0s autopkgtest [00:45:39]: starting date and time: 2025-02-20 00:45:39+0000 0s autopkgtest [00:45:39]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [00:45:39]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dv53sos8/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sphinx --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-16.secgroup --name adt-plucky-ppc64el-tombo-20250220-004539-juju-7f2275-prod-proposed-migration-environment-15-11177a40-ec92-4bf4-bca8-41e248e30f09 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -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/ 134s autopkgtest [00:47:53]: testbed dpkg architecture: ppc64el 134s autopkgtest [00:47:53]: testbed apt version: 2.9.30 135s autopkgtest [00:47:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 135s autopkgtest [00:47:54]: testbed release detected to be: None 136s autopkgtest [00:47:55]: updating testbed package index (apt update) 136s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 136s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 136s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 136s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 137s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 137s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [739 kB] 137s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [81.0 kB] 137s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.3 kB] 137s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [107 kB] 137s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el Packages [760 B] 137s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [685 kB] 137s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [5948 B] 137s Fetched 1749 kB in 1s (1677 kB/s) 138s Reading package lists... 139s + lsb_release --codename --short 139s + RELEASE=plucky 139s + cat 139s + [ plucky != trusty ] 139s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 140s Calculating upgrade... 140s The following packages will be upgraded: 140s lto-disabled-list 140s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Need to get 12.3 kB of archives. 140s After this operation, 1024 B of additional disk space will be used. 140s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el lto-disabled-list all 55 [12.3 kB] 141s Fetched 12.3 kB in 0s (84.4 kB/s) 141s (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 ... 106420 files and directories currently installed.) 141s Preparing to unpack .../lto-disabled-list_55_all.deb ... 141s Unpacking lto-disabled-list (55) over (54) ... 141s Setting up lto-disabled-list (55) ... 141s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 141s + /usr/lib/apt/apt-helper analyze-pattern ?true 141s + uname -r 141s + sed s/\./\\./g 141s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 141s + apt list ?obsolete 141s + + tail -n+2 141s cut -d/ -f1 141s + grep -v ^linux-.*6\.12\.0-15-generic.* 141s + true 141s + obsolete_pkgs= 141s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 142s + grep -q trusty /etc/lsb-release 142s + [ ! -d /usr/share/doc/unattended-upgrades ] 142s + [ ! -d /usr/share/doc/lxd ] 142s + [ ! -d /usr/share/doc/lxd-client ] 142s + [ ! -d /usr/share/doc/snapd ] 142s + type iptables 142s + cat 142s + chmod 755 /etc/rc.local 142s + . /etc/rc.local 142s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 142s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 142s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 142s + uname -m 142s + [ ppc64le = ppc64le ] 142s + systemctl is-active keyboard-setup.service 142s + [ active = failed ] 142s + [ -d /run/systemd/system ] 142s + systemd-detect-virt --quiet --vm 142s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 142s + cat 142s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 142s + echo COMPRESS=lz4 142s autopkgtest [00:48:01]: upgrading testbed (apt dist-upgrade and autopurge) 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 144s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 144s Starting 2 pkgProblemResolver with broken count: 0 144s Done 144s Entering ResolveByKeep 144s 145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Starting pkgProblemResolver with broken count: 0 145s Starting 2 pkgProblemResolver with broken count: 0 145s Done 146s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s autopkgtest [00:48:08]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP Tue Feb 4 16:32:08 UTC 2025 149s autopkgtest [00:48:08]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 153s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (dsc) [2291 B] 153s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (tar) [22.3 MB] 153s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build1 (diff) [9600 B] 153s gpgv: Signature made Wed Jan 29 22:42:44 2025 UTC 153s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 153s gpgv: Can't check signature: No public key 153s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7build1.dsc: no acceptable signature found 154s autopkgtest [00:48:13]: testing package tombo version 1.5.1-7build1 154s autopkgtest [00:48:13]: build not needed 155s autopkgtest [00:48:14]: test run-unit-test: preparing testbed 155s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Starting pkgProblemResolver with broken count: 0 156s Starting 2 pkgProblemResolver with broken count: 0 156s Done 157s The following NEW packages will be installed: 157s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 157s libhdf5-310 libhdf5-hl-310 libjs-jquery libjs-mathjax libjs-sphinxdoc 157s libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 python3-decorator 157s python3-h5py python3-h5py-serial python3-mappy python3-numpy 157s python3-packaging python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 157s tombo-doc 157s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 157s Need to get 70.1 MB of archives. 157s After this operation, 298 MB of additional disk space will be used. 157s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-lato all 2.015-1 [2781 kB] 157s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 157s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 158s Get:4 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libaec0 ppc64el 1.1.3-1 [30.1 kB] 158s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.1-2 [239 kB] 158s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 15-20250213-1ubuntu1 [613 kB] 158s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libsz2 ppc64el 1.1.3-1 [5566 B] 158s Get:8 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-310 ppc64el 1.14.5+repack-3 [1523 kB] 158s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-hl-310 ppc64el 1.14.5+repack-3 [74.9 kB] 158s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 158s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 158s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 158s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.1-2 [2813 kB] 158s Get:14 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 158s Get:15 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 