and downstream over which 168s to compute Fisher's method combined p-values. Note: 168s Not applicable for alternative model likelihood ratio 168s tests. Default: 1. 168s --minimum-test-reads MINIMUM_TEST_READS 168s Number of reads required at a position to perform 168s significance testing or contribute to model 168s estimation. Default: 1 168s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 168s P-value threshold when computing fraction of 168s significant reads at each genomic position. If two 168s values are provided, statistics between these values 168s are not considered. Default thresholds: DNA:0.15-0.5 , 168s RNA:0.05-0.4 168s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 168s Dampen fraction modified estimates for low coverage 168s sites. Two parameters are unmodified and modified 168s pseudo read counts. This is equivalent to a beta prior 168s on the fraction estimate. Set to "0 0" to disable 168s dampened fraction estimation. Default: [2, 0] 168s 168s Output Argument: 168s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 168s Base for binary files containing per-read statistics 168s from statistical testing. Filenames will be [--per- 168s read-statistics-basename].[--alternate- 168s bases]?.tombo.per_read_stats 168s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 168s Number of the most significant sites to store for 168s faster access. If a longer list of most significant 168s sites is required the list must be re-computed from 168s all batches. Very large values can increase RAM usage. 168s Default: 100000 168s 168s Multiprocessing Arguments: 168s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 168s Size of regions over which to multiprocesses statistic 168s computation. For very deep samples a smaller value is 168s recommmended in order to control memory consumption. 168s Default: 10000 168s --processes PROCESSES 168s Number of processes. Default: 1 168s 168s FAST5 Data Arguments: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 168s FAST5 subgroup(s) (under /Analyses/[--basecall- 168s group]/) containing basecalls and created within 168s [--corrected-group] containing re-squiggle results. 168s Default: ['BaseCalled_template'] 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo detect_modifications level_sample_compare 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s --statistics-file-basename STATISTICS_FILE_BASENAME 168s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 168s [--fishers-method-context FISHERS_METHOD_CONTEXT] 168s [--minimum-test-reads MINIMUM_TEST_READS] 168s [--statistic-type {ks,u,t}] 168s [--store-p-value] 168s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 168s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 168s [--processes PROCESSES] 168s [--corrected-group CORRECTED_GROUP] 168s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 168s [--quiet] [--help] 168s 168s Required Argument: 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s Directories containing fast5 files. 168s --statistics-file-basename STATISTICS_FILE_BASENAME 168s File base name to save base by base statistics from 168s testing. Filenames will be [--statistics-file- 168s basename].[--alternate-bases]?.tombo.stats 168s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 168s Set of directories containing fast5 files for 168s alternate set of reads. 168s 168s Significance Test Arguments: 168s --fishers-method-context FISHERS_METHOD_CONTEXT 168s Number of context bases up and downstream over which 168s to compute Fisher's method combined p-values. Note: 168s Not applicable for alternative model likelihood ratio 168s tests. Default: 1. 168s --minimum-test-reads MINIMUM_TEST_READS 168s Number of reads required at a position to perform 168s significance testing or contribute to model 168s estimation. Default: 50 168s --statistic-type {ks,u,t} 168s Type of statistical test to apply. Default: "ks" 168s --store-p-value Store p-value instead of effect-size statistic. 168s Statistics are D-statistic (KS-test), deviation from 168s even common language effect size (u-test), and Cohen's 168s D (t-test). 168s 168s Output Argument: 168s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 168s Number of the most significant sites to store for 168s faster access. If a longer list of most significant 168s sites is required the list must be re-computed from 168s all batches. Very large values can increase RAM usage. 168s Default: 100000 168s 168s Multiprocessing Arguments: 168s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 168s Size of regions over which to multiprocesses statistic 168s computation. For very deep samples a smaller value is 168s recommmended in order to control memory consumption. 168s Default: 10000 168s --processes PROCESSES 168s Number of processes. Default: 1 168s 168s FAST5 Data Arguments: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 168s FAST5 subgroup(s) (under /Analyses/[--basecall- 168s group]/) containing basecalls and created within 168s [--corrected-group] containing re-squiggle results. 168s Default: ['BaseCalled_template'] 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo detect_modifications aggregate_per_read_stats 168s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 168s --statistics-filename STATISTICS_FILENAME 168s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 168s [--minimum-test-reads MINIMUM_TEST_READS] 168s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 168s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 168s [--processes PROCESSES] 168s [--corrected-group CORRECTED_GROUP] 168s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 168s [--quiet] [--help] 168s 168s Required Argument: 168s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 168s Binary file containing per-read statistics from 168s statistical testing. 168s --statistics-filename STATISTICS_FILENAME 168s File to save/load genomic base anchored statistics. 168s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 168s P-value or log likelihood ratio threshold when 168s computing fraction of significant reads at each 168s genomic position. If two values are provided, 168s statistics between these values are not considered. 