0s autopkgtest [19:31:50]: starting date and time: 2025-03-15 19:31:50+0000 0s autopkgtest [19:31:50]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [19:31:50]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6hslk65x/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-21.secgroup --name adt-plucky-s390x-tombo-20250315-193150-juju-7f2275-prod-proposed-migration-environment-2-7cbd9197-1027-4db4-847f-4566ca894592 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 101s autopkgtest [19:33:31]: testbed dpkg architecture: s390x 102s autopkgtest [19:33:32]: testbed apt version: 2.9.33 102s autopkgtest [19:33:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 102s autopkgtest [19:33:32]: testbed release detected to be: None 103s autopkgtest [19:33:33]: updating testbed package index (apt update) 104s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 104s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 104s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 104s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 104s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 104s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [45.1 kB] 104s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 105s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [77.3 kB] 105s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 105s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 105s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [314 kB] 105s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.3 kB] 105s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3532 B] 105s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 105s Fetched 965 kB in 1s (788 kB/s) 105s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Calculating upgrade... 106s Calculating upgrade... 106s The following packages were automatically installed and are no longer required: 106s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 106s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 106s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 106s linux-tools-6.11.0-8-generic 106s Use 'sudo apt autoremove' to remove them. 106s The following packages will be upgraded: 106s pinentry-curses python3-jinja2 strace 107s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 652 kB of archives. 107s After this operation, 27.6 kB of additional disk space will be used. 107s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 107s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 107s Fetched 652 kB in 1s (1121 kB/s) 107s (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 ... 81428 files and directories currently installed.) 107s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 107s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 107s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 107s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 107s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 107s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 107s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 107s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 108s Setting up strace (6.13+ds-1ubuntu1) ... 108s Processing triggers for man-db (2.13.0-1) ... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Solving dependencies... 108s The following packages will be REMOVED: 108s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 108s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 108s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 108s linux-tools-6.11.0-8-generic* 109s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 109s After this operation, 167 MB disk space will be freed. 109s (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 ... 81428 files and directories currently installed.) 109s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 109s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 109s Removing libpython3.12t64:s390x (3.12.9-1) ... 109s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 109s Removing libnsl2:s390x (1.3.0-3build3) ... 109s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 109s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 109s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 110s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 110s Processing triggers for libc-bin (2.41-1ubuntu1) ... 110s (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 ... 56328 files and directories currently installed.) 110s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 110s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 110s autopkgtest [19:33:40]: upgrading testbed (apt dist-upgrade and autopurge) 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 110s Starting 2 pkgProblemResolver with broken count: 0 110s Done 111s Entering ResolveByKeep 111s 111s Calculating upgrade... 111s The following packages will be upgraded: 111s libc-bin libc-dev-bin libc6 libc6-dev locales 111s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Need to get 9512 kB of archives. 111s After this operation, 8192 B of additional disk space will be used. 111s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 112s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 112s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 112s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 112s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 112s Preconfiguring packages ... 112s Fetched 9512 kB in 1s (8982 kB/s) 112s (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 ... 56326 files and directories currently installed.) 112s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 112s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 112s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 112s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 112s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 112s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 113s Setting up libc6:s390x (2.41-1ubuntu2) ... 113s (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 ... 56326 files and directories currently installed.) 113s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 113s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 113s Setting up libc-bin (2.41-1ubuntu2) ... 113s (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 ... 56326 files and directories currently installed.) 113s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 113s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 113s Setting up locales (2.41-1ubuntu2) ... 113s Generating locales (this might take a while)... 114s en_US.UTF-8... done 114s Generation complete. 114s Setting up libc-dev-bin (2.41-1ubuntu2) ... 114s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 114s Processing triggers for man-db (2.13.0-1) ... 115s Processing triggers for systemd (257.3-1ubuntu3) ... 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Starting pkgProblemResolver with broken count: 0 116s Starting 2 pkgProblemResolver with broken count: 0 116s Done 116s Solving dependencies... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s autopkgtest [19:33:46]: rebooting testbed after setup commands that affected boot 138s autopkgtest [19:34:08]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 141s autopkgtest [19:34:11]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 144s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build2 (dsc) [2291 B] 144s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build2 (tar) [22.3 MB] 144s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build2 (diff) [9628 B] 145s gpgv: Signature made Tue Mar 4 15:27:30 2025 UTC 145s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 145s gpgv: Can't check signature: No public key 145s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7build2.dsc: no acceptable signature found 145s autopkgtest [19:34:15]: testing package tombo version 1.5.1-7build2 145s autopkgtest [19:34:15]: build not needed 148s autopkgtest [19:34:18]: test run-unit-test: preparing testbed 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Starting pkgProblemResolver with broken count: 0 149s Starting 2 pkgProblemResolver with broken count: 0 149s Done 149s The following NEW packages will be installed: 149s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 149s libhdf5-310 libhdf5-hl-310 libjs-jquery libjs-mathjax libjs-sphinxdoc 149s libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 python3-decorator 149s python3-h5py python3-h5py-serial python3-mappy python3-numpy 149s python3-numpy-dev python3-packaging python3-scipy python3-tqdm 149s sphinx-rtd-theme-common tombo tombo-doc 149s 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded. 149s Need to get 64.4 MB of archives. 149s After this operation, 205 MB of additional disk space will be used. 149s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-lato all 2.015-1 [2781 kB] 151s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy-dev s390x 1:2.2.3+ds-5 [147 kB] 151s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 151s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 151s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 152s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:2.2.3+ds-5 [4396 kB] 152s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 152s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 153s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 153s Get:10 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 153s Get:11 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-310 s390x 1.14.5+repack-3 [1477 kB] 153s Get:12 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-310 s390x 1.14.5+repack-3 [61.0 kB] 153s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 153s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 153s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-sphinxdoc all 8.1.3-4 [30.9 kB] 153s Get:16 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 153s Get:17 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B] 153s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 153s Get:19 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py-serial s390x 3.13.0-1 [1185 kB] 153s Get:20 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py all 3.13.0-1 [7978 B] 153s Get:21 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mappy s390x 2.27+dfsg-1build2 [213 kB] 153s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.2-1 [51.5 kB] 153s Get:23 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-tqdm all 4.67.1-2 [92.5 kB] 153s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 153s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.14.1-4ubuntu2 [18.0 MB] 155s Get:26 http://ftpmaster.internal/ubuntu plucky/universe s390x tombo s390x 1.5.1-7build2 [466 kB] 155s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 155s Get:28 http://ftpmaster.internal/ubuntu plucky/universe s390x tombo-doc all 1.5.1-7build2 [21.7 MB] 157s Fetched 64.4 MB in 8s (8111 kB/s) 157s Selecting previously unselected package fonts-lato. 157s (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 ... 