158s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 158s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-13 [5146 kB] 158s Get:18 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py-serial ppc64el 3.12.1-1 [1603 kB] 158s Get:19 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py all 3.12.1-1 [7970 B] 158s Get:20 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mappy ppc64el 2.27+dfsg-1build1 [223 kB] 158s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.2-1 [51.5 kB] 158s Get:22 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-tqdm all 4.67.1-2 [92.5 kB] 158s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 158s Get:24 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.14.1-4ubuntu1 [22.7 MB] 159s Get:25 http://ftpmaster.internal/ubuntu plucky/universe ppc64el tombo ppc64el 1.5.1-7build1 [529 kB] 159s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 159s Get:27 http://ftpmaster.internal/ubuntu plucky/universe ppc64el tombo-doc all 1.5.1-7build1 [21.7 MB] 160s Fetched 70.1 MB in 3s (23.5 MB/s) 160s Selecting previously unselected package fonts-lato. 160s (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 ... 106420 files and directories currently installed.) 160s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 160s Unpacking fonts-lato (2.015-1) ... 161s Selecting previously unselected package fonts-font-awesome. 161s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 161s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 161s Selecting previously unselected package fonts-mathjax. 161s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 161s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 161s Selecting previously unselected package libaec0:ppc64el. 161s Preparing to unpack .../03-libaec0_1.1.3-1_ppc64el.deb ... 161s Unpacking libaec0:ppc64el (1.1.3-1) ... 161s Selecting previously unselected package libblas3:ppc64el. 161s Preparing to unpack .../04-libblas3_3.12.1-2_ppc64el.deb ... 161s Unpacking libblas3:ppc64el (3.12.1-2) ... 161s Selecting previously unselected package libgfortran5:ppc64el. 161s Preparing to unpack .../05-libgfortran5_15-20250213-1ubuntu1_ppc64el.deb ... 161s Unpacking libgfortran5:ppc64el (15-20250213-1ubuntu1) ... 161s Selecting previously unselected package libsz2:ppc64el. 161s Preparing to unpack .../06-libsz2_1.1.3-1_ppc64el.deb ... 161s Unpacking libsz2:ppc64el (1.1.3-1) ... 161s Selecting previously unselected package libhdf5-310:ppc64el. 161s Preparing to unpack .../07-libhdf5-310_1.14.5+repack-3_ppc64el.deb ... 161s Unpacking libhdf5-310:ppc64el (1.14.5+repack-3) ... 161s Selecting previously unselected package libhdf5-hl-310:ppc64el. 161s Preparing to unpack .../08-libhdf5-hl-310_1.14.5+repack-3_ppc64el.deb ... 161s Unpacking libhdf5-hl-310:ppc64el (1.14.5+repack-3) ... 161s Selecting previously unselected package libjs-jquery. 161s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 161s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 161s Selecting previously unselected package libjs-underscore. 161s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 161s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 161s Selecting previously unselected package libjs-sphinxdoc. 161s Preparing to unpack .../11-libjs-sphinxdoc_8.1.3-5_all.deb ... 161s Unpacking libjs-sphinxdoc (8.1.3-5) ... 161s Selecting previously unselected package liblapack3:ppc64el. 161s Preparing to unpack .../12-liblapack3_3.12.1-2_ppc64el.deb ... 161s Unpacking liblapack3:ppc64el (3.12.1-2) ... 161s Selecting previously unselected package liblbfgsb0:ppc64el. 161s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 161s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 161s Selecting previously unselected package liblzf1:ppc64el. 161s Preparing to unpack .../14-liblzf1_3.6-4_ppc64el.deb ... 161s Unpacking liblzf1:ppc64el (3.6-4) ... 161s Selecting previously unselected package python3-decorator. 161s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 161s Unpacking python3-decorator (5.1.1-5) ... 161s Selecting previously unselected package python3-numpy. 161s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-13_ppc64el.deb ... 161s Unpacking python3-numpy (1:1.26.4+ds-13) ... 162s Selecting previously unselected package python3-h5py-serial. 162s Preparing to unpack .../17-python3-h5py-serial_3.12.1-1_ppc64el.deb ... 162s Unpacking python3-h5py-serial (3.12.1-1) ... 162s Selecting previously unselected package python3-h5py. 162s Preparing to unpack .../18-python3-h5py_3.12.1-1_all.deb ... 162s Unpacking python3-h5py (3.12.1-1) ... 162s Selecting previously unselected package python3-mappy. 162s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1build1_ppc64el.deb ... 162s Unpacking python3-mappy (2.27+dfsg-1build1) ... 162s Selecting previously unselected package python3-packaging. 162s Preparing to unpack .../20-python3-packaging_24.2-1_all.deb ... 162s Unpacking python3-packaging (24.2-1) ... 162s Selecting previously unselected package python3-tqdm. 162s Preparing to unpack .../21-python3-tqdm_4.67.1-2_all.deb ... 162s Unpacking python3-tqdm (4.67.1-2) ... 162s Selecting previously unselected package sphinx-rtd-theme-common. 162s Preparing to unpack .../22-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 162s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 162s Selecting previously unselected package python3-scipy. 162s Preparing to unpack .../23-python3-scipy_1.14.1-4ubuntu1_ppc64el.deb ... 162s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 163s Selecting previously unselected package tombo. 163s Preparing to unpack .../24-tombo_1.5.1-7build1_ppc64el.deb ... 163s Unpacking tombo (1.5.1-7build1) ... 163s Selecting previously unselected package libjs-mathjax. 163s Preparing to unpack .../25-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 163s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 164s Selecting previously unselected package tombo-doc. 164s Preparing to unpack .../26-tombo-doc_1.5.1-7build1_all.deb ... 164s Unpacking tombo-doc (1.5.1-7build1) ... 165s Setting up fonts-lato (2.015-1) ... 165s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 165s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 165s Setting up python3-tqdm (4.67.1-2) ... 165s Setting up python3-mappy (2.27+dfsg-1build1) ... 165s Setting up libaec0:ppc64el (1.1.3-1) ... 165s Setting up python3-decorator (5.1.1-5) ... 165s Setting up libblas3:ppc64el (3.12.1-2) ... 165s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 165s Setting up python3-packaging (24.2-1) ... 166s Setting up liblzf1:ppc64el (3.6-4) ... 166s Setting up libgfortran5:ppc64el (15-20250213-1ubuntu1) ... 166s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 166s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 166s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 166s Setting up libsz2:ppc64el (1.1.3-1) ... 166s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 166s Setting up liblapack3:ppc64el (3.12.1-2) ... 166s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 166s Setting up python3-numpy (1:1.26.4+ds-13) ... 