168s 168s Significance Test Arguments: 168s --minimum-test-reads MINIMUM_TEST_READS 168s Number of reads required at a position to perform 168s significance testing or contribute to model 168s estimation. Default: 1 168s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 168s Dampen fraction modified estimates for low coverage 168s sites. Two parameters are unmodified and modified 168s pseudo read counts. This is equivalent to a beta prior 168s on the fraction estimate. Set to "0 0" to disable 168s dampened fraction estimation. Default: [2, 0] 168s 168s Output Argument: 168s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 168s Number of the most significant sites to store for 168s faster access. If a longer list of most significant 168s sites is required the list must be re-computed from 168s all batches. Very large values can increase RAM usage. 168s Default: 100000 168s 168s Multiprocessing Arguments: 168s --processes PROCESSES 168s Number of processes. Default: 1 168s 168s FAST5 Data Arguments: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 168s FAST5 subgroup(s) (under /Analyses/[--basecall- 168s group]/) containing basecalls and created within 168s [--corrected-group] containing re-squiggle results. 168s Default: ['BaseCalled_template'] 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo text_output browser_files 168s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 168s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 168s [--statistics-filename STATISTICS_FILENAME] 168s [--genome-fasta GENOME_FASTA] 168s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 168s [--browser-file-basename BROWSER_FILE_BASENAME] 168s [--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} ...]] 168s [--corrected-group CORRECTED_GROUP] 168s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 168s [--quiet] [--help] 168s 168s Data Arguments: 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s Directories containing fast5 files. 168s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 168s Set of directories containing fast5 files for control 168s reads, containing only canonical nucleotides. 168s --statistics-filename STATISTICS_FILENAME 168s File to save/load genomic base anchored statistics. 168s 168s Statistic Motif Filter Arguments: 168s --genome-fasta GENOME_FASTA 168s FASTA file used to re-squiggle. For faster sequence 168s access. 168s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 168s Ground truth, motif centered, modified base 168s descriptions for output filtering. Format descriptions 168s as: "motif:mod_pos:name". The mod_pos indicates the 168s modified base within the motif (1-based index). 168s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 168s output for identification of E. coli dam and dcm 168s methylation. 168s 168s Output Arguments: 168s --browser-file-basename BROWSER_FILE_BASENAME 168s Basename for output browser files. Two files (plus and 168s minus strand) will be produced for each --file-types 168s supplied. Filenames formatted as "[browser-file- 168s basename].[file- 168s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 168s Default: tombo_results 168s --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} ...] 168s Data types of genome browser files to produce. 168s Produced coverage files are in bedGraph format, while 168s all other file types will be in wiggle format 168s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 168s Default: "coverage" 168s 168s FAST5 Data Arguments: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 168s FAST5 subgroup(s) (under /Analyses/[--basecall- 168s group]/) containing basecalls and created within 168s [--corrected-group] containing re-squiggle results. 168s Default: ['BaseCalled_template'] 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo text_output signif_sequence_context 168s --statistics-filename STATISTICS_FILENAME 168s [--genome-fasta GENOME_FASTA] 168s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 168s [--num-regions NUM_REGIONS] 168s [--num-bases NUM_BASES] 168s [--sequences-filename SEQUENCES_FILENAME] 168s [--corrected-group CORRECTED_GROUP] 168s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 168s [--quiet] [--help] 168s 168s Required Argument: 168s --statistics-filename STATISTICS_FILENAME 168s File to save/load genomic base anchored statistics. 168s 168s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 168s --genome-fasta GENOME_FASTA 168s FASTA file used to re-squiggle. For faster sequence 168s access. 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s Directories containing fast5 files. 168s 168s Region Selection Arguments: 168s --num-regions NUM_REGIONS 168s Number of regions to plot. Default: 100 168s --num-bases NUM_BASES 168s Number of bases to plot/output. Default: 15 168s 168s Output Arguments: 168s --sequences-filename SEQUENCES_FILENAME 168s File for sequences from selected regions. Sequences 168s will be stored in FASTA format. Default: 168s tombo_results.significant_regions.fasta. 168s 168s FAST5 Data Arguments: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 168s FAST5 subgroup(s) (under /Analyses/[--basecall- 168s group]/) containing basecalls and created within 168s [--corrected-group] containing re-squiggle results. 168s Default: ['BaseCalled_template'] 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo plot max_coverage 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 168s [--plot-standard-model] 168s [--plot-alternate-model {6mA,dcm,dam,CpG,5mC}] 168s [--overplot-threshold OVERPLOT_THRESHOLD] 168s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 168s [--num-regions NUM_REGIONS] 168s [--num-bases NUM_BASES] 168s [--pdf-filename PDF_FILENAME] 168s [--corrected-group CORRECTED_GROUP] 168s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 168s [--quiet] [--help] 168s 168s Required Argument: 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s Directories containing fast5 files. 168s 168s Comparison Arguments: 168s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 168s Set of directories containing fast5 files for control 168s reads, containing only canonical nucleotides. 168s --plot-standard-model 168s Add default standard model distribution to the plot. 168s --plot-alternate-model {6mA,dcm,dam,CpG,5mC} 168s Add alternative model distribution to the plot. 168s 168s Overplotting Arguments: 168s --overplot-threshold OVERPLOT_THRESHOLD 168s Coverage level to trigger alternative plot type 168s instead of raw signal. Default: 50 168s --overplot-type {Downsample,Boxplot,Quantile,Density} 168s Plot type for regions with higher coverage. Default: 168s Downsample 168s 168s Plotting Region Arguments: 168s --num-regions NUM_REGIONS 168s Number of regions to plot. Default: 10 168s --num-bases NUM_BASES 168s Number of bases to plot/output. Default: 21 168s 168s Output Argument: 168s --pdf-filename PDF_FILENAME 168s PDF filename to store plot(s). Default: 168s tombo_results.max_coverage.pdf 168s 168s FAST5 Data Arguments: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 168s FAST5 subgroup(s) (under /Analyses/[--basecall- 168s group]/) containing basecalls and created within 168s [--corrected-group] containing re-squiggle results. 