56326 files and directories currently installed.) 157s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 157s Unpacking fonts-lato (2.015-1) ... 158s Selecting previously unselected package python3-numpy-dev:s390x. 158s Preparing to unpack .../01-python3-numpy-dev_1%3a2.2.3+ds-5_s390x.deb ... 158s Unpacking python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 158s Selecting previously unselected package libblas3:s390x. 158s Preparing to unpack .../02-libblas3_3.12.1-2_s390x.deb ... 158s Unpacking libblas3:s390x (3.12.1-2) ... 158s Selecting previously unselected package libgfortran5:s390x. 158s Preparing to unpack .../03-libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 158s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 158s Selecting previously unselected package liblapack3:s390x. 158s Preparing to unpack .../04-liblapack3_3.12.1-2_s390x.deb ... 158s Unpacking liblapack3:s390x (3.12.1-2) ... 158s Selecting previously unselected package python3-numpy. 158s Preparing to unpack .../05-python3-numpy_1%3a2.2.3+ds-5_s390x.deb ... 158s Unpacking python3-numpy (1:2.2.3+ds-5) ... 158s Selecting previously unselected package fonts-font-awesome. 158s Preparing to unpack .../06-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 158s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 158s Selecting previously unselected package fonts-mathjax. 158s Preparing to unpack .../07-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 158s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 158s Selecting previously unselected package libaec0:s390x. 158s Preparing to unpack .../08-libaec0_1.1.3-1_s390x.deb ... 158s Unpacking libaec0:s390x (1.1.3-1) ... 158s Selecting previously unselected package libsz2:s390x. 158s Preparing to unpack .../09-libsz2_1.1.3-1_s390x.deb ... 158s Unpacking libsz2:s390x (1.1.3-1) ... 158s Selecting previously unselected package libhdf5-310:s390x. 158s Preparing to unpack .../10-libhdf5-310_1.14.5+repack-3_s390x.deb ... 158s Unpacking libhdf5-310:s390x (1.14.5+repack-3) ... 158s Selecting previously unselected package libhdf5-hl-310:s390x. 158s Preparing to unpack .../11-libhdf5-hl-310_1.14.5+repack-3_s390x.deb ... 158s Unpacking libhdf5-hl-310:s390x (1.14.5+repack-3) ... 158s Selecting previously unselected package libjs-jquery. 158s Preparing to unpack .../12-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 158s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 158s Selecting previously unselected package libjs-underscore. 158s Preparing to unpack .../13-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 158s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 158s Selecting previously unselected package libjs-sphinxdoc. 158s Preparing to unpack .../14-libjs-sphinxdoc_8.1.3-4_all.deb ... 158s Unpacking libjs-sphinxdoc (8.1.3-4) ... 158s Selecting previously unselected package liblbfgsb0:s390x. 158s Preparing to unpack .../15-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 158s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 158s Selecting previously unselected package liblzf1:s390x. 158s Preparing to unpack .../16-liblzf1_3.6-4_s390x.deb ... 158s Unpacking liblzf1:s390x (3.6-4) ... 158s Selecting previously unselected package python3-decorator. 158s Preparing to unpack .../17-python3-decorator_5.1.1-5_all.deb ... 158s Unpacking python3-decorator (5.1.1-5) ... 158s Selecting previously unselected package python3-h5py-serial. 158s Preparing to unpack .../18-python3-h5py-serial_3.13.0-1_s390x.deb ... 158s Unpacking python3-h5py-serial (3.13.0-1) ... 158s Selecting previously unselected package python3-h5py. 158s Preparing to unpack .../19-python3-h5py_3.13.0-1_all.deb ... 158s Unpacking python3-h5py (3.13.0-1) ... 158s Selecting previously unselected package python3-mappy. 158s Preparing to unpack .../20-python3-mappy_2.27+dfsg-1build2_s390x.deb ... 158s Unpacking python3-mappy (2.27+dfsg-1build2) ... 158s Selecting previously unselected package python3-packaging. 158s Preparing to unpack .../21-python3-packaging_24.2-1_all.deb ... 158s Unpacking python3-packaging (24.2-1) ... 158s Selecting previously unselected package python3-tqdm. 158s Preparing to unpack .../22-python3-tqdm_4.67.1-2_all.deb ... 158s Unpacking python3-tqdm (4.67.1-2) ... 158s Selecting previously unselected package sphinx-rtd-theme-common. 158s Preparing to unpack .../23-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 158s Unpacking sphinx-rtd-theme-common 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python3-numpy (1:2.2.3+ds-5) ... 161s Setting up libjs-sphinxdoc (8.1.3-4) ... 161s Setting up tombo-doc (1.5.1-7build2) ... 161s Setting up libhdf5-310:s390x (1.14.5+repack-3) ... 161s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 161s Setting up libhdf5-hl-310:s390x (1.14.5+repack-3) ... 161s Setting up python3-scipy (1.14.1-4ubuntu2) ... 163s Setting up python3-h5py-serial (3.13.0-1) ... 163s Setting up python3-h5py (3.13.0-1) ... 163s Setting up tombo (1.5.1-7build2) ... 164s Processing triggers for man-db (2.13.0-1) ... 164s Processing triggers for libc-bin (2.41-1ubuntu2) ... 165s autopkgtest [19:34:35]: test run-unit-test: [----------------------- 165s ********* Testing help commands ********** 165s usage: tombo [-h] [-v] 165s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} ... 165s 165s ********** Tombo ********* 165s 165s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 165s 165s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 165s 165s Tombo command groups (additional help available within each command group): 165s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 165s preprocess Pre-process nanopore reads for Tombo processing. 165s filter Apply filter to Tombo index file for specified criterion. 165s detect_modifications Perform statistical testing to detect non-standard nucleotides. 165s text_output Output Tombo results in text files. 165s build_model Create canonical and alternative base Tombo models. 165s plot Save plots to visualize raw nanopore signal or testing results. 165s 165s options: 165s -h, --help show this help message and exit 165s -v, --version show Tombo version and exit. 165s usage: tombo resquiggle [--dna] [--rna] 165s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 165s [--q-score Q_SCORE] 165s [--signal-matching-score SIGNAL_MATCHING_SCORE] 165s [--processes PROCESSES] 165s [--corrected-group CORRECTED_GROUP] 165s [--basecall-group BASECALL_GROUP] 165s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 165s [--overwrite] 165s [--failed-reads-filename FAILED_READS_FILENAME] 165s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 165s [--print-advanced-arguments] [--quiet] [--help] 165s fast5s_basedir reference 165s 165s Required Arguments: 165s fast5s_basedir Directory containing fast5 files. All files ending in 165s "fast5" found recursively within this base directory 165s will be processed. 165s reference Reference genome/transcriptome FASTA file or minimap2 165s index (with "map-ont" preset) for mapping. 165s 165s Model Parameters: 165s --dna Explicitly select canonical DNA model. Default: 165s Automatically determine from FAST5s 165s --rna Explicitly select canonical RNA model. Default: 165s Automatically determine from FAST5s 165s 165s Read Filtering Argument: 165s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 165s Filter reads based on observations per base percentile 165s thresholds. Format thresholds as "percentile:thresh 165s [pctl2:thresh2 ...]". For example to filter reads with 165s 99th pctl > 200 obs/base or max > 5k obs/base use 165s "99:200 100:5000". 165s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 165s Default: 0.000000 165s --signal-matching-score SIGNAL_MATCHING_SCORE 165s Observed to expected signal matching score (higher 165s score indicates poor matching). Sample type defaults: 165s RNA : 2 || DNA : 1.1 165s 165s Multiprocessing Arguments: 165s --processes PROCESSES 165s Number of processes. Default: 1 165s 165s FAST5 Data Arguments: 165s --corrected-group CORRECTED_GROUP 165s FAST5 group created by resquiggle command. Default: 165s RawGenomeCorrected_000 165s --basecall-group BASECALL_GROUP 165s FAST5 group obtain original basecalls (under Analyses 165s group). Default: Basecall_1D_000 165s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 165s FAST5 subgroup(s) (under /Analyses/[--basecall- 165s group]/) containing basecalls and created within 165s [--corrected-group] containing re-squiggle results. 165s Default: ['BaseCalled_template'] 165s --overwrite Overwrite previous corrected group in FAST5 files. 165s Note: only effects --corrected-group or --new- 165s corrected-group. 165s 165s Input/Output Arguments: 165s --failed-reads-filename FAILED_READS_FILENAME 165s Output failed read filenames with assoicated error. 165s Default: Do not store failed reads. 165s --num-most-common-errors NUM_MOST_COMMON_ERRORS 165s Dynamically show this many most common errors so far 165s through run. Default: 0; Just show progress 165s 165s Advanced Arguments: 165s --print-advanced-arguments 165s Print advanced re-squiggle arguments and exit. 