169s Setting up libjs-sphinxdoc (8.1.3-5) ... 169s Setting up tombo-doc (1.5.1-7build1) ... 169s Setting up libhdf5-310:ppc64el (1.14.5+repack-3) ... 169s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 169s Setting up libhdf5-hl-310:ppc64el (1.14.5+repack-3) ... 169s Setting up python3-scipy (1.14.1-4ubuntu1) ... 176s Setting up python3-h5py-serial (3.12.1-1) ... 177s Setting up python3-h5py (3.12.1-1) ... 177s Setting up tombo (1.5.1-7build1) ... 177s Processing triggers for man-db (2.13.0-1) ... 178s Processing triggers for libc-bin (2.40-4ubuntu1) ... 179s autopkgtest [00:48:38]: test run-unit-test: [----------------------- 180s ********* Testing help commands ********** 180s usage: tombo [-h] [-v] 180s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} ... 180s 180s ********** Tombo ********* 180s 180s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 180s 180s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 180s 180s Tombo command groups (additional help available within each command group): 180s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 180s preprocess Pre-process nanopore reads for Tombo processing. 180s filter Apply filter to Tombo index file for specified criterion. 180s detect_modifications Perform statistical testing to detect non-standard nucleotides. 180s text_output Output Tombo results in text files. 180s build_model Create canonical and alternative base Tombo models. 180s plot Save plots to visualize raw nanopore signal or testing results. 180s 180s options: 180s -h, --help show this help message and exit 180s -v, --version show Tombo version and exit. 180s usage: tombo resquiggle [--dna] [--rna] 180s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 180s [--q-score Q_SCORE] 180s [--signal-matching-score SIGNAL_MATCHING_SCORE] 180s [--processes PROCESSES] 180s [--corrected-group CORRECTED_GROUP] 180s [--basecall-group BASECALL_GROUP] 180s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 180s [--overwrite] 180s [--failed-reads-filename FAILED_READS_FILENAME] 180s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 180s [--print-advanced-arguments] [--quiet] [--help] 180s fast5s_basedir reference 180s 180s Required Arguments: 180s fast5s_basedir Directory containing fast5 files. All files ending in 180s "fast5" found recursively within this base directory 180s will be processed. 180s reference Reference genome/transcriptome FASTA file or minimap2 180s index (with "map-ont" preset) for mapping. 180s 180s Model Parameters: 180s --dna Explicitly select canonical DNA model. Default: 180s Automatically determine from FAST5s 180s --rna Explicitly select canonical RNA model. Default: 180s Automatically determine from FAST5s 180s 180s Read Filtering Argument: 180s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 180s Filter reads based on observations per base percentile 180s thresholds. Format thresholds as "percentile:thresh 180s [pctl2:thresh2 ...]". For example to filter reads with 180s 99th pctl > 200 obs/base or max > 5k obs/base use 180s "99:200 100:5000". 180s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 180s Default: 0.000000 180s --signal-matching-score SIGNAL_MATCHING_SCORE 180s Observed to expected signal matching score (higher 180s score indicates poor matching). Sample type defaults: 180s RNA : 2 || DNA : 1.1 180s 180s Multiprocessing Arguments: 180s --processes PROCESSES 180s Number of processes. Default: 1 180s 180s FAST5 Data Arguments: 180s --corrected-group CORRECTED_GROUP 180s FAST5 group created by resquiggle command. Default: 180s RawGenomeCorrected_000 180s --basecall-group BASECALL_GROUP 180s FAST5 group obtain original basecalls (under Analyses 180s group). Default: Basecall_1D_000 180s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 180s FAST5 subgroup(s) (under /Analyses/[--basecall- 180s group]/) containing basecalls and created within 180s [--corrected-group] containing re-squiggle results. 180s Default: ['BaseCalled_template'] 180s --overwrite Overwrite previous corrected group in FAST5 files. 180s Note: only effects --corrected-group or --new- 180s corrected-group. 180s 180s Input/Output Arguments: 180s --failed-reads-filename FAILED_READS_FILENAME 180s Output failed read filenames with assoicated error. 180s Default: Do not store failed reads. 180s --num-most-common-errors NUM_MOST_COMMON_ERRORS 180s Dynamically show this many most common errors so far 180s through run. Default: 0; Just show progress 180s 180s Advanced Arguments: 180s --print-advanced-arguments 180s Print advanced re-squiggle arguments and exit. 180s 180s Miscellaneous Arguments: 180s --quiet, -q Don't print status information. 180s --help, -h Print this help message and exit 180s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 180s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 180s [--basecall-group BASECALL_GROUP] 180s [--basecall-subgroup BASECALL_SUBGROUP] 180s [--overwrite] 180s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 180s [--processes PROCESSES] 180s [--quiet] [--help] 180s 180s Required Arguments: 180s --fast5-basedir FAST5_BASEDIR 180s Directory containing fast5 files. 180s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 180s FASTQ filenames containing basecalls to be added to 180s raw FAST5 files. 180s 180s FAST5 Data Arguments: 180s --basecall-group BASECALL_GROUP 180s FAST5 group obtain original basecalls (under Analyses 180s group). Default: Basecall_1D_000 180s --basecall-subgroup BASECALL_SUBGROUP 180s FAST5 subgroup (under /Analyses/[--basecall-group]/) 180s under which to store basecalls from FASTQs. Default: 180s BaseCalled_template 180s --overwrite Overwrite previous corrected group in FAST5 files. 180s Note: only effects --corrected-group or --new- 180s corrected-group. 180s 180s Sequencing Summary Argument: 180s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 180s Sequencing summary filenames produced by albacore. 180s These can make annotation of raw FAST5 files with 180s FASTQ sequence much faster. 180s 180s Multiprocessing Argument: 180s --processes PROCESSES 180s Number of processes. Default: 1 180s 180s Miscellaneous Arguments: 180s --quiet, -q Don't print status information. 180s --help, -h Print this help message and exit 180s usage: tombo filter clear_filters 180s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 180s [--corrected-group CORRECTED_GROUP] 180s [--quiet] [--help] 180s 180s Required Argument: 180s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 180s Directories containing fast5 files. 180s 180s FAST5 Data Argument: 180s --corrected-group CORRECTED_GROUP 180s FAST5 group created by resquiggle command. Default: 180s RawGenomeCorrected_000 180s 180s Miscellaneous Arguments: 180s --quiet, -q Don't print status information. 180s --help, -h Print this help message and exit 180s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 180s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 180s [--corrected-group CORRECTED_GROUP] [--quiet] 180s [--help] 180s 180s Required Argument: 180s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 180s Directories containing fast5 files. 