168s Default: ['BaseCalled_template'] 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 168s usage: tombo plot genome_locations 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 168s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 168s [--plot-standard-model] 168s [--plot-alternate-model {6mA,5mC,CpG,dam,dcm}] 168s [--overplot-threshold OVERPLOT_THRESHOLD] 168s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 168s [--num-bases NUM_BASES] 168s [--pdf-filename PDF_FILENAME] 168s [--corrected-group CORRECTED_GROUP] 168s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 168s [--quiet] [--help] 168s 168s Required Arguments: 168s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 168s Directories containing fast5 files. 168s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 168s Genomic locations at which to plot signal. Format 168s locations as "chrm:position[:strand] 168s [chrm2:position2[:strand2] ...]" (strand not 168s applicable for all applications) 168s 168s Comparison Arguments: 168s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 168s Set of directories containing fast5 files for control 168s reads, containing only canonical nucleotides. 168s --plot-standard-model 168s Add default standard model distribution to the plot. 168s --plot-alternate-model {6mA,5mC,CpG,dam,dcm} 168s Add alternative model distribution to the plot. 168s 168s Overplotting Arguments: 168s --overplot-threshold OVERPLOT_THRESHOLD 168s Coverage level to trigger alternative plot type 168s instead of raw signal. Default: 50 168s --overplot-type {Downsample,Boxplot,Quantile,Density} 168s Plot type for regions with higher coverage. Default: 168s Downsample 168s 168s Plotting Region Argument: 168s --num-bases NUM_BASES 168s Number of bases to plot/output. Default: 21 168s 168s Output Argument: 168s --pdf-filename PDF_FILENAME 168s PDF filename to store plot(s). Default: 168s tombo_results.genome_locations.pdf 168s 168s FAST5 Data Arguments: 168s --corrected-group CORRECTED_GROUP 168s FAST5 group created by resquiggle command. Default: 168s RawGenomeCorrected_000 168s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 168s FAST5 subgroup(s) (under /Analyses/[--basecall- 168s group]/) containing basecalls and created within 168s [--corrected-group] containing re-squiggle results. 168s Default: ['BaseCalled_template'] 168s 168s Miscellaneous Arguments: 168s --quiet, -q Don't print status information. 168s --help, -h Print this help message and exit 169s usage: tombo plot motif_centered 169s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s --motif MOTIF --genome-fasta GENOME_FASTA 169s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 169s [--plot-standard-model] 169s [--plot-alternate-model {6mA,CpG,dcm,5mC,dam}] 169s [--overplot-threshold OVERPLOT_THRESHOLD] 169s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 169s [--num-regions NUM_REGIONS] 169s [--num-bases NUM_BASES] [--deepest-coverage] 169s [--pdf-filename PDF_FILENAME] 169s [--corrected-group CORRECTED_GROUP] 169s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 169s [--quiet] [--help] 169s 169s Required Arguments: 169s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s Directories containing fast5 files. 169s --motif MOTIF Motif of interest at which to plot signal and 169s statsitics. Supports IUPAC single letter codes (use T 169s for RNA). 169s --genome-fasta GENOME_FASTA 169s FASTA file used to re-squiggle. For faster sequence 169s access. 169s 169s Comparison Arguments: 169s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 169s Set of directories containing fast5 files for control 169s reads, containing only canonical nucleotides. 169s --plot-standard-model 169s Add default standard model distribution to the plot. 169s --plot-alternate-model {6mA,CpG,dcm,5mC,dam} 169s Add alternative model distribution to the plot. 169s 169s Overplotting Arguments: 169s --overplot-threshold OVERPLOT_THRESHOLD 169s Coverage level to trigger alternative plot type 169s instead of raw signal. Default: 50 169s --overplot-type {Downsample,Boxplot,Quantile,Density} 169s Plot type for regions with higher coverage. Default: 169s Downsample 169s 169s Plotting Region Arguments: 169s --num-regions NUM_REGIONS 169s Number of regions to plot. Default: 10 169s --num-bases NUM_BASES 169s Number of bases to plot/output. Default: 21 169s --deepest-coverage Plot the deepest coverage regions. 169s 169s Output Argument: 169s --pdf-filename PDF_FILENAME 169s PDF filename to store plot(s). Default: 169s tombo_results.motif_centered.pdf 169s 169s FAST5 Data Arguments: 169s --corrected-group CORRECTED_GROUP 169s FAST5 group created by resquiggle command. Default: 169s RawGenomeCorrected_000 169s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 169s FAST5 subgroup(s) (under /Analyses/[--basecall- 169s group]/) containing basecalls and created within 169s [--corrected-group] containing re-squiggle results. 169s Default: ['BaseCalled_template'] 169s 169s Miscellaneous Arguments: 169s --quiet, -q Don't print status information. 169s --help, -h Print this help message and exit 169s usage: tombo plot max_difference 169s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 169s [--overplot-threshold OVERPLOT_THRESHOLD] 169s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 169s [--num-regions NUM_REGIONS] 169s [--num-bases NUM_BASES] 169s [--pdf-filename PDF_FILENAME] 169s [--sequences-filename SEQUENCES_FILENAME] 169s [--corrected-group CORRECTED_GROUP] 169s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 169s [--quiet] [--help] 169s 169s Required Arguments: 169s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s Directories containing fast5 files. 169s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 169s Set of directories containing fast5 files for control 169s reads, containing only canonical nucleotides. 