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 165s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 165s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 165s [--basecall-group BASECALL_GROUP] 165s [--basecall-subgroup BASECALL_SUBGROUP] 165s [--overwrite] 165s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 165s [--processes PROCESSES] 165s [--quiet] [--help] 165s 165s Required Arguments: 165s --fast5-basedir FAST5_BASEDIR 165s Directory containing fast5 files. 165s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 165s FASTQ filenames containing basecalls to be added to 165s raw FAST5 files. 165s 165s FAST5 Data Arguments: 165s --basecall-group BASECALL_GROUP 165s FAST5 group obtain original basecalls (under Analyses 165s group). Default: Basecall_1D_000 165s --basecall-subgroup BASECALL_SUBGROUP 165s FAST5 subgroup (under /Analyses/[--basecall-group]/) 165s under which to store basecalls from FASTQs. Default: 165s BaseCalled_template 165s --overwrite Overwrite previous corrected group in FAST5 files. 165s Note: only effects --corrected-group or --new- 165s corrected-group. 165s 165s Sequencing Summary Argument: 165s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 165s Sequencing summary filenames produced by albacore. 165s These can make annotation of raw FAST5 files with 165s FASTQ sequence much faster. 165s 165s Multiprocessing Argument: 165s --processes PROCESSES 165s Number of processes. Default: 1 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 165s usage: tombo filter clear_filters 165s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s [--corrected-group CORRECTED_GROUP] 165s [--quiet] [--help] 165s 165s Required Argument: 165s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s Directories containing fast5 files. 165s 165s FAST5 Data Argument: 165s --corrected-group CORRECTED_GROUP 165s FAST5 group created by resquiggle command. Default: 165s RawGenomeCorrected_000 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 165s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 165s [--corrected-group CORRECTED_GROUP] [--quiet] 165s [--help] 165s 165s Required Argument: 165s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s Directories containing fast5 files. 165s 165s Read Filtering Argument: 165s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 165s Filter reads based on observations per base percentile 165s thresholds. Format thresholds as "percentile:thresh 165s [pctl2:thresh2 ...]". For example to filter reads with 165s 99th pctl > 200 obs/base or max > 5k obs/base use 165s "99:200 100:5000". 165s 165s FAST5 Data Argument: 165s --corrected-group CORRECTED_GROUP 165s FAST5 group created by resquiggle command. Default: 165s RawGenomeCorrected_000 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 165s usage: tombo filter level_coverage 165s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s [--percent-to-filter PERCENT_TO_FILTER] 165s [--corrected-group CORRECTED_GROUP] 165s [--quiet] [--help] 165s 165s Required Arguments: 165s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s Directories containing fast5 files. 165s 165s Read Filtering Argument: 165s --percent-to-filter PERCENT_TO_FILTER 165s Percentage of all reads to filter. Reads are randomly 165s selected weighted according to the approximate 165s coverage at the mapped genomic location. This can be 165s useful in modeling and testing. Default: 10.000000 165s 165s FAST5 Data Arguments: 165s --corrected-group CORRECTED_GROUP 165s FAST5 group created by resquiggle command. Default: 165s RawGenomeCorrected_000 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 165s usage: tombo filter q_score 165s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s [--q-score Q_SCORE] 165s [--corrected-group CORRECTED_GROUP] 165s [--basecall-group BASECALL_GROUP] [--quiet] 165s [--help] 165s 165s Required Arguments: 165s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 165s Directories containing fast5 files. 165s 165s Read Filtering Argument: 165s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 165s Default: 7.000000 165s 165s FAST5 Data Arguments: 165s --corrected-group CORRECTED_GROUP 165s FAST5 group created by resquiggle command. Default: 165s RawGenomeCorrected_000 165s --basecall-group BASECALL_GROUP 165s FAST5 group obtain original basecalls (under Analyses 165s group). Default: Basecall_1D_000 165s 165s Miscellaneous Arguments: 165s --quiet, -q Don't print status information. 165s --help, -h Print this help message and exit 166s usage: tombo filter raw_signal_matching 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s --signal-matching-score SIGNAL_MATCHING_SCORE 166s [--corrected-group CORRECTED_GROUP] 166s [--quiet] [--help] 166s 166s Required Arguments: 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s --signal-matching-score SIGNAL_MATCHING_SCORE 166s Observed to expected signal matching score (higher 166s score indicates poor matching). Sample type defaults: 166s RNA : 2 || DNA : 1.1 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo filter genome_locations 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 166s [--include-partial-overlap] 166s [--corrected-group CORRECTED_GROUP] 166s [--quiet] [--help] 166s 166s Required Arguments: 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 166s Filter out reads not falling completely within include 166s regions. Omit start and end coordinates to include an 166s entire chromosome/sequence record. Format regions as 166s "chrm[:start-end] [chrm2[:start2-end2] ...]". 166s 166s Filter Argument: 166s --include-partial-overlap 166s Include reads that partially overlap the specified 166s region. Default: Only include reads completely 166s contained in a specified region 166s 166s FAST5 Data Argument: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo detect_modifications de_novo 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s --statistics-file-basename STATISTICS_FILE_BASENAME 166s [--dna] [--rna] 166s [--fishers-method-context FISHERS_METHOD_CONTEXT] 166s [--minimum-test-reads MINIMUM_TEST_READS] 166s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 166s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 166s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 166s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 166s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 166s [--processes PROCESSES] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Argument: 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s --statistics-file-basename STATISTICS_FILE_BASENAME 166s File base name to save base by base statistics from 166s testing. Filenames will be [--statistics-file- 166s basename].[--alternate-bases]?.tombo.stats 166s 166s Comparison Model Arguments: 166s --dna Explicitly select canonical DNA model. Default: 166s Automatically determine from FAST5s 166s --rna Explicitly select canonical RNA model. Default: 166s Automatically determine from FAST5s 166s 166s Significance Test Arguments: 166s --fishers-method-context FISHERS_METHOD_CONTEXT 166s Number of context bases up and downstream over which 166s to compute Fisher's method combined p-values. Note: 166s Not applicable for alternative model likelihood ratio 166s tests. Default: 1. 166s --minimum-test-reads MINIMUM_TEST_READS 166s Number of reads required at a position to perform 166s significance testing or contribute to model 166s estimation. Default: 1 166s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 166s P-value threshold when computing fraction of 166s significant reads at each genomic position. If two 166s values are provided, statistics between these values 166s are not considered. Default thresholds: DNA:0.15-0.5 , 166s RNA:0.05-0.4 166s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 166s Dampen fraction modified estimates for low coverage 166s sites. Two parameters are unmodified and modified 166s pseudo read counts. This is equivalent to a beta prior 166s on the fraction estimate. Set to "0 0" to disable 166s dampened fraction estimation. Default: [2, 0] 166s 166s Output Argument: 166s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 166s Base for binary files containing per-read statistics 166s from statistical testing. Filenames will be [--per- 166s read-statistics-basename].[--alternate- 166s bases]?.tombo.per_read_stats 166s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 166s Number of the most significant sites to store for 166s faster access. If a longer list of most significant 166s sites is required the list must be re-computed from 166s all batches. Very large values can increase RAM usage. 166s Default: 100000 166s 166s Multiprocessing Arguments: 166s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 166s Size of regions over which to multiprocesses statistic 166s computation. For very deep samples a smaller value is 166s recommmended in order to control memory consumption. 166s Default: 10000 166s --processes PROCESSES 166s Number of processes. Default: 1 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo detect_modifications alternative_model 166s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 166s [--statistics-file-basename STATISTICS_FILE_BASENAME] 166s [--alternate-bases {dcm,dam,5mC,6mA,CpG} [{dcm,dam,5mC,6mA,CpG} ...]] 166s [--print-available-models] 166s [--dna] [--rna] 166s [--minimum-test-reads MINIMUM_TEST_READS] 166s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 166s [--standard-log-likelihood-ratio] 166s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 166s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 166s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 166s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 166s [--processes PROCESSES] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Argument: 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s --statistics-file-basename STATISTICS_FILE_BASENAME 166s File base name to save base by base statistics from 166s testing. Filenames will be [--statistics-file- 166s basename].[--alternate-bases]?.tombo.stats 166s --alternate-bases {dcm,dam,5mC,6mA,CpG} [{dcm,dam,5mC,6mA,CpG} ...] 166s Default non-standard base model for testing (not 166s required if user created --alternate-model-filenames 166s is provided). 