180s 180s Read Filtering Argument: 180s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 180s Filter reads based on observations per base percentile 180s thresholds. Format thresholds as "percentile:thresh 180s [pctl2:thresh2 ...]". For example to filter reads with 180s 99th pctl > 200 obs/base or max > 5k obs/base use 180s "99:200 100:5000". 180s 180s FAST5 Data Argument: 180s --corrected-group CORRECTED_GROUP 180s FAST5 group created by resquiggle command. Default: 180s RawGenomeCorrected_000 180s 180s Miscellaneous Arguments: 180s --quiet, -q Don't print status information. 180s --help, -h Print this help message and exit 180s usage: tombo filter level_coverage 180s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 180s [--percent-to-filter PERCENT_TO_FILTER] 180s [--corrected-group CORRECTED_GROUP] 180s [--quiet] [--help] 180s 180s Required Arguments: 180s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 180s Directories containing fast5 files. 180s 180s Read Filtering Argument: 180s --percent-to-filter PERCENT_TO_FILTER 180s Percentage of all reads to filter. Reads are randomly 180s selected weighted according to the approximate 180s coverage at the mapped genomic location. This can be 180s useful in modeling and testing. Default: 10.000000 180s 180s FAST5 Data Arguments: 180s --corrected-group CORRECTED_GROUP 180s FAST5 group created by resquiggle command. Default: 180s RawGenomeCorrected_000 180s 180s Miscellaneous Arguments: 180s --quiet, -q Don't print status information. 180s --help, -h Print this help message and exit 180s usage: tombo filter q_score 180s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 180s [--q-score Q_SCORE] 180s [--corrected-group CORRECTED_GROUP] 180s [--basecall-group BASECALL_GROUP] [--quiet] 180s [--help] 180s 180s Required Arguments: 180s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 180s Directories containing fast5 files. 180s 180s Read Filtering Argument: 180s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 180s Default: 7.000000 180s 180s FAST5 Data Arguments: 180s --corrected-group CORRECTED_GROUP 180s FAST5 group created by resquiggle command. Default: 180s RawGenomeCorrected_000 180s --basecall-group BASECALL_GROUP 180s FAST5 group obtain original basecalls (under Analyses 180s group). Default: Basecall_1D_000 180s 180s Miscellaneous Arguments: 180s --quiet, -q Don't print status information. 180s --help, -h Print this help message and exit 181s usage: tombo filter raw_signal_matching 181s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 181s --signal-matching-score SIGNAL_MATCHING_SCORE 181s [--corrected-group CORRECTED_GROUP] 181s [--quiet] [--help] 181s 181s Required Arguments: 181s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 181s Directories containing fast5 files. 181s --signal-matching-score SIGNAL_MATCHING_SCORE 181s Observed to expected signal matching score (higher 181s score indicates poor matching). Sample type defaults: 181s RNA : 2 || DNA : 1.1 181s 181s FAST5 Data Arguments: 181s --corrected-group CORRECTED_GROUP 181s FAST5 group created by resquiggle command. Default: 181s RawGenomeCorrected_000 181s 181s Miscellaneous Arguments: 181s --quiet, -q Don't print status information. 181s --help, -h Print this help message and exit 181s usage: tombo filter genome_locations 181s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 181s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 181s [--include-partial-overlap] 181s [--corrected-group CORRECTED_GROUP] 181s [--quiet] [--help] 181s 181s Required Arguments: 181s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 181s Directories containing fast5 files. 181s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 181s Filter out reads not falling completely within include 181s regions. Omit start and end coordinates to include an 181s entire chromosome/sequence record. Format regions as 181s "chrm[:start-end] [chrm2[:start2-end2] ...]". 181s 181s Filter Argument: 181s --include-partial-overlap 181s Include reads that partially overlap the specified 181s region. Default: Only include reads completely 181s contained in a specified region 181s 181s FAST5 Data Argument: 181s --corrected-group CORRECTED_GROUP 181s FAST5 group created by resquiggle command. Default: 181s RawGenomeCorrected_000 181s 181s Miscellaneous Arguments: 181s --quiet, -q Don't print status information. 181s --help, -h Print this help message and exit 181s usage: tombo detect_modifications de_novo 181s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 181s --statistics-file-basename STATISTICS_FILE_BASENAME 181s [--dna] [--rna] 181s [--fishers-method-context FISHERS_METHOD_CONTEXT] 181s [--minimum-test-reads MINIMUM_TEST_READS] 181s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 181s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 181s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 181s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 181s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 181s [--processes PROCESSES] 181s [--corrected-group CORRECTED_GROUP] 181s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 181s [--quiet] [--help] 181s 181s Required Argument: 181s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 181s Directories containing fast5 files. 181s --statistics-file-basename STATISTICS_FILE_BASENAME 181s File base name to save base by base statistics from 181s testing. Filenames will be [--statistics-file- 181s basename].[--alternate-bases]?.tombo.stats 181s 181s Comparison Model Arguments: 181s --dna Explicitly select canonical DNA model. Default: 181s Automatically determine from FAST5s 181s --rna Explicitly select canonical RNA model. Default: 181s Automatically determine from FAST5s 181s 181s Significance Test Arguments: 181s --fishers-method-context FISHERS_METHOD_CONTEXT 181s Number of context bases up and downstream over which 181s to compute Fisher's method combined p-values. Note: 181s Not applicable for alternative model likelihood ratio 181s tests. Default: 1. 181s --minimum-test-reads MINIMUM_TEST_READS 181s Number of reads required at a position to perform 181s significance testing or contribute to model 181s estimation. Default: 1 181s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 181s P-value threshold when computing fraction of 181s significant reads at each genomic position. If two 181s values are provided, statistics between these values 181s are not considered. Default thresholds: DNA:0.15-0.5 , 181s RNA:0.05-0.4 181s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 181s Dampen fraction modified estimates for low coverage 181s sites. Two parameters are unmodified and modified 181s pseudo read counts. This is equivalent to a beta prior 181s on the fraction estimate. Set to "0 0" to disable 181s dampened fraction estimation. Default: [2, 0] 181s 181s Output Argument: 181s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 181s Base for binary files containing per-read statistics 181s from statistical testing. Filenames will be [--per- 181s read-statistics-basename].