169s 169s Overplotting Arguments: 169s --overplot-threshold OVERPLOT_THRESHOLD 169s Coverage level to trigger alternative plot type 169s instead of raw signal. Default: 50 169s --overplot-type {Downsample,Boxplot,Quantile,Density} 169s Plot type for regions with higher coverage. Default: 169s Downsample 169s 169s Plotting Region Arguments: 169s --num-regions NUM_REGIONS 169s Number of regions to plot. Default: 10 169s --num-bases NUM_BASES 169s Number of bases to plot/output. Default: 21 169s 169s Output Arguments: 169s --pdf-filename PDF_FILENAME 169s PDF filename to store plot(s). Default: 169s tombo_results.max_difference.pdf 169s --sequences-filename SEQUENCES_FILENAME 169s File for sequences from selected regions. Sequences 169s will be stored in FASTA format. Default: None. 169s 169s FAST5 Data Arguments: 169s --corrected-group CORRECTED_GROUP 169s FAST5 group created by resquiggle command. Default: 169s RawGenomeCorrected_000 169s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 169s FAST5 subgroup(s) (under /Analyses/[--basecall- 169s group]/) containing basecalls and created within 169s [--corrected-group] containing re-squiggle results. 169s Default: ['BaseCalled_template'] 169s 169s Miscellaneous Arguments: 169s --quiet, -q Don't print status information. 169s --help, -h Print this help message and exit 169s usage: tombo plot most_significant 169s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s --statistics-filename STATISTICS_FILENAME 169s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 169s [--plot-standard-model] 169s [--plot-alternate-model {dam,6mA,CpG,dcm,5mC}] 169s [--overplot-threshold OVERPLOT_THRESHOLD] 169s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 169s [--num-regions NUM_REGIONS] 169s [--num-bases NUM_BASES] 169s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 169s [--pdf-filename PDF_FILENAME] 169s [--sequences-filename SEQUENCES_FILENAME] 169s [--corrected-group CORRECTED_GROUP] 169s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 169s [--quiet] [--help] 169s 169s Required Arguments: 169s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s Directories containing fast5 files. 169s --statistics-filename STATISTICS_FILENAME 169s File to save/load genomic base anchored statistics. 169s 169s Comparison Arguments: 169s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 169s Set of directories containing fast5 files for control 169s reads, containing only canonical nucleotides. 169s --plot-standard-model 169s Add default standard model distribution to the plot. 169s --plot-alternate-model {dam,6mA,CpG,dcm,5mC} 169s Add alternative model distribution to the plot. 169s 169s Overplotting Arguments: 169s --overplot-threshold OVERPLOT_THRESHOLD 169s Coverage level to trigger alternative plot type 169s instead of raw signal. Default: 50 169s --overplot-type {Downsample,Boxplot,Quantile,Density} 169s Plot type for regions with higher coverage. Default: 169s Downsample 169s 169s Plotting Region Arguments: 169s --num-regions NUM_REGIONS 169s Number of regions to plot. Default: 10 169s --num-bases NUM_BASES 169s Number of bases to plot/output. Default: 21 169s 169s Statistical Argument: 169s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 169s Dampen fraction modified estimates for low coverage 169s sites. Two parameters are unmodified and modified 169s pseudo read counts. This is equivalent to a beta prior 169s on the fraction estimate. Set to "0 0" to disable 169s dampened fraction estimation. Default: [2, 0] 169s 169s Output Arguments: 169s --pdf-filename PDF_FILENAME 169s PDF filename to store plot(s). Default: 169s tombo_results.significant_difference.pdf 169s --sequences-filename SEQUENCES_FILENAME 169s File for sequences from selected regions. Sequences 169s will be stored in FASTA format. Default: None. 169s 169s FAST5 Data Arguments: 169s --corrected-group CORRECTED_GROUP 169s FAST5 group created by resquiggle command. Default: 169s RawGenomeCorrected_000 169s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 169s FAST5 subgroup(s) (under /Analyses/[--basecall- 169s group]/) containing basecalls and created within 169s [--corrected-group] containing re-squiggle results. 169s Default: ['BaseCalled_template'] 169s 169s Miscellaneous Arguments: 169s --quiet, -q Don't print status information. 169s --help, -h Print this help message and exit 169s usage: tombo plot motif_with_stats 169s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s --motif MOTIF 169s --statistics-filename STATISTICS_FILENAME 169s --genome-fasta GENOME_FASTA 169s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 169s [--plot-standard-model] 169s [--plot-alternate-model {CpG,dcm,6mA,5mC,dam}] 169s [--overplot-threshold OVERPLOT_THRESHOLD] 169s [--num-regions NUM_REGIONS] 169s [--num-context NUM_CONTEXT] 169s [--num-statistics NUM_STATISTICS] 169s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 169s [--pdf-filename PDF_FILENAME] 169s [--corrected-group CORRECTED_GROUP] 169s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 169s [--quiet] [--help] 169s 169s Required Arguments: 169s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s Directories containing fast5 files. 169s --motif MOTIF Motif of interest at which to plot signal and 169s statsitics. Supports IUPAC single letter codes (use T 169s for RNA). 169s --statistics-filename STATISTICS_FILENAME 169s File to save/load genomic base anchored statistics. 169s --genome-fasta GENOME_FASTA 169s FASTA file used to re-squiggle. For faster sequence 169s access. 169s 169s Comparison Arguments: 169s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 169s Set of directories containing fast5 files for control 169s reads, containing only canonical nucleotides. 169s --plot-standard-model 169s Add default standard model distribution to the plot. 169s --plot-alternate-model {CpG,dcm,6mA,5mC,dam} 169s Add alternative model distribution to the plot. 169s 169s Overplotting Argument: 169s --overplot-threshold OVERPLOT_THRESHOLD 169s Coverage level to trigger alternative plot type 169s instead of raw signal. Default: 50 169s 169s Plotting Region Arguments: 169s --num-regions NUM_REGIONS 169s Number of regions to plot. Default: 3 169s --num-context NUM_CONTEXT 169s Number of context bases around motif. Default: 5 169s --num-statistics NUM_STATISTICS 169s Number of motif centered regions to include in 169s statistic distributions. Default: 200 169s 169s Statistical Argument: 169s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 169s Dampen fraction modified estimates for low coverage 169s sites. Two parameters are unmodified and modified 169s pseudo read counts. This is equivalent to a beta prior 169s on the fraction estimate. Set to "0 0" to disable 169s dampened fraction estimation. Default: [2, 0] 169s 169s Output Argument: 169s --pdf-filename PDF_FILENAME 169s PDF filename to store plot(s). Default: 169s tombo_results.motif_statistics.pdf 169s 169s FAST5 Data Arguments: 169s --corrected-group CORRECTED_GROUP 169s FAST5 group created by resquiggle command. Default: 169s RawGenomeCorrected_000 169s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 169s FAST5 subgroup(s) (under /Analyses/[--basecall- 169s group]/) containing basecalls and created within 169s [--corrected-group] containing re-squiggle results. 