166s 166s Comparison Arguments: 166s --print-available-models 166s Print available alternative models and exit. 166s --dna Explicitly select canonical DNA model. Default: 166s Automatically determine from FAST5s 166s --rna Explicitly select canonical RNA model. Default: 166s Automatically determine from FAST5s 166s 166s Significance Test Arguments: 166s --minimum-test-reads MINIMUM_TEST_READS 166s Number of reads required at a position to perform 166s significance testing or contribute to model 166s estimation. Default: 1 166s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 166s Log likelihood ratio threshold when computing fraction 166s of significant reads at each genomic position. If two 166s values are provided, statistics between these values 166s are not considered. Default thresholds: DNA:-1.5-2.5 , 166s RNA:-2.5-2.5 166s --standard-log-likelihood-ratio 166s Use a standard log likelihood ratio (LLR) statistic. 166s Default is to use an outlier-robust LLR-like 166s statistic. Detail in full online documentation. 166s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 166s Dampen fraction modified estimates for low coverage 166s sites. Two parameters are unmodified and modified 166s pseudo read counts. This is equivalent to a beta prior 166s on the fraction estimate. Set to "0 0" to disable 166s dampened fraction estimation. Default: [2, 0] 166s 166s Output Argument: 166s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 166s Base for binary files containing per-read statistics 166s from statistical testing. Filenames will be [--per- 166s read-statistics-basename].[--alternate- 166s bases]?.tombo.per_read_stats 166s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 166s Number of the most significant sites to store for 166s faster access. If a longer list of most significant 166s sites is required the list must be re-computed from 166s all batches. Very large values can increase RAM usage. 166s Default: 100000 166s 166s Multiprocessing Arguments: 166s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 166s Size of regions over which to multiprocesses statistic 166s computation. For very deep samples a smaller value is 166s recommmended in order to control memory consumption. 166s Default: 10000 166s --processes PROCESSES 166s Number of processes. Default: 1 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo detect_modifications model_sample_compare 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s --statistics-file-basename STATISTICS_FILE_BASENAME 166s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 166s [--sample-only-estimates] 166s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 166s [--dna] [--rna] 166s [--fishers-method-context FISHERS_METHOD_CONTEXT] 166s [--minimum-test-reads MINIMUM_TEST_READS] 166s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 166s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 166s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 166s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 166s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 166s [--processes PROCESSES] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Argument: 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s --statistics-file-basename STATISTICS_FILE_BASENAME 166s File base name to save base by base statistics from 166s testing. Filenames will be [--statistics-file- 166s basename].[--alternate-bases]?.tombo.stats 166s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 166s Set of directories containing fast5 files for control 166s reads, containing only canonical nucleotides. 166s 166s Model Prior Arguments: 166s --sample-only-estimates 166s Only use canonical sample to estimate expected signal 166s level and spread. Default: Use canonical model to 166s improve estimtates (esp. for low coverage regions) 166s using baysian posterior estimates. 166s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 166s Prior weights (one each for mean and spread) applied 166s to canonical base model for estimating posterior model 166s parameters for sample comparison. Default: [5, 40] 166s --dna Explicitly select canonical DNA model. Default: 166s Automatically determine from FAST5s 166s --rna Explicitly select canonical RNA model. Default: 166s Automatically determine from FAST5s 166s 166s Significance Test Arguments: 166s --fishers-method-context FISHERS_METHOD_CONTEXT 166s Number of context bases up and downstream over which 166s to compute Fisher's method combined p-values. Note: 166s Not applicable for alternative model likelihood ratio 166s tests. Default: 1. 166s --minimum-test-reads MINIMUM_TEST_READS 166s Number of reads required at a position to perform 166s significance testing or contribute to model 166s estimation. Default: 1 166s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 166s P-value threshold when computing fraction of 166s significant reads at each genomic position. If two 166s values are provided, statistics between these values 166s are not considered. Default thresholds: DNA:0.15-0.5 , 166s RNA:0.05-0.4 166s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 166s Dampen fraction modified estimates for low coverage 166s sites. Two parameters are unmodified and modified 166s pseudo read counts. This is equivalent to a beta prior 166s on the fraction estimate. Set to "0 0" to disable 166s dampened fraction estimation. Default: [2, 0] 166s 166s Output Argument: 166s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 166s Base for binary files containing per-read statistics 166s from statistical testing. Filenames will be [--per- 166s read-statistics-basename].[--alternate- 166s bases]?.tombo.per_read_stats 166s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 166s Number of the most significant sites to store for 166s faster access. If a longer list of most significant 166s sites is required the list must be re-computed from 166s all batches. Very large values can increase RAM usage. 166s Default: 100000 166s 166s Multiprocessing Arguments: 166s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 166s Size of regions over which to multiprocesses statistic 166s computation. For very deep samples a smaller value is 166s recommmended in order to control memory consumption. 166s Default: 10000 166s --processes PROCESSES 166s Number of processes. Default: 1 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo detect_modifications level_sample_compare 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s --statistics-file-basename STATISTICS_FILE_BASENAME 166s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 166s [--fishers-method-context FISHERS_METHOD_CONTEXT] 166s [--minimum-test-reads MINIMUM_TEST_READS] 166s [--statistic-type {ks,u,t}] 166s [--store-p-value] 166s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 166s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 166s [--processes PROCESSES] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Argument: 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s --statistics-file-basename STATISTICS_FILE_BASENAME 166s File base name to save base by base statistics from 166s testing. Filenames will be [--statistics-file- 166s basename].[--alternate-bases]?.tombo.stats 166s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 166s Set of directories containing fast5 files for 166s alternate set of reads. 166s 166s Significance Test Arguments: 166s --fishers-method-context FISHERS_METHOD_CONTEXT 166s Number of context bases up and downstream over which 166s to compute Fisher's method combined p-values. Note: 166s Not applicable for alternative model likelihood ratio 166s tests. Default: 1. 166s --minimum-test-reads MINIMUM_TEST_READS 166s Number of reads required at a position to perform 166s significance testing or contribute to model 166s estimation. Default: 50 166s --statistic-type {ks,u,t} 166s Type of statistical test to apply. Default: "ks" 166s --store-p-value Store p-value instead of effect-size statistic. 166s Statistics are D-statistic (KS-test), deviation from 166s even common language effect size (u-test), and Cohen's 166s D (t-test). 166s 166s Output Argument: 166s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 166s Number of the most significant sites to store for 166s faster access. If a longer list of most significant 166s sites is required the list must be re-computed from 166s all batches. Very large values can increase RAM usage. 166s Default: 100000 166s 166s Multiprocessing Arguments: 166s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 166s Size of regions over which to multiprocesses statistic 166s computation. For very deep samples a smaller value is 166s recommmended in order to control memory consumption. 166s Default: 10000 166s --processes PROCESSES 166s Number of processes. Default: 1 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo detect_modifications aggregate_per_read_stats 166s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 166s --statistics-filename STATISTICS_FILENAME 166s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 166s [--minimum-test-reads MINIMUM_TEST_READS] 166s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 166s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 166s [--processes PROCESSES] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Argument: 166s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 166s Binary file containing per-read statistics from 166s statistical testing. 166s --statistics-filename STATISTICS_FILENAME 166s File to save/load genomic base anchored statistics. 166s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 166s P-value or log likelihood ratio threshold when 166s computing fraction of significant reads at each 166s genomic position. If two values are provided, 166s statistics between these values are not considered. 