[--alternate- 181s bases]?.tombo.per_read_stats 181s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 181s Number of the most significant sites to store for 181s faster access. If a longer list of most significant 181s sites is required the list must be re-computed from 181s all batches. Very large values can increase RAM usage. 181s Default: 100000 181s 181s Multiprocessing Arguments: 181s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 181s Size of regions over which to multiprocesses statistic 181s computation. For very deep samples a smaller value is 181s recommmended in order to control memory consumption. 181s Default: 10000 181s --processes PROCESSES 181s Number of processes. Default: 1 181s 181s FAST5 Data Arguments: 181s --corrected-group CORRECTED_GROUP 181s FAST5 group created by resquiggle command. Default: 181s RawGenomeCorrected_000 181s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 181s FAST5 subgroup(s) (under /Analyses/[--basecall- 181s group]/) containing basecalls and created within 181s [--corrected-group] containing re-squiggle results. 181s Default: ['BaseCalled_template'] 181s 181s Miscellaneous Arguments: 181s --quiet, -q Don't print status information. 181s --help, -h Print this help message and exit 181s usage: tombo detect_modifications alternative_model 181s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 181s [--statistics-file-basename STATISTICS_FILE_BASENAME] 181s [--alternate-bases {dcm,CpG,6mA,5mC,dam} [{dcm,CpG,6mA,5mC,dam} ...]] 181s [--print-available-models] 181s [--dna] [--rna] 181s [--minimum-test-reads MINIMUM_TEST_READS] 181s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 181s [--standard-log-likelihood-ratio] 181s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 181s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 181s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 181s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 181s [--processes PROCESSES] 181s [--corrected-group CORRECTED_GROUP] 181s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 181s [--quiet] [--help] 181s 181s Required Argument: 181s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 181s Directories containing fast5 files. 181s --statistics-file-basename STATISTICS_FILE_BASENAME 181s File base name to save base by base statistics from 181s testing. Filenames will be [--statistics-file- 181s basename].[--alternate-bases]?.tombo.stats 181s --alternate-bases {dcm,CpG,6mA,5mC,dam} [{dcm,CpG,6mA,5mC,dam} ...] 181s Default non-standard base model for testing (not 181s required if user created --alternate-model-filenames 181s is provided). 181s 181s Comparison Arguments: 181s --print-available-models 181s Print available alternative models and exit. 181s --dna Explicitly select canonical DNA model. Default: 181s Automatically determine from FAST5s 181s --rna Explicitly select canonical RNA model. Default: 181s Automatically determine from FAST5s 181s 181s Significance Test Arguments: 181s --minimum-test-reads MINIMUM_TEST_READS 181s Number of reads required at a position to perform 181s significance testing or contribute to model 181s estimation. Default: 1 181s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 181s Log likelihood ratio threshold when computing fraction 181s of significant reads at each genomic position. If two 181s values are provided, statistics between these values 181s are not considered. Default thresholds: DNA:-1.5-2.5 , 181s RNA:-2.5-2.5 181s --standard-log-likelihood-ratio 181s Use a standard log likelihood ratio (LLR) statistic. 181s Default is to use an outlier-robust LLR-like 181s statistic. Detail in full online documentation. 181s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 181s Dampen fraction modified estimates for low coverage 181s sites. Two parameters are unmodified and modified 181s pseudo read counts. This is equivalent to a beta prior 181s on the fraction estimate. Set to "0 0" to disable 181s dampened fraction estimation. Default: [2, 0] 181s 181s Output Argument: 181s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 181s Base for binary files containing per-read statistics 181s from statistical testing. Filenames will be [--per- 181s read-statistics-basename].[--alternate- 181s bases]?.tombo.per_read_stats 181s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 181s Number of the most significant sites to store for 181s faster access. If a longer list of most significant 181s sites is required the list must be re-computed from 181s all batches. Very large values can increase RAM usage. 181s Default: 100000 181s 181s Multiprocessing Arguments: 181s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 181s Size of regions over which to multiprocesses statistic 181s computation. For very deep samples a smaller value is 181s recommmended in order to control memory consumption. 181s Default: 10000 181s --processes PROCESSES 181s Number of processes. Default: 1 181s 181s FAST5 Data Arguments: 181s --corrected-group CORRECTED_GROUP 181s FAST5 group created by resquiggle command. Default: 181s RawGenomeCorrected_000 181s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 181s FAST5 subgroup(s) (under /Analyses/[--basecall- 181s group]/) containing basecalls and created within 181s [--corrected-group] containing re-squiggle results. 181s Default: ['BaseCalled_template'] 181s 181s Miscellaneous Arguments: 181s --quiet, -q Don't print status information. 181s --help, -h Print this help message and exit 181s usage: tombo detect_modifications model_sample_compare 181s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 181s --statistics-file-basename STATISTICS_FILE_BASENAME 181s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 181s [--sample-only-estimates] 181s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 181s [--dna] [--rna] 181s [--fishers-method-context FISHERS_METHOD_CONTEXT] 181s [--minimum-test-reads MINIMUM_TEST_READS] 181s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 181s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 181s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 181s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 181s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 181s [--processes PROCESSES] 181s [--corrected-group CORRECTED_GROUP] 181s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 181s [--quiet] [--help] 181s 181s Required Argument: 181s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 181s Directories containing fast5 files. 181s --statistics-file-basename STATISTICS_FILE_BASENAME 181s File base name to save base by base statistics from 181s testing. Filenames will be [--statistics-file- 181s basename].[--alternate-bases]?.tombo.stats 181s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 181s Set of directories containing fast5 files for control 181s reads, containing only canonical nucleotides. 