169s Default: ['BaseCalled_template'] 169s 169s Miscellaneous Arguments: 169s --quiet, -q Don't print status information. 169s --help, -h Print this help message and exit 169s usage: tombo plot per_read 169s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 169s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 169s [--genome-fasta GENOME_FASTA] 169s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 169s [--num-reads NUM_READS] [--num-bases NUM_BASES] 169s [--box-center] [--pdf-filename PDF_FILENAME] 169s [--corrected-group CORRECTED_GROUP] 169s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 169s [--quiet] [--help] 169s 169s Required Arguments: 169s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 169s Genomic locations at which to plot signal. Format 169s locations as "chrm:position[:strand] 169s [chrm2:position2[:strand2] ...]" (strand not 169s applicable for all applications) 169s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 169s Binary file containing per-read statistics from 169s statistical testing. 169s 169s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 169s --genome-fasta GENOME_FASTA 169s FASTA file used to re-squiggle. For faster sequence 169s access. 169s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s Directories containing fast5 files. 169s 169s Plotting Region Arguments: 169s --num-reads NUM_READS 169s Number of reads to plot. Default: 100 169s --num-bases NUM_BASES 169s Number of bases to plot/output. Default: 51 169s --box-center Plot a box around the central base. 169s 169s Output Argument: 169s --pdf-filename PDF_FILENAME 169s PDF filename to store plot(s). Default: 169s tombo_results.per_read_stats.pdf 169s 169s FAST5 Data Arguments: 169s --corrected-group CORRECTED_GROUP 169s FAST5 group created by resquiggle command. Default: 169s RawGenomeCorrected_000 169s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 169s FAST5 subgroup(s) (under /Analyses/[--basecall- 169s group]/) containing basecalls and created within 169s [--corrected-group] containing re-squiggle results. 169s Default: ['BaseCalled_template'] 169s 169s Miscellaneous Arguments: 169s --quiet, -q Don't print status information. 169s --help, -h Print this help message and exit 169s usage: tombo plot roc 169s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 169s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 169s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 169s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 169s [--genome-fasta GENOME_FASTA] 169s [--pdf-filename PDF_FILENAME] 169s [--statistics-per-block STATISTICS_PER_BLOCK] 169s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 169s [--quiet] [--help] 169s 169s Required Argument: 169s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 169s Files to load genomic base anchored statistics. 169s 169s Ground Truth Arguments (provide bed files or motifs): 169s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 169s Modification description and bed format files 169s containing single base locations of ground truth 169s modified sites. Bed files should contain 6 fields 169s including strand. Format descriptions as 169s "mod_name:locs.bed". Example: "CpG 169s bisulfite":bisulfite_locs.bed 169s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 169s Bed format files containing single base locations of 169s ground truth unmodified sites. Bed files should 169s contain 6 fields including strand. 169s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 169s Ground truth, motif centered, modified base 169s descriptions for computing ROC and PR curves. Each 169s statistics file is associated with a set of motif 169s descriptions. Format descriptions as: 169s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 169s mod_pos indicates the alternate-base within the motif 169s (1-based index). Example: CCWGG:2:"dcm 169s 5mC"::GATC:2:"dam 6mA" would assess the performance of 169s a single Tombo statistics file for identification of 169s E. coli dam and dcm methylation. 169s --genome-fasta GENOME_FASTA 169s FASTA file used to re-squiggle. For faster sequence 169s access. 169s 169s Output Arguments: 169s --pdf-filename PDF_FILENAME 169s PDF filename to store plot(s). Default: 169s tombo_results.roc.pdf 169s 169s Down-sampling Arguments: 169s --statistics-per-block STATISTICS_PER_BLOCK 169s Number of randomly selected per-read, per-base 169s statistics to extract from each genomic block for 169s plotting. Default: Include all stats 169s --total-statistics-limit TOTAL_STATISTICS_LIMIT 169s Total per-read statistics to be extracted for 169s plotting. Avoids memory overflow for large runs. 169s Default: 5000000 169s 169s Miscellaneous Arguments: 169s --quiet, -q Don't print status information. 169s --help, -h Print this help message and exit 169s usage: tombo plot per_read_roc 169s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 169s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 169s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 169s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 169s [--genome-fasta GENOME_FASTA] 169s [--statistics-per-block STATISTICS_PER_BLOCK] 169s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 169s [--pdf-filename PDF_FILENAME] [--quiet] 169s [--help] 169s 169s Required Argument: 169s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 169s Binary files containing per-read statistics from 169s statistical testing. 169s 169s Ground Truth Arguments (provide bed files or motifs): 169s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 169s Modification description and bed format files 169s containing single base locations of ground truth 169s modified sites. Bed files should contain 6 fields 169s including strand. Format descriptions as 169s "mod_name:locs.bed". Example: "CpG 169s bisulfite":bisulfite_locs.bed 169s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 169s Bed format files containing single base locations of 169s ground truth unmodified sites. Bed files should 169s contain 6 fields including strand. 