166s 166s Significance Test Arguments: 166s --minimum-test-reads MINIMUM_TEST_READS 166s Number of reads required at a position to perform 166s significance testing or contribute to model 166s estimation. Default: 1 166s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 166s Dampen fraction modified estimates for low coverage 166s sites. Two parameters are unmodified and modified 166s pseudo read counts. This is equivalent to a beta prior 166s on the fraction estimate. Set to "0 0" to disable 166s dampened fraction estimation. Default: [2, 0] 166s 166s Output Argument: 166s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 166s Number of the most significant sites to store for 166s faster access. If a longer list of most significant 166s sites is required the list must be re-computed from 166s all batches. Very large values can increase RAM usage. 166s Default: 100000 166s 166s Multiprocessing Arguments: 166s --processes PROCESSES 166s Number of processes. Default: 1 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo text_output browser_files 166s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 166s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 166s [--statistics-filename STATISTICS_FILENAME] 166s [--genome-fasta GENOME_FASTA] 166s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 166s [--browser-file-basename BROWSER_FILE_BASENAME] 166s [--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} ...]] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Data Arguments: 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 166s Set of directories containing fast5 files for control 166s reads, containing only canonical nucleotides. 166s --statistics-filename STATISTICS_FILENAME 166s File to save/load genomic base anchored statistics. 166s 166s Statistic Motif Filter Arguments: 166s --genome-fasta GENOME_FASTA 166s FASTA file used to re-squiggle. For faster sequence 166s access. 166s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 166s Ground truth, motif centered, modified base 166s descriptions for output filtering. Format descriptions 166s as: "motif:mod_pos:name". The mod_pos indicates the 166s modified base within the motif (1-based index). 166s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 166s output for identification of E. coli dam and dcm 166s methylation. 166s 166s Output Arguments: 166s --browser-file-basename BROWSER_FILE_BASENAME 166s Basename for output browser files. Two files (plus and 166s minus strand) will be produced for each --file-types 166s supplied. Filenames formatted as "[browser-file- 166s basename].[file- 166s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 166s Default: tombo_results 166s --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} ...] 166s Data types of genome browser files to produce. 166s Produced coverage files are in bedGraph format, while 166s all other file types will be in wiggle format 166s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 166s Default: "coverage" 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo text_output signif_sequence_context 166s --statistics-filename STATISTICS_FILENAME 166s [--genome-fasta GENOME_FASTA] 166s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 166s [--num-regions NUM_REGIONS] 166s [--num-bases NUM_BASES] 166s [--sequences-filename SEQUENCES_FILENAME] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Argument: 166s --statistics-filename STATISTICS_FILENAME 166s File to save/load genomic base anchored statistics. 166s 166s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 166s --genome-fasta GENOME_FASTA 166s FASTA file used to re-squiggle. For faster sequence 166s access. 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s 166s Region Selection Arguments: 166s --num-regions NUM_REGIONS 166s Number of regions to plot. Default: 100 166s --num-bases NUM_BASES 166s Number of bases to plot/output. Default: 15 166s 166s Output Arguments: 166s --sequences-filename SEQUENCES_FILENAME 166s File for sequences from selected regions. Sequences 166s will be stored in FASTA format. Default: 166s tombo_results.significant_regions.fasta. 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo plot max_coverage 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 166s [--plot-standard-model] 166s [--plot-alternate-model {6mA,5mC,dcm,dam,CpG}] 166s [--overplot-threshold OVERPLOT_THRESHOLD] 166s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 166s [--num-regions NUM_REGIONS] 166s [--num-bases NUM_BASES] 166s [--pdf-filename PDF_FILENAME] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Argument: 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s 166s Comparison Arguments: 166s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 166s Set of directories containing fast5 files for control 166s reads, containing only canonical nucleotides. 166s --plot-standard-model 166s Add default standard model distribution to the plot. 166s --plot-alternate-model {6mA,5mC,dcm,dam,CpG} 166s Add alternative model distribution to the plot. 166s 166s Overplotting Arguments: 166s --overplot-threshold OVERPLOT_THRESHOLD 166s Coverage level to trigger alternative plot type 166s instead of raw signal. Default: 50 166s --overplot-type {Downsample,Boxplot,Quantile,Density} 166s Plot type for regions with higher coverage. Default: 166s Downsample 166s 166s Plotting Region Arguments: 166s --num-regions NUM_REGIONS 166s Number of regions to plot. Default: 10 166s --num-bases NUM_BASES 166s Number of bases to plot/output. Default: 21 166s 166s Output Argument: 166s --pdf-filename PDF_FILENAME 166s PDF filename to store plot(s). Default: 166s tombo_results.max_coverage.pdf 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo plot genome_locations 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 166s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 166s [--plot-standard-model] 166s [--plot-alternate-model {dam,CpG,dcm,6mA,5mC}] 166s [--overplot-threshold OVERPLOT_THRESHOLD] 166s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 166s [--num-bases NUM_BASES] 166s [--pdf-filename PDF_FILENAME] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Arguments: 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 166s Genomic locations at which to plot signal. Format 166s locations as "chrm:position[:strand] 166s [chrm2:position2[:strand2] ...]" (strand not 166s applicable for all applications) 166s 166s Comparison Arguments: 166s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 166s Set of directories containing fast5 files for control 166s reads, containing only canonical nucleotides. 166s --plot-standard-model 166s Add default standard model distribution to the plot. 166s --plot-alternate-model {dam,CpG,dcm,6mA,5mC} 166s Add alternative model distribution to the plot. 166s 166s Overplotting Arguments: 166s --overplot-threshold OVERPLOT_THRESHOLD 166s Coverage level to trigger alternative plot type 166s instead of raw signal. Default: 50 166s --overplot-type {Downsample,Boxplot,Quantile,Density} 166s Plot type for regions with higher coverage. Default: 166s Downsample 166s 166s Plotting Region Argument: 166s --num-bases NUM_BASES 166s Number of bases to plot/output. Default: 21 166s 166s Output Argument: 166s --pdf-filename PDF_FILENAME 166s PDF filename to store plot(s). Default: 166s tombo_results.genome_locations.pdf 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo plot motif_centered 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s --motif MOTIF --genome-fasta GENOME_FASTA 166s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 166s [--plot-standard-model] 166s [--plot-alternate-model {5mC,6mA,CpG,dcm,dam}] 166s [--overplot-threshold OVERPLOT_THRESHOLD] 166s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 166s [--num-regions NUM_REGIONS] 166s [--num-bases NUM_BASES] [--deepest-coverage] 166s [--pdf-filename PDF_FILENAME] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Arguments: 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s --motif MOTIF Motif of interest at which to plot signal and 166s statsitics. Supports IUPAC single letter codes (use T 166s for RNA). 166s --genome-fasta GENOME_FASTA 166s FASTA file used to re-squiggle. For faster sequence 166s access. 166s 166s Comparison Arguments: 166s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 166s Set of directories containing fast5 files for control 166s reads, containing only canonical nucleotides. 166s --plot-standard-model 166s Add default standard model distribution to the plot. 166s --plot-alternate-model {5mC,6mA,CpG,dcm,dam} 166s Add alternative model distribution to the plot. 166s 166s Overplotting Arguments: 166s --overplot-threshold OVERPLOT_THRESHOLD 166s Coverage level to trigger alternative plot type 166s instead of raw signal. Default: 50 166s --overplot-type {Downsample,Boxplot,Quantile,Density} 166s Plot type for regions with higher coverage. Default: 166s Downsample 166s 166s Plotting Region Arguments: 166s --num-regions NUM_REGIONS 166s Number of regions to plot. Default: 10 166s --num-bases NUM_BASES 166s Number of bases to plot/output. Default: 21 166s --deepest-coverage Plot the deepest coverage regions. 166s 166s Output Argument: 166s --pdf-filename PDF_FILENAME 166s PDF filename to store plot(s). Default: 166s tombo_results.motif_centered.pdf 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo plot max_difference 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 166s [--overplot-threshold OVERPLOT_THRESHOLD] 166s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 166s [--num-regions NUM_REGIONS] 166s [--num-bases NUM_BASES] 166s [--pdf-filename PDF_FILENAME] 166s [--sequences-filename SEQUENCES_FILENAME] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Arguments: 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 166s Set of directories containing fast5 files for control 166s reads, containing only canonical nucleotides. 166s 166s Overplotting Arguments: 166s --overplot-threshold OVERPLOT_THRESHOLD 166s Coverage level to trigger alternative plot type 166s instead of raw signal. Default: 50 166s --overplot-type {Downsample,Boxplot,Quantile,Density} 166s Plot type for regions with higher coverage. Default: 166s Downsample 166s 166s Plotting Region Arguments: 166s --num-regions NUM_REGIONS 166s Number of regions to plot. Default: 10 166s --num-bases NUM_BASES 166s Number of bases to plot/output. Default: 21 166s 166s Output Arguments: 166s --pdf-filename PDF_FILENAME 166s PDF filename to store plot(s). Default: 166s tombo_results.max_difference.pdf 166s --sequences-filename SEQUENCES_FILENAME 166s File for sequences from selected regions. Sequences 166s will be stored in FASTA format. Default: None. 