181s 181s Model Prior Arguments: 181s --sample-only-estimates 181s Only use canonical sample to estimate expected signal 181s level and spread. Default: Use canonical model to 181s improve estimtates (esp. for low coverage regions) 181s using baysian posterior estimates. 181s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 181s Prior weights (one each for mean and spread) applied 181s to canonical base model for estimating posterior model 181s parameters for sample comparison. Default: [5, 40] 181s --dna Explicitly select canonical DNA model. Default: 181s Automatically determine from FAST5s 181s --rna Explicitly select canonical RNA model. Default: 181s Automatically determine from FAST5s 181s 181s Significance Test Arguments: 181s --fishers-method-context FISHERS_METHOD_CONTEXT 181s Number of context bases up and downstream over which 181s to compute Fisher's method combined p-values. Note: 181s Not applicable for alternative model likelihood ratio 181s tests. Default: 1. 181s --minimum-test-reads MINIMUM_TEST_READS 181s Number of reads required at a position to perform 181s significance testing or contribute to model 181s estimation. Default: 1 181s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 181s P-value threshold when computing fraction of 181s significant reads at each genomic position. If two 181s values are provided, statistics between these values 181s are not considered. Default thresholds: DNA:0.15-0.5 , 181s RNA:0.05-0.4 181s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 181s Dampen fraction modified estimates for low coverage 181s sites. Two parameters are unmodified and modified 181s pseudo read counts. This is equivalent to a beta prior 181s on the fraction estimate. Set to "0 0" to disable 181s dampened fraction estimation. Default: [2, 0] 181s 181s Output Argument: 181s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 181s Base for binary files containing per-read statistics 181s from statistical testing. Filenames will be [--per- 181s read-statistics-basename].[--alternate- 181s bases]?.tombo.per_read_stats 181s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 181s Number of the most significant sites to store for 181s faster access. If a longer list of most significant 181s sites is required the list must be re-computed from 181s all batches. Very large values can increase RAM usage. 181s Default: 100000 181s 181s Multiprocessing Arguments: 181s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 181s Size of regions over which to multiprocesses statistic 181s computation. For very deep samples a smaller value is 181s recommmended in order to control memory consumption. 181s Default: 10000 181s --processes PROCESSES 181s Number of processes. Default: 1 181s 181s FAST5 Data Arguments: 181s --corrected-group CORRECTED_GROUP 181s FAST5 group created by resquiggle command. Default: 181s RawGenomeCorrected_000 181s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 181s FAST5 subgroup(s) (under /Analyses/[--basecall- 181s group]/) containing basecalls and created within 181s [--corrected-group] containing re-squiggle results. 181s Default: ['BaseCalled_template'] 181s 181s Miscellaneous Arguments: 181s --quiet, -q Don't print status information. 181s --help, -h Print this help message and exit 181s usage: tombo detect_modifications level_sample_compare 181s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 181s --statistics-file-basename STATISTICS_FILE_BASENAME 181s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 181s [--fishers-method-context FISHERS_METHOD_CONTEXT] 181s [--minimum-test-reads MINIMUM_TEST_READS] 181s [--statistic-type {ks,u,t}] 181s [--store-p-value] 181s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 181s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 181s [--processes PROCESSES] 181s [--corrected-group CORRECTED_GROUP] 181s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 181s [--quiet] [--help] 181s 181s Required Argument: 181s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 181s Directories containing fast5 files. 181s --statistics-file-basename STATISTICS_FILE_BASENAME 181s File base name to save base by base statistics from 181s testing. Filenames will be [--statistics-file- 181s basename].[--alternate-bases]?.tombo.stats 181s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 181s Set of directories containing fast5 files for 181s alternate set of reads. 181s 181s Significance Test Arguments: 181s --fishers-method-context FISHERS_METHOD_CONTEXT 181s Number of context bases up and downstream over which 181s to compute Fisher's method combined p-values. Note: 181s Not applicable for alternative model likelihood ratio 181s tests. Default: 1. 181s --minimum-test-reads MINIMUM_TEST_READS 181s Number of reads required at a position to perform 181s significance testing or contribute to model 181s estimation. Default: 50 181s --statistic-type {ks,u,t} 181s Type of statistical test to apply. Default: "ks" 181s --store-p-value Store p-value instead of effect-size statistic. 181s Statistics are D-statistic (KS-test), deviation from 181s even common language effect size (u-test), and Cohen's 181s D (t-test). 181s 181s Output Argument: 181s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 181s Number of the most significant sites to store for 181s faster access. If a longer list of most significant 181s sites is required the list must be re-computed from 181s all batches. Very large values can increase RAM usage. 181s Default: 100000 181s 181s Multiprocessing Arguments: 181s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 181s Size of regions over which to multiprocesses statistic 181s computation. For very deep samples a smaller value is 181s recommmended in order to control memory consumption. 181s Default: 10000 181s --processes PROCESSES 181s Number of processes. Default: 1 181s 181s FAST5 Data Arguments: 181s --corrected-group CORRECTED_GROUP 181s FAST5 group created by resquiggle command. Default: 181s RawGenomeCorrected_000 181s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 181s FAST5 subgroup(s) (under /Analyses/[--basecall- 181s group]/) containing basecalls and created within 181s [--corrected-group] containing re-squiggle results. 181s Default: ['BaseCalled_template'] 181s 181s Miscellaneous Arguments: 181s --quiet, -q Don't print status information. 181s --help, -h Print this help message and exit 181s usage: tombo detect_modifications aggregate_per_read_stats 181s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 181s --statistics-filename STATISTICS_FILENAME 181s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 181s [--minimum-test-reads MINIMUM_TEST_READS] 181s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 181s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 181s [--processes PROCESSES] 181s [--corrected-group CORRECTED_GROUP] 181s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 181s [--quiet] [--help] 181s 181s Required Argument: 181s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 181s Binary file containing per-read statistics from 181s statistical testing. 