169s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 169s Ground truth, motif centered, modified base 169s descriptions for computing ROC and PR curves. Each 169s statistics file is associated with a set of motif 169s descriptions. Format descriptions as: 169s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 169s mod_pos indicates the alternate-base within the motif 169s (1-based index). Example: CCWGG:2:"dcm 169s 5mC"::GATC:2:"dam 6mA" would assess the performance of 169s a single Tombo statistics file for identification of 169s E. coli dam and dcm methylation. 169s --genome-fasta GENOME_FASTA 169s FASTA file used to re-squiggle. For faster sequence 169s access. 169s 169s Down-sampling Arguments: 169s --statistics-per-block STATISTICS_PER_BLOCK 169s Number of randomly selected per-read, per-base 169s statistics to extract from each genomic block for 169s plotting. Default: 100000 169s --total-statistics-limit TOTAL_STATISTICS_LIMIT 169s Total per-read statistics to be extracted for 169s plotting. Avoids memory overflow for large runs. 169s Default: 5000000 169s 169s Output Arguments: 169s --pdf-filename PDF_FILENAME 169s PDF filename to store plot(s). Default: 169s tombo_results.per_reads_roc.pdf 169s 169s Miscellaneous Arguments: 169s --quiet, -q Don't print status information. 169s --help, -h Print this help message and exit 169s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s [--upstream-bases {0,1,2,3,4}] 169s [--downstream-bases {0,1,2,3,4}] [--read-mean] 169s [--num-kmer-threshold NUM_KMER_THRESHOLD] 169s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 169s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 169s [--corrected-group CORRECTED_GROUP] 169s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 169s [--quiet] [--help] 169s 169s Required Argument: 169s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s Directories containing fast5 files. 169s 169s Data Processing Arguments: 169s --upstream-bases {0,1,2,3,4} 169s Upstream bases in k-mer. Default: 1 169s --downstream-bases {0,1,2,3,4} 169s Downstream bases in k-mer. Default: 2 169s --read-mean Plot k-mer means across whole reads as opposed to 169s individual k-mer event levels. 169s --num-kmer-threshold NUM_KMER_THRESHOLD 169s Observations of each k-mer required to include a read 169s in read level averages. Default: 1 169s 169s Plotting Region Arguments: 169s --num-reads NUM_READS 169s Number of reads to plot. Default: 100 169s 169s Output Arguments: 169s --pdf-filename PDF_FILENAME 169s PDF filename to store plot(s). Default: 169s tombo_results.kmer_distribution.pdf 169s --r-data-filename R_DATA_FILENAME 169s Filename to save R data structure. Default: Don't save 169s --dont-plot Don't plot result. Useful to produce only R data file. 169s 169s FAST5 Data Arguments: 169s --corrected-group CORRECTED_GROUP 169s FAST5 group created by resquiggle command. Default: 169s RawGenomeCorrected_000 169s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 169s FAST5 subgroup(s) (under /Analyses/[--basecall- 169s group]/) containing basecalls and created within 169s [--corrected-group] containing re-squiggle results. 169s Default: ['BaseCalled_template'] 169s 169s Miscellaneous Arguments: 169s --quiet, -q Don't print status information. 169s --help, -h Print this help message and exit 169s usage: tombo plot cluster_most_significant 169s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 169s --statistics-filename STATISTICS_FILENAME 169s [--genome-fasta GENOME_FASTA] 169s [--processes PROCESSES] 169s [--num-regions NUM_REGIONS] 169s [--num-bases NUM_BASES] 169s [--slide-span SLIDE_SPAN] 169s [--pdf-filename PDF_FILENAME] 169s [--r-data-filename R_DATA_FILENAME] 169s [--corrected-group CORRECTED_GROUP] 169s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 169s [--quiet] [--help] 169s 169s Required Arguments: 169s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s Directories containing fast5 files. 169s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 169s Set of directories containing fast5 files for control 169s reads, containing only canonical nucleotides. 169s --statistics-filename STATISTICS_FILENAME 169s File to save/load genomic base anchored statistics. 169s 169s FASTA Sequence Argument: 169s --genome-fasta GENOME_FASTA 169s FASTA file used to re-squiggle. For faster sequence 169s access. 169s 169s Multiprocessing Argument: 169s --processes PROCESSES 169s Number of processes. Default: 1 169s 169s Plotting Region Arguments: 169s --num-regions NUM_REGIONS 169s Number of regions to plot. Default: 10 169s --num-bases NUM_BASES 169s Number of bases to plot/output. Default: 21 169s --slide-span SLIDE_SPAN 169s Number of bases offset over which to search when 169s computing distances for signal cluster plotting. 169s Default: 0 (exact position) 169s 169s Output Arguments: 169s --pdf-filename PDF_FILENAME 169s PDF filename to store plot(s). Default: 169s tombo_results.signal_clusters.pdf 169s --r-data-filename R_DATA_FILENAME 169s Filename to save R data structure. Default: Don't save 169s 169s FAST5 Data Arguments: 169s --corrected-group CORRECTED_GROUP 169s FAST5 group created by resquiggle command. Default: 169s RawGenomeCorrected_000 169s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 169s FAST5 subgroup(s) (under /Analyses/[--basecall- 169s group]/) containing basecalls and created within 169s [--corrected-group] containing re-squiggle results. 169s Default: ['BaseCalled_template'] 169s 169s Miscellaneous Arguments: 169s --quiet, -q Don't print status information. 169s --help, -h Print this help message and exit 169s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 169s 169s Required Arguments: 169s fast5s_basedir Directory containing fast5 files. All files ending in 169s "fast5" found recursively within this base directory will be 169s processed. 169s 169s Miscellaneous Arguments: 169s --quiet, -q Don't print status information. 