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo plot most_significant 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s --statistics-filename STATISTICS_FILENAME 166s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 166s [--plot-standard-model] 166s [--plot-alternate-model {CpG,dcm,6mA,5mC,dam}] 166s [--overplot-threshold OVERPLOT_THRESHOLD] 166s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 166s [--num-regions NUM_REGIONS] 166s [--num-bases NUM_BASES] 166s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 166s [--pdf-filename PDF_FILENAME] 166s [--sequences-filename SEQUENCES_FILENAME] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Arguments: 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s --statistics-filename STATISTICS_FILENAME 166s File to save/load genomic base anchored statistics. 166s 166s Comparison Arguments: 166s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 166s Set of directories containing fast5 files for control 166s reads, containing only canonical nucleotides. 166s --plot-standard-model 166s Add default standard model distribution to the plot. 166s --plot-alternate-model {CpG,dcm,6mA,5mC,dam} 166s Add alternative model distribution to the plot. 166s 166s Overplotting Arguments: 166s --overplot-threshold OVERPLOT_THRESHOLD 166s Coverage level to trigger alternative plot type 166s instead of raw signal. Default: 50 166s --overplot-type {Downsample,Boxplot,Quantile,Density} 166s Plot type for regions with higher coverage. Default: 166s Downsample 166s 166s Plotting Region Arguments: 166s --num-regions NUM_REGIONS 166s Number of regions to plot. Default: 10 166s --num-bases NUM_BASES 166s Number of bases to plot/output. Default: 21 166s 166s Statistical Argument: 166s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 166s Dampen fraction modified estimates for low coverage 166s sites. Two parameters are unmodified and modified 166s pseudo read counts. This is equivalent to a beta prior 166s on the fraction estimate. Set to "0 0" to disable 166s dampened fraction estimation. Default: [2, 0] 166s 166s Output Arguments: 166s --pdf-filename PDF_FILENAME 166s PDF filename to store plot(s). Default: 166s tombo_results.significant_difference.pdf 166s --sequences-filename SEQUENCES_FILENAME 166s File for sequences from selected regions. Sequences 166s will be stored in FASTA format. Default: None. 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo plot motif_with_stats 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s --motif MOTIF 166s --statistics-filename STATISTICS_FILENAME 166s --genome-fasta GENOME_FASTA 166s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 166s [--plot-standard-model] 166s [--plot-alternate-model {dam,6mA,CpG,5mC,dcm}] 166s [--overplot-threshold OVERPLOT_THRESHOLD] 166s [--num-regions NUM_REGIONS] 166s [--num-context NUM_CONTEXT] 166s [--num-statistics NUM_STATISTICS] 166s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 166s [--pdf-filename PDF_FILENAME] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Arguments: 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s --motif MOTIF Motif of interest at which to plot signal and 166s statsitics. Supports IUPAC single letter codes (use T 166s for RNA). 166s --statistics-filename STATISTICS_FILENAME 166s File to save/load genomic base anchored statistics. 166s --genome-fasta GENOME_FASTA 166s FASTA file used to re-squiggle. For faster sequence 166s access. 166s 166s Comparison Arguments: 166s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 166s Set of directories containing fast5 files for control 166s reads, containing only canonical nucleotides. 166s --plot-standard-model 166s Add default standard model distribution to the plot. 166s --plot-alternate-model {dam,6mA,CpG,5mC,dcm} 166s Add alternative model distribution to the plot. 166s 166s Overplotting Argument: 166s --overplot-threshold OVERPLOT_THRESHOLD 166s Coverage level to trigger alternative plot type 166s instead of raw signal. Default: 50 166s 166s Plotting Region Arguments: 166s --num-regions NUM_REGIONS 166s Number of regions to plot. Default: 3 166s --num-context NUM_CONTEXT 166s Number of context bases around motif. Default: 5 166s --num-statistics NUM_STATISTICS 166s Number of motif centered regions to include in 166s statistic distributions. Default: 200 166s 166s Statistical Argument: 166s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 166s Dampen fraction modified estimates for low coverage 166s sites. Two parameters are unmodified and modified 166s pseudo read counts. This is equivalent to a beta prior 166s on the fraction estimate. Set to "0 0" to disable 166s dampened fraction estimation. Default: [2, 0] 166s 166s Output Argument: 166s --pdf-filename PDF_FILENAME 166s PDF filename to store plot(s). Default: 166s tombo_results.motif_statistics.pdf 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo plot per_read 166s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 166s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 166s [--genome-fasta GENOME_FASTA] 166s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 166s [--num-reads NUM_READS] [--num-bases NUM_BASES] 166s [--box-center] [--pdf-filename PDF_FILENAME] 166s [--corrected-group CORRECTED_GROUP] 166s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 166s [--quiet] [--help] 166s 166s Required Arguments: 166s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 166s Genomic locations at which to plot signal. Format 166s locations as "chrm:position[:strand] 166s [chrm2:position2[:strand2] ...]" (strand not 166s applicable for all applications) 166s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 166s Binary file containing per-read statistics from 166s statistical testing. 166s 166s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 166s --genome-fasta GENOME_FASTA 166s FASTA file used to re-squiggle. For faster sequence 166s access. 166s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 166s Directories containing fast5 files. 166s 166s Plotting Region Arguments: 166s --num-reads NUM_READS 166s Number of reads to plot. Default: 100 166s --num-bases NUM_BASES 166s Number of bases to plot/output. Default: 51 166s --box-center Plot a box around the central base. 166s 166s Output Argument: 166s --pdf-filename PDF_FILENAME 166s PDF filename to store plot(s). Default: 166s tombo_results.per_read_stats.pdf 166s 166s FAST5 Data Arguments: 166s --corrected-group CORRECTED_GROUP 166s FAST5 group created by resquiggle command. Default: 166s RawGenomeCorrected_000 166s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 166s FAST5 subgroup(s) (under /Analyses/[--basecall- 166s group]/) containing basecalls and created within 166s [--corrected-group] containing re-squiggle results. 166s Default: ['BaseCalled_template'] 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 166s usage: tombo plot roc 166s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 166s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 166s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 166s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 166s [--genome-fasta GENOME_FASTA] 166s [--pdf-filename PDF_FILENAME] 166s [--statistics-per-block STATISTICS_PER_BLOCK] 166s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 166s [--quiet] [--help] 166s 166s Required Argument: 166s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 166s Files to load genomic base anchored statistics. 166s 166s Ground Truth Arguments (provide bed files or motifs): 166s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 166s Modification description and bed format files 166s containing single base locations of ground truth 166s modified sites. Bed files should contain 6 fields 166s including strand. Format descriptions as 166s "mod_name:locs.bed". Example: "CpG 166s bisulfite":bisulfite_locs.bed 166s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 166s Bed format files containing single base locations of 166s ground truth unmodified sites. Bed files should 166s contain 6 fields including strand. 166s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 166s Ground truth, motif centered, modified base 166s descriptions for computing ROC and PR curves. Each 166s statistics file is associated with a set of motif 166s descriptions. Format descriptions as: 166s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 166s mod_pos indicates the alternate-base within the motif 166s (1-based index). Example: CCWGG:2:"dcm 166s 5mC"::GATC:2:"dam 6mA" would assess the performance of 166s a single Tombo statistics file for identification of 166s E. coli dam and dcm methylation. 166s --genome-fasta GENOME_FASTA 166s FASTA file used to re-squiggle. For faster sequence 166s access. 166s 166s Output Arguments: 166s --pdf-filename PDF_FILENAME 166s PDF filename to store plot(s). Default: 166s tombo_results.roc.pdf 166s 166s Down-sampling Arguments: 166s --statistics-per-block STATISTICS_PER_BLOCK 166s Number of randomly selected per-read, per-base 166s statistics to extract from each genomic block for 166s plotting. Default: Include all stats 166s --total-statistics-limit TOTAL_STATISTICS_LIMIT 166s Total per-read statistics to be extracted for 166s plotting. Avoids memory overflow for large runs. 166s Default: 5000000 166s 166s Miscellaneous Arguments: 166s --quiet, -q Don't print status information. 166s --help, -h Print this help message and exit 167s usage: tombo plot per_read_roc 167s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 167s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 167s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 167s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 167s [--genome-fasta GENOME_FASTA] 167s [--statistics-per-block STATISTICS_PER_BLOCK] 167s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 167s [--pdf-filename PDF_FILENAME] [--quiet] 167s [--help] 167s 167s Required Argument: 167s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 167s Binary files containing per-read statistics from 167s statistical testing. 