181s --statistics-filename STATISTICS_FILENAME 181s File to save/load genomic base anchored statistics. 181s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 181s P-value or log likelihood ratio threshold when 181s computing fraction of significant reads at each 181s genomic position. If two values are provided, 181s statistics between these values are not considered. 181s 181s Significance Test Arguments: 181s --minimum-test-reads MINIMUM_TEST_READS 181s Number of reads required at a position to perform 181s significance testing or contribute to model 181s estimation. Default: 1 181s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 181s Dampen fraction modified estimates for low coverage 181s sites. Two parameters are unmodified and modified 181s pseudo read counts. This is equivalent to a beta prior 181s on the fraction estimate. Set to "0 0" to disable 181s dampened fraction estimation. Default: [2, 0] 181s 181s Output Argument: 181s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 181s Number of the most significant sites to store for 181s faster access. If a longer list of most significant 181s sites is required the list must be re-computed from 181s all batches. Very large values can increase RAM usage. 181s Default: 100000 181s 181s Multiprocessing Arguments: 181s --processes PROCESSES 181s Number of processes. Default: 1 181s 181s FAST5 Data Arguments: 181s --corrected-group CORRECTED_GROUP 181s FAST5 group created by resquiggle command. Default: 181s RawGenomeCorrected_000 181s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 181s FAST5 subgroup(s) (under /Analyses/[--basecall- 181s group]/) containing basecalls and created within 181s [--corrected-group] containing re-squiggle results. 181s Default: ['BaseCalled_template'] 181s 181s Miscellaneous Arguments: 181s --quiet, -q Don't print status information. 181s --help, -h Print this help message and exit 181s usage: tombo text_output browser_files 181s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 181s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 181s [--statistics-filename STATISTICS_FILENAME] 181s [--genome-fasta GENOME_FASTA] 181s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 181s [--browser-file-basename BROWSER_FILE_BASENAME] 181s [--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} ...]] 181s [--corrected-group CORRECTED_GROUP] 181s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 181s [--quiet] [--help] 181s 181s Data Arguments: 181s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 181s Directories containing fast5 files. 181s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 181s Set of directories containing fast5 files for control 181s reads, containing only canonical nucleotides. 181s --statistics-filename STATISTICS_FILENAME 181s File to save/load genomic base anchored statistics. 181s 181s Statistic Motif Filter Arguments: 181s --genome-fasta GENOME_FASTA 181s FASTA file used to re-squiggle. For faster sequence 181s access. 181s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 181s Ground truth, motif centered, modified base 181s descriptions for output filtering. Format descriptions 181s as: "motif:mod_pos:name". The mod_pos indicates the 181s modified base within the motif (1-based index). 181s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 181s output for identification of E. coli dam and dcm 181s methylation. 181s 181s Output Arguments: 181s --browser-file-basename BROWSER_FILE_BASENAME 181s Basename for output browser files. Two files (plus and 181s minus strand) will be produced for each --file-types 181s supplied. Filenames formatted as "[browser-file- 181s basename].[file- 181s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 181s Default: tombo_results 181s --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} ...] 181s Data types of genome browser files to produce. 181s Produced coverage files are in bedGraph format, while 181s all other file types will be in wiggle format 181s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 181s Default: "coverage" 181s 181s FAST5 Data Arguments: 181s --corrected-group CORRECTED_GROUP 181s FAST5 group created by resquiggle command. Default: 181s RawGenomeCorrected_000 181s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 181s FAST5 subgroup(s) (under /Analyses/[--basecall- 181s group]/) containing basecalls and created within 181s [--corrected-group] containing re-squiggle results. 181s Default: ['BaseCalled_template'] 181s 181s Miscellaneous Arguments: 181s --quiet, -q Don't print status information. 181s --help, -h Print this help message and exit 182s usage: tombo text_output signif_sequence_context 182s --statistics-filename STATISTICS_FILENAME 182s [--genome-fasta GENOME_FASTA] 182s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 182s [--num-regions NUM_REGIONS] 182s [--num-bases NUM_BASES] 182s [--sequences-filename SEQUENCES_FILENAME] 182s [--corrected-group CORRECTED_GROUP] 182s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 182s [--quiet] [--help] 182s 182s Required Argument: 182s --statistics-filename STATISTICS_FILENAME 182s File to save/load genomic base anchored statistics. 182s 182s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 182s --genome-fasta GENOME_FASTA 182s FASTA file used to re-squiggle. For faster sequence 182s access. 182s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 182s Directories containing fast5 files. 182s 182s Region Selection Arguments: 182s --num-regions NUM_REGIONS 182s Number of regions to plot. Default: 100 182s --num-bases NUM_BASES 182s Number of bases to plot/output. Default: 15 182s 182s Output Arguments: 182s --sequences-filename SEQUENCES_FILENAME 182s File for sequences from selected regions. Sequences 182s will be stored in FASTA format. Default: 182s tombo_results.significant_regions.fasta. 182s 182s FAST5 Data Arguments: 182s --corrected-group CORRECTED_GROUP 182s FAST5 group created by resquiggle command. Default: 182s RawGenomeCorrected_000 182s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 182s FAST5 subgroup(s) (under /Analyses/[--basecall- 182s group]/) containing basecalls and created within 182s [--corrected-group] containing re-squiggle results. 182s Default: ['BaseCalled_template'] 182s 182s Miscellaneous Arguments: 182s --quiet, -q Don't print status information. 182s --help, -h Print this help message and exit 182s usage: tombo plot max_coverage 182s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 182s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 182s [--plot-standard-model] 182s [--plot-alternate-model {dcm,CpG,dam,6mA,5mC}] 182s [--overplot-threshold OVERPLOT_THRESHOLD] 182s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 182s [--num-regions NUM_REGIONS] 182s [--num-bases NUM_BASES] 182s [--pdf-filename PDF_FILENAME] 182s [--corrected-group CORRECTED_GROUP] 182s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 182s [--quiet] [--help] 182s 182s Required Argument: 182s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 182s Directories containing fast5 files. 