169s --help, -h Print this help message and exit 169s usage: tombo build_model event_resquiggle 169s [--minimap2-executable MINIMAP2_EXECUTABLE] 169s [--minimap2-index MINIMAP2_INDEX] 169s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 169s [--graphmap-executable GRAPHMAP_EXECUTABLE] 169s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 169s [--normalization-type {median,pA,pA_raw,none}] 169s [--pore-model-filename PORE_MODEL_FILENAME] 169s [--outlier-threshold OUTLIER_THRESHOLD] 169s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 169s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 169s [--timeout TIMEOUT] 169s [--cpts-limit CPTS_LIMIT] 169s [--skip-index] [--overwrite] 169s [--failed-reads-filename FAILED_READS_FILENAME] 169s [--include-event-stdev] 169s [--corrected-group CORRECTED_GROUP] 169s [--basecall-group BASECALL_GROUP] 169s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 169s [--processes PROCESSES] 169s [--align-processes ALIGN_PROCESSES] 169s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 169s [--resquiggle-processes RESQUIGGLE_PROCESSES] 169s [--quiet] [--help] 169s fast5s_basedir reference_fasta 169s 169s Required Arguments: 169s fast5s_basedir Directory containing fast5 files. All files ending in 169s "fast5" found recursively within this base directory 169s will be processed. 169s reference_fasta Reference genome/transcriptome FASTA file for mapping. 169s 169s Mapper Arguments (One mapper is required): 169s --minimap2-executable MINIMAP2_EXECUTABLE 169s Path to minimap2 executable. 169s --minimap2-index MINIMAP2_INDEX 169s Path to minimap2 index (with map-ont preset) file 169s corresponding to the [genome_fasta] provided. 169s --bwa-mem-executable BWA_MEM_EXECUTABLE 169s Path to bwa-mem executable. 169s --graphmap-executable GRAPHMAP_EXECUTABLE 169s Path to graphmap executable. 169s --alignment-batch-size ALIGNMENT_BATCH_SIZE 169s Number of reads included in each alignment call. Note: 169s A new system mapping call is made for each batch 169s (including loading of the genome), so it is advised to 169s use larger values for larger genomes. Default: 1000 169s 169s Signal Processing Arguments: 169s --normalization-type {median,pA,pA_raw,none} 169s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 169s as in the ONT events (using offset, range and 169s digitization), "pA": k-mer-based correction for pA 169s drift as in nanopolish (requires [--pore-model- 169s filename]), "median": median and MAD from raw signal. 169s Default: median 169s --pore-model-filename PORE_MODEL_FILENAME 169s File containing kmer model parameters (level_mean and 169s level_stdv) used in order to compute kmer-based 169s corrected pA values. E.g. https://github.com/jts/nanop 169s olish/blob/master/etc/r9- 169s models/template_median68pA.5mers.model 169s --outlier-threshold OUTLIER_THRESHOLD 169s Windosrize the signal at this number of scale values. 169s Negative value disables outlier clipping. Default: 169s 5.000000 169s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 169s Specify the 2 parameters for segmentation 1) running 169s neighboring windows width 2) minimum raw observations 169s per genomic base. Sample type defaults: RNA : 12 6 || 169s DNA : 5 3 169s 169s Read Filtering Arguments: 169s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 169s Filter reads based on observations per base percentile 169s thresholds. Format thresholds as "percentile:thresh 169s [pctl2:thresh2 ...]". For example to filter reads with 169s 99th pctl > 200 obs/base or max > 5k obs/base use 169s "99:200 100:5000". 169s --timeout TIMEOUT Timeout in seconds for processing a single read. 169s Default: No timeout. 169s --cpts-limit CPTS_LIMIT 169s Maximum number of changepoints to find within a single 169s indel group. Default: No limit. 169s 169s Input/Output Arguments: 169s --skip-index Skip creation of tombo index. This drastically slows 169s downstream tombo commands. Default stores tombo index 169s named ".[--fast5-basedir].[--corrected- 169s group].tombo.index" to be loaded automatically for 169s downstream commands. 169s --overwrite Overwrite previous corrected group in FAST5 files. 169s Note: only effects --corrected-group or --new- 169s corrected-group. 169s --failed-reads-filename FAILED_READS_FILENAME 169s Output failed read filenames with assoicated error. 169s Default: Do not store failed reads. 169s --include-event-stdev 169s Include corrected event standard deviation in output 169s FAST5 data. 169s 169s FAST5 Data Arguments: 169s --corrected-group CORRECTED_GROUP 169s FAST5 group created by resquiggle command. Default: 169s RawGenomeCorrected_000 169s --basecall-group BASECALL_GROUP 169s FAST5 group obtain original basecalls (under Analyses 169s group). Default: Basecall_1D_000 169s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 169s FAST5 subgroup(s) (under /Analyses/[--basecall- 169s group]/) containing basecalls and created within 169s [--corrected-group] containing re-squiggle results. 169s Default: ['BaseCalled_template'] 169s 169s Multiprocessing Arguments: 169s --processes PROCESSES 169s Number of processes. Default: 2 169s --align-processes ALIGN_PROCESSES 169s Number of processes to use for parsing and aligning 169s original basecalls. Each process will independently 169s load the genome into memory, so use caution with 169s larger genomes (e.g. human). Default: 1 169s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 169s Number of threads to use for aligner system call. 169s Default: [--processes] / (2 * [--align-processes)] 169s --resquiggle-processes RESQUIGGLE_PROCESSES 169s Number of processes to use for resquiggle algorithm. 169s Default: [--processes] / 2 169s 169s Miscellaneous Arguments: 169s --quiet, -q Don't print status information. 169s --help, -h Print this help message and exit 169s usage: tombo build_model estimate_reference 169s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s --tombo-model-filename TOMBO_MODEL_FILENAME 169s [--estimate-mean] 169s [--kmer-specific-sd] 169s [--upstream-bases {0,1,2,3,4}] 169s [--downstream-bases {0,1,2,3,4}] 169s [--minimum-test-reads MINIMUM_TEST_READS] 169s [--coverage-threshold COVERAGE_THRESHOLD] 169s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 169s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 169s [--processes PROCESSES] 169s [--corrected-group CORRECTED_GROUP] 169s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 169s [--quiet] [--help] 169s 169s Required Arguments: 169s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 169s Directories containing fast5 files. 169s --tombo-model-filename TOMBO_MODEL_FILENAME 169s Filename to save Tombo model. 169s 169s Modeling Arguments: 169s --estimate-mean Use the mean instead of median for model level 169s estimation. Note: This can cause poor fits due to 169s outliers 169s --kmer-specific-sd Estimate standard deviation for each k-mers 169s individually. 