167s 167s Ground Truth Arguments (provide bed files or motifs): 167s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 167s Modification description and bed format files 167s containing single base locations of ground truth 167s modified sites. Bed files should contain 6 fields 167s including strand. Format descriptions as 167s "mod_name:locs.bed". Example: "CpG 167s bisulfite":bisulfite_locs.bed 167s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 167s Bed format files containing single base locations of 167s ground truth unmodified sites. Bed files should 167s contain 6 fields including strand. 167s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 167s Ground truth, motif centered, modified base 167s descriptions for computing ROC and PR curves. Each 167s statistics file is associated with a set of motif 167s descriptions. Format descriptions as: 167s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 167s mod_pos indicates the alternate-base within the motif 167s (1-based index). Example: CCWGG:2:"dcm 167s 5mC"::GATC:2:"dam 6mA" would assess the performance of 167s a single Tombo statistics file for identification of 167s E. coli dam and dcm methylation. 167s --genome-fasta GENOME_FASTA 167s FASTA file used to re-squiggle. For faster sequence 167s access. 167s 167s Down-sampling Arguments: 167s --statistics-per-block STATISTICS_PER_BLOCK 167s Number of randomly selected per-read, per-base 167s statistics to extract from each genomic block for 167s plotting. Default: 100000 167s --total-statistics-limit TOTAL_STATISTICS_LIMIT 167s Total per-read statistics to be extracted for 167s plotting. Avoids memory overflow for large runs. 167s Default: 5000000 167s 167s Output Arguments: 167s --pdf-filename PDF_FILENAME 167s PDF filename to store plot(s). Default: 167s tombo_results.per_reads_roc.pdf 167s 167s Miscellaneous Arguments: 167s --quiet, -q Don't print status information. 167s --help, -h Print this help message and exit 167s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 167s [--upstream-bases {0,1,2,3,4}] 167s [--downstream-bases {0,1,2,3,4}] [--read-mean] 167s [--num-kmer-threshold NUM_KMER_THRESHOLD] 167s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 167s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 167s [--corrected-group CORRECTED_GROUP] 167s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 167s [--quiet] [--help] 167s 167s Required Argument: 167s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 167s Directories containing fast5 files. 167s 167s Data Processing Arguments: 167s --upstream-bases {0,1,2,3,4} 167s Upstream bases in k-mer. Default: 1 167s --downstream-bases {0,1,2,3,4} 167s Downstream bases in k-mer. Default: 2 167s --read-mean Plot k-mer means across whole reads as opposed to 167s individual k-mer event levels. 167s --num-kmer-threshold NUM_KMER_THRESHOLD 167s Observations of each k-mer required to include a read 167s in read level averages. Default: 1 167s 167s Plotting Region Arguments: 167s --num-reads NUM_READS 167s Number of reads to plot. Default: 100 167s 167s Output Arguments: 167s --pdf-filename PDF_FILENAME 167s PDF filename to store plot(s). Default: 167s tombo_results.kmer_distribution.pdf 167s --r-data-filename R_DATA_FILENAME 167s Filename to save R data structure. Default: Don't save 167s --dont-plot Don't plot result. Useful to produce only R data file. 167s 167s FAST5 Data Arguments: 167s --corrected-group CORRECTED_GROUP 167s FAST5 group created by resquiggle command. Default: 167s RawGenomeCorrected_000 167s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 167s FAST5 subgroup(s) (under /Analyses/[--basecall- 167s group]/) containing basecalls and created within 167s [--corrected-group] containing re-squiggle results. 167s Default: ['BaseCalled_template'] 167s 167s Miscellaneous Arguments: 167s --quiet, -q Don't print status information. 167s --help, -h Print this help message and exit 167s usage: tombo plot cluster_most_significant 167s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 167s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 167s --statistics-filename STATISTICS_FILENAME 167s [--genome-fasta GENOME_FASTA] 167s [--processes PROCESSES] 167s [--num-regions NUM_REGIONS] 167s [--num-bases NUM_BASES] 167s [--slide-span SLIDE_SPAN] 167s [--pdf-filename PDF_FILENAME] 167s [--r-data-filename R_DATA_FILENAME] 167s [--corrected-group CORRECTED_GROUP] 167s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 167s [--quiet] [--help] 167s 167s Required Arguments: 167s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 167s Directories containing fast5 files. 167s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 167s Set of directories containing fast5 files for control 167s reads, containing only canonical nucleotides. 167s --statistics-filename STATISTICS_FILENAME 167s File to save/load genomic base anchored statistics. 167s 167s FASTA Sequence Argument: 167s --genome-fasta GENOME_FASTA 167s FASTA file used to re-squiggle. For faster sequence 167s access. 167s 167s Multiprocessing Argument: 167s --processes PROCESSES 167s Number of processes. Default: 1 167s 167s Plotting Region Arguments: 167s --num-regions NUM_REGIONS 167s Number of regions to plot. Default: 10 167s --num-bases NUM_BASES 167s Number of bases to plot/output. Default: 21 167s --slide-span SLIDE_SPAN 167s Number of bases offset over which to search when 167s computing distances for signal cluster plotting. 167s Default: 0 (exact position) 167s 167s Output Arguments: 167s --pdf-filename PDF_FILENAME 167s PDF filename to store plot(s). Default: 167s tombo_results.signal_clusters.pdf 167s --r-data-filename R_DATA_FILENAME 167s Filename to save R data structure. Default: Don't save 167s 167s FAST5 Data Arguments: 167s --corrected-group CORRECTED_GROUP 167s FAST5 group created by resquiggle command. Default: 167s RawGenomeCorrected_000 167s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 167s FAST5 subgroup(s) (under /Analyses/[--basecall- 167s group]/) containing basecalls and created within 167s [--corrected-group] containing re-squiggle results. 167s Default: ['BaseCalled_template'] 167s 167s Miscellaneous Arguments: 167s --quiet, -q Don't print status information. 167s --help, -h Print this help message and exit 167s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 167s 167s Required Arguments: 167s fast5s_basedir Directory containing fast5 files. All files ending in 167s "fast5" found recursively within this base directory will be 167s processed. 167s 167s Miscellaneous Arguments: 167s --quiet, -q Don't print status information. 167s --help, -h Print this help message and exit 167s usage: tombo build_model event_resquiggle 167s [--minimap2-executable MINIMAP2_EXECUTABLE] 167s [--minimap2-index MINIMAP2_INDEX] 167s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 167s [--graphmap-executable GRAPHMAP_EXECUTABLE] 167s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 167s [--normalization-type {median,pA,pA_raw,none}] 167s [--pore-model-filename PORE_MODEL_FILENAME] 167s [--outlier-threshold OUTLIER_THRESHOLD] 167s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 167s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 167s [--timeout TIMEOUT] 167s [--cpts-limit CPTS_LIMIT] 167s [--skip-index] [--overwrite] 167s [--failed-reads-filename FAILED_READS_FILENAME] 167s [--include-event-stdev] 167s [--corrected-group CORRECTED_GROUP] 167s [--basecall-group BASECALL_GROUP] 167s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 167s [--processes PROCESSES] 167s [--align-processes ALIGN_PROCESSES] 167s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 167s [--resquiggle-processes RESQUIGGLE_PROCESSES] 167s [--quiet] [--help] 167s fast5s_basedir reference_fasta 167s 167s Required Arguments: 167s fast5s_basedir Directory containing fast5 files. All files ending in 167s "fast5" found recursively within this base directory 167s will be processed. 167s reference_fasta Reference genome/transcriptome FASTA file for mapping. 167s 167s Mapper Arguments (One mapper is required): 167s --minimap2-executable MINIMAP2_EXECUTABLE 167s Path to minimap2 executable. 167s --minimap2-index MINIMAP2_INDEX 167s Path to minimap2 index (with map-ont preset) file 167s corresponding to the [genome_fasta] provided. 167s --bwa-mem-executable BWA_MEM_EXECUTABLE 167s Path to bwa-mem executable. 167s --graphmap-executable GRAPHMAP_EXECUTABLE 167s Path to graphmap executable. 167s --alignment-batch-size ALIGNMENT_BATCH_SIZE 167s Number of reads included in each alignment call. Note: 167s A new system mapping call is made for each batch 167s (including loading of the genome), so it is advised to 167s use larger values for larger genomes. Default: 1000 167s 167s Signal Processing Arguments: 167s --normalization-type {median,pA,pA_raw,none} 167s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 167s as in the ONT events (using offset, range and 167s digitization), "pA": k-mer-based correction for pA 167s drift as in nanopolish (requires [--pore-model- 167s filename]), "median": median and MAD from raw signal. 167s Default: median 167s --pore-model-filename PORE_MODEL_FILENAME 167s File containing kmer model parameters (level_mean and 167s level_stdv) used in order to compute kmer-based 167s corrected pA values. E.g. https://github.com/jts/nanop 167s olish/blob/master/etc/r9- 167s models/template_median68pA.5mers.model 167s --outlier-threshold OUTLIER_THRESHOLD 167s Windosrize the signal at this number of scale values. 167s Negative value disables outlier clipping. Default: 167s 5.000000 167s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 167s Specify the 2 parameters for segmentation 1) running 167s neighboring windows width 2) minimum raw observations 167s per genomic base. Sample type defaults: RNA : 12 6 || 167s DNA : 5 3 167s 167s Read Filtering Arguments: 167s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 167s Filter reads based on observations per base percentile 167s thresholds. Format thresholds as "percentile:thresh 167s [pctl2:thresh2 ...]". For example to filter reads with 167s 99th pctl > 200 obs/base or max > 5k obs/base use 167s "99:200 100:5000". 