169s --upstream-bases {0,1,2,3,4} 169s Upstream bases in k-mer. Default: 1 169s --downstream-bases {0,1,2,3,4} 169s Downstream bases in k-mer. Default: 2 169s 169s Filtering Arguments: 169s --minimum-test-reads MINIMUM_TEST_READS 169s Number of reads required at a position to perform 169s significance testing or contribute to model 169s estimation. Default: 10 169s --coverage-threshold COVERAGE_THRESHOLD 169s Maximum mean coverage per region when estimating k-mer 169s model (limits compute time for deep samples). Default: 169s 100 169s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 169s Number of each k-mer observations required in order to 169s produce a reference (genomic locations for standard 169s reference and per-read for alternative reference). 169s Default: 5 169s 169s Multiprocessing Arguments: 169s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 169s Size of regions over which to multiprocesses statistic 169s computation. For very deep samples a smaller value is 169s recommmended in order to control memory consumption. 169s Default: 10000 169s --processes PROCESSES 169s Number of processes. Default: 1 169s 169s FAST5 Data Arguments: 169s --corrected-group CORRECTED_GROUP 169s FAST5 group created by resquiggle command. Default: 169s RawGenomeCorrected_000 169s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 169s FAST5 subgroup(s) (under /Analyses/[--basecall- 169s group]/) containing basecalls and created within 169s [--corrected-group] containing re-squiggle results. 169s Default: ['BaseCalled_template'] 169s 169s Miscellaneous Arguments: 169s --quiet, -q Don't print status information. 169s --help, -h Print this help message and exit 170s usage: tombo build_model estimate_alt_reference 170s --alternate-model-filename ALTERNATE_MODEL_FILENAME 170s --alternate-model-name ALTERNATE_MODEL_NAME 170s --alternate-model-base {A,C,G,T} 170s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 170s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 170s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 170s [--control-density-filename CONTROL_DENSITY_FILENAME] 170s [--dna] [--rna] 170s [--tombo-model-filename TOMBO_MODEL_FILENAME] 170s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 170s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 170s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 170s [--save-density-basename SAVE_DENSITY_BASENAME] 170s [--processes PROCESSES] 170s [--corrected-group CORRECTED_GROUP] 170s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 170s [--quiet] [--help] 170s 170s Required Arguments: 170s --alternate-model-filename ALTERNATE_MODEL_FILENAME 170s Tombo model for alternative likelihood ratio 170s significance testing. 170s --alternate-model-name ALTERNATE_MODEL_NAME 170s A short name to associate with this alternate model 170s (e.g. 5mC, 6mA, etc.). This text will be included in 170s output filenames when this model is used for testing. 170s --alternate-model-base {A,C,G,T} 170s Non-standard base is an alternative to this base. 170s 170s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 170s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 170s Directories containing fast5 files. 170s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 170s Set of directories containing fast5 files for control 170s reads, containing only canonical nucleotides. 170s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 170s File containing k-mer level kernel density estimates 170s for the alternative sample saved using --save-density- 170s basename. 170s --control-density-filename CONTROL_DENSITY_FILENAME 170s File containing k-mer level kernel density estimates 170s for the control sample saved using --save-density- 170s basename. 170s 170s Standard Model Arguments: 170s --dna Explicitly select canonical DNA model. Default: 170s Automatically determine from FAST5s 170s --rna Explicitly select canonical RNA model. Default: 170s Automatically determine from FAST5s 170s --tombo-model-filename TOMBO_MODEL_FILENAME 170s Tombo model filename. If no file is provided, the 170s default DNA or RNA Tombo model will be used. 170s 170s Model Fitting Arguments: 170s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 170s When esitmating the alternative base incorporation 170s rate, this percent of k-mers are assumed to have 170s significantly shifted signal so the alternative 170s distribution minimally overlaps the standard base 170s distribution. Default: 5.000000 170s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 170s Bandwidth applied when performing Gaussian kernal 170s density esitmation on standard and alternative base 170s signal distributions. Default: 0.050000 170s 170s Filtering Argument: 170s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 170s Number of each k-mer observations required in order to 170s produce a reference (genomic locations for standard 170s reference and per-read for alternative reference). 170s Default: 1000 170s 170s Output Argument: 170s --save-density-basename SAVE_DENSITY_BASENAME 170s Basename to save alternative model estimation density 170s estimation information. See scripts/debug_est_alt.R 170s for info use example. Default: Don't save. 170s 170s Multiprocessing Arguments: 170s --processes PROCESSES 170s Number of processes. Default: 1 170s 170s FAST5 Data Arguments: 170s --corrected-group CORRECTED_GROUP 170s FAST5 group created by resquiggle command. Default: 170s RawGenomeCorrected_000 170s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 170s FAST5 subgroup(s) (under /Analyses/[--basecall- 170s group]/) containing basecalls and created within 170s [--corrected-group] containing re-squiggle results. 170s Default: ['BaseCalled_template'] 170s 170s Miscellaneous Arguments: 170s --quiet, -q Don't print status information. 170s --help, -h Print this help message and exit 170s This test only tests the help system 170s There is an extensive test in 170s 170s tombo/tests/shell_tests.sh 170s 170s but this requires to download larger data 170s sets which is not done for the moment. 170s autopkgtest [13:08:37]: test run-unit-test: -----------------------] 170s run-unit-test PASS 170s autopkgtest [13:08:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 171s autopkgtest [13:08:38]: @@@@@@@@@@@@@@@@@@@@ summary 171s run-unit-test PASS 188s nova [W] Using flock in prodstack6-s390x 188s Creating nova instance adt-plucky-s390x-tombo-20250219-130547-juju-7f2275-prod-proposed-migration-environment-20-2777983d-1f01-4d8e-92af-c6db160edaf3 from image adt/ubuntu-plucky-s390x-server-20250219.img (UUID 7af5aa59-4155-4177-a560-02c7dd963d23)... 188s nova [W] Timed out waiting for f819494b-90c2-40d9-a82c-64295c18e88a to get deleted.