167s --timeout TIMEOUT Timeout in seconds for processing a single read. 167s Default: No timeout. 167s --cpts-limit CPTS_LIMIT 167s Maximum number of changepoints to find within a single 167s indel group. Default: No limit. 167s 167s Input/Output Arguments: 167s --skip-index Skip creation of tombo index. This drastically slows 167s downstream tombo commands. Default stores tombo index 167s named ".[--fast5-basedir].[--corrected- 167s group].tombo.index" to be loaded automatically for 167s downstream commands. 167s --overwrite Overwrite previous corrected group in FAST5 files. 167s Note: only effects --corrected-group or --new- 167s corrected-group. 167s --failed-reads-filename FAILED_READS_FILENAME 167s Output failed read filenames with assoicated error. 167s Default: Do not store failed reads. 167s --include-event-stdev 167s Include corrected event standard deviation in output 167s FAST5 data. 167s 167s FAST5 Data Arguments: 167s --corrected-group CORRECTED_GROUP 167s FAST5 group created by resquiggle command. Default: 167s RawGenomeCorrected_000 167s --basecall-group BASECALL_GROUP 167s FAST5 group obtain original basecalls (under Analyses 167s group). Default: Basecall_1D_000 167s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 167s FAST5 subgroup(s) (under /Analyses/[--basecall- 167s group]/) containing basecalls and created within 167s [--corrected-group] containing re-squiggle results. 167s Default: ['BaseCalled_template'] 167s 167s Multiprocessing Arguments: 167s --processes PROCESSES 167s Number of processes. Default: 2 167s --align-processes ALIGN_PROCESSES 167s Number of processes to use for parsing and aligning 167s original basecalls. Each process will independently 167s load the genome into memory, so use caution with 167s larger genomes (e.g. human). Default: 1 167s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 167s Number of threads to use for aligner system call. 167s Default: [--processes] / (2 * [--align-processes)] 167s --resquiggle-processes RESQUIGGLE_PROCESSES 167s Number of processes to use for resquiggle algorithm. 167s Default: [--processes] / 2 167s 167s Miscellaneous Arguments: 167s --quiet, -q Don't print status information. 167s --help, -h Print this help message and exit 167s usage: tombo build_model estimate_reference 167s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 167s --tombo-model-filename TOMBO_MODEL_FILENAME 167s [--estimate-mean] 167s [--kmer-specific-sd] 167s [--upstream-bases {0,1,2,3,4}] 167s [--downstream-bases {0,1,2,3,4}] 167s [--minimum-test-reads MINIMUM_TEST_READS] 167s [--coverage-threshold COVERAGE_THRESHOLD] 167s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 167s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 167s [--processes PROCESSES] 167s [--corrected-group CORRECTED_GROUP] 167s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 167s [--quiet] [--help] 167s 167s Required Arguments: 167s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 167s Directories containing fast5 files. 167s --tombo-model-filename TOMBO_MODEL_FILENAME 167s Filename to save Tombo model. 167s 167s Modeling Arguments: 167s --estimate-mean Use the mean instead of median for model level 167s estimation. Note: This can cause poor fits due to 167s outliers 167s --kmer-specific-sd Estimate standard deviation for each k-mers 167s individually. 167s --upstream-bases {0,1,2,3,4} 167s Upstream bases in k-mer. Default: 1 167s --downstream-bases {0,1,2,3,4} 167s Downstream bases in k-mer. Default: 2 167s 167s Filtering Arguments: 167s --minimum-test-reads MINIMUM_TEST_READS 167s Number of reads required at a position to perform 167s significance testing or contribute to model 167s estimation. Default: 10 167s --coverage-threshold COVERAGE_THRESHOLD 167s Maximum mean coverage per region when estimating k-mer 167s model (limits compute time for deep samples). Default: 167s 100 167s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 167s Number of each k-mer observations required in order to 167s produce a reference (genomic locations for standard 167s reference and per-read for alternative reference). 167s Default: 5 167s 167s Multiprocessing Arguments: 167s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 167s Size of regions over which to multiprocesses statistic 167s computation. For very deep samples a smaller value is 167s recommmended in order to control memory consumption. 167s Default: 10000 167s --processes PROCESSES 167s Number of processes. Default: 1 167s 167s FAST5 Data Arguments: 167s --corrected-group CORRECTED_GROUP 167s FAST5 group created by resquiggle command. Default: 167s RawGenomeCorrected_000 167s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 167s FAST5 subgroup(s) (under /Analyses/[--basecall- 167s group]/) containing basecalls and created within 167s [--corrected-group] containing re-squiggle results. 167s Default: ['BaseCalled_template'] 167s 167s Miscellaneous Arguments: 167s --quiet, -q Don't print status information. 167s --help, -h Print this help message and exit 167s usage: tombo build_model estimate_alt_reference 167s --alternate-model-filename ALTERNATE_MODEL_FILENAME 167s --alternate-model-name ALTERNATE_MODEL_NAME 167s --alternate-model-base {A,C,G,T} 167s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 167s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 167s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 167s [--control-density-filename CONTROL_DENSITY_FILENAME] 167s [--dna] [--rna] 167s [--tombo-model-filename TOMBO_MODEL_FILENAME] 167s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 167s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 167s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 167s [--save-density-basename SAVE_DENSITY_BASENAME] 167s [--processes PROCESSES] 167s [--corrected-group CORRECTED_GROUP] 167s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 167s [--quiet] [--help] 167s 167s Required Arguments: 167s --alternate-model-filename ALTERNATE_MODEL_FILENAME 167s Tombo model for alternative likelihood ratio 167s significance testing. 167s --alternate-model-name ALTERNATE_MODEL_NAME 167s A short name to associate with this alternate model 167s (e.g. 5mC, 6mA, etc.). This text will be included in 167s output filenames when this model is used for testing. 167s --alternate-model-base {A,C,G,T} 167s Non-standard base is an alternative to this base. 167s 167s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 167s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 167s Directories containing fast5 files. 167s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 167s Set of directories containing fast5 files for control 167s reads, containing only canonical nucleotides. 167s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 167s File containing k-mer level kernel density estimates 167s for the alternative sample saved using --save-density- 167s basename. 167s --control-density-filename CONTROL_DENSITY_FILENAME 167s File containing k-mer level kernel density estimates 167s for the control sample saved using --save-density- 167s basename. 167s 167s Standard Model Arguments: 167s --dna Explicitly select canonical DNA model. Default: 167s Automatically determine from FAST5s 167s --rna Explicitly select canonical RNA model. Default: 167s Automatically determine from FAST5s 167s --tombo-model-filename TOMBO_MODEL_FILENAME 167s Tombo model filename. If no file is provided, the 167s default DNA or RNA Tombo model will be used. 167s 167s Model Fitting Arguments: 167s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 167s When esitmating the alternative base incorporation 167s rate, this percent of k-mers are assumed to have 167s significantly shifted signal so the alternative 167s distribution minimally overlaps the standard base 167s distribution. Default: 5.000000 167s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 167s Bandwidth applied when performing Gaussian kernal 167s density esitmation on standard and alternative base 167s signal distributions. Default: 0.050000 167s 167s Filtering Argument: 167s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 167s Number of each k-mer observations required in order to 167s produce a reference (genomic locations for standard 167s reference and per-read for alternative reference). 167s Default: 1000 167s 167s Output Argument: 167s --save-density-basename SAVE_DENSITY_BASENAME 167s Basename to save alternative model estimation density 167s estimation information. See scripts/debug_est_alt.R 167s for info use example. Default: Don't save. 167s 167s Multiprocessing Arguments: 167s --processes PROCESSES 167s Number of processes. Default: 1 167s 167s FAST5 Data Arguments: 167s --corrected-group CORRECTED_GROUP 167s FAST5 group created by resquiggle command. Default: 167s RawGenomeCorrected_000 167s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 167s FAST5 subgroup(s) (under /Analyses/[--basecall- 167s group]/) containing basecalls and created within 167s [--corrected-group] containing re-squiggle results. 167s Default: ['BaseCalled_template'] 167s 167s Miscellaneous Arguments: 167s --quiet, -q Don't print status information. 167s --help, -h Print this help message and exit 167s This test only tests the help system 167s There is an extensive test in 167s 167s tombo/tests/shell_tests.sh 167s 167s but this requires to download larger data 167s sets which is not done for the moment. 167s autopkgtest [19:34:37]: test run-unit-test: -----------------------] 168s run-unit-test PASS 168s autopkgtest [19:34:38]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 168s autopkgtest [19:34:38]: @@@@@@@@@@@@@@@@@@@@ summary 168s run-unit-test PASS 187s nova [W] Using flock in prodstack6-s390x 187s flock: timeout while waiting to get lock 187s Creating nova instance adt-plucky-s390x-tombo-20250315-193150-juju-7f2275-prod-proposed-migration-environment-2-7cbd9197-1027-4db4-847f-4566ca894592 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 187s nova [W] Timed out waiting for 21d891fd-7912-4e66-998f-590ec4ca31c8 to get deleted.