182s 182s Comparison Arguments: 182s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 182s Set of directories containing fast5 files for control 182s reads, containing only canonical nucleotides. 182s --plot-standard-model 182s Add default standard model distribution to the plot. 182s --plot-alternate-model {dcm,CpG,dam,6mA,5mC} 182s Add alternative model distribution to the plot. 182s 182s Overplotting Arguments: 182s --overplot-threshold OVERPLOT_THRESHOLD 182s Coverage level to trigger alternative plot type 182s instead of raw signal. Default: 50 182s --overplot-type {Downsample,Boxplot,Quantile,Density} 182s Plot type for regions with higher coverage. Default: 182s Downsample 182s 182s Plotting Region Arguments: 182s --num-regions NUM_REGIONS 182s Number of regions to plot. Default: 10 182s --num-bases NUM_BASES 182s Number of bases to plot/output. Default: 21 182s 182s Output Argument: 182s --pdf-filename PDF_FILENAME 182s PDF filename to store plot(s). Default: 182s tombo_results.max_coverage.pdf 182s 182s FAST5 Data Arguments: 182s --corrected-group CORRECTED_GROUP 182s FAST5 group created by resquiggle command. Default: 182s RawGenomeCorrected_000 182s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 182s FAST5 subgroup(s) (under /Analyses/[--basecall- 182s group]/) containing basecalls and created within 182s [--corrected-group] containing re-squiggle results. 182s Default: ['BaseCalled_template'] 182s 182s Miscellaneous Arguments: 182s --quiet, -q Don't print status information. 182s --help, -h Print this help message and exit 182s usage: tombo plot genome_locations 182s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 182s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 182s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 182s [--plot-standard-model] 182s [--plot-alternate-model {dam,dcm,6mA,5mC,CpG}] 182s [--overplot-threshold OVERPLOT_THRESHOLD] 182s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 182s [--num-bases NUM_BASES] 182s [--pdf-filename PDF_FILENAME] 182s [--corrected-group CORRECTED_GROUP] 182s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 182s [--quiet] [--help] 182s 182s Required Arguments: 182s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 182s Directories containing fast5 files. 182s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 182s Genomic locations at which to plot signal. Format 182s locations as "chrm:position[:strand] 182s [chrm2:position2[:strand2] ...]" (strand not 182s applicable for all applications) 182s 182s Comparison Arguments: 182s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 182s Set of directories containing fast5 files for control 182s reads, containing only canonical nucleotides. 182s --plot-standard-model 182s Add default standard model distribution to the plot. 182s --plot-alternate-model {dam,dcm,6mA,5mC,CpG} 182s Add alternative model distribution to the plot. 182s 182s Overplotting Arguments: 182s --overplot-threshold OVERPLOT_THRESHOLD 182s Coverage level to trigger alternative plot type 182s instead of raw signal. Default: 50 182s --overplot-type {Downsample,Boxplot,Quantile,Density} 182s Plot type for regions with higher coverage. Default: 182s Downsample 182s 182s Plotting Region Argument: 182s --num-bases NUM_BASES 182s Number of bases to plot/output. Default: 21 182s 182s Output Argument: 182s --pdf-filename PDF_FILENAME 182s PDF filename to store plot(s). Default: 182s tombo_results.genome_locations.pdf 182s 182s FAST5 Data Arguments: 182s --corrected-group CORRECTED_GROUP 182s FAST5 group created by resquiggle command. Default: 182s RawGenomeCorrected_000 182s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 182s FAST5 subgroup(s) (under /Analyses/[--basecall- 182s group]/) containing basecalls and created within 182s [--corrected-group] containing re-squiggle results. 182s Default: ['BaseCalled_template'] 182s 182s Miscellaneous Arguments: 182s --quiet, -q Don't print status information. 182s --help, -h Print this help message and exit 182s usage: tombo plot motif_centered 182s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 182s --motif MOTIF --genome-fasta GENOME_FASTA 182s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 182s [--plot-standard-model] 182s [--plot-alternate-model {5mC,6mA,dam,dcm,CpG}] 182s [--overplot-threshold OVERPLOT_THRESHOLD] 182s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 182s [--num-regions NUM_REGIONS] 182s [--num-bases NUM_BASES] [--deepest-coverage] 182s [--pdf-filename PDF_FILENAME] 182s [--corrected-group CORRECTED_GROUP] 182s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 182s [--quiet] [--help] 182s 182s Required Arguments: 182s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 182s Directories containing fast5 files. 182s --motif MOTIF Motif of interest at which to plot signal and 182s statsitics. Supports IUPAC single letter codes (use T 182s for RNA). 182s --genome-fasta GENOME_FASTA 182s FASTA file used to re-squiggle. For faster sequence 182s access. 182s 182s Comparison Arguments: 182s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 182s Set of directories containing fast5 files for control 182s reads, containing only canonical nucleotides. 182s --plot-standard-model 182s Add default standard model distribution to the plot. 182s --plot-alternate-model {5mC,6mA,dam,dcm,CpG} 182s Add alternative model distribution to the plot. 182s 182s Overplotting Arguments: 182s --overplot-threshold OVERPLOT_THRESHOLD 182s Coverage level to trigger alternative plot type 182s instead of raw signal. Default: 50 182s --overplot-type {Downsample,Boxplot,Quantile,Density} 182s Plot type for regions with higher coverage. Default: 182s Downsample 182s 182s Plotting Region Arguments: 182s --num-regions NUM_REGIONS 182s Number of regions to plot. Default: 10 182s --num-bases NUM_BASES 182s Number of bases to plot/output. Default: 21 182s --deepest-coverage Plot the deepest coverage regions. 182s 182s Output Argument: 182s --pdf-filename PDF_FILENAME 182s PDF filename to store plot(s). Default: 182s tombo_results.motif_centered.pdf 182s 182s FAST5 Data Arguments: 182s --corrected-group CORRECTED_GROUP 182s FAST5 group created by resquiggle command. Default: 182s RawGenomeCorrected_000 182s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 182s FAST5 subgroup(s) (under /Analyses/[--basecall- 182s group]/) containing basecalls and created within 182s [--corrected-group] containing re-squiggle results. 182s Default: ['BaseCalled_template'] 182s 182s Miscellaneous Arguments: 182s --quiet, -q Don't print status information. 182s --help, -h Print this help message and exit 182s usage: tombo plot max_difference 182s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 182s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 182s [--overplot-threshold OVERPLOT_THRESHOLD] 182s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 182s [--num-regions NUM_REGIONS] 182s [--num-bases NUM_BASES] 182s [--pdf-filename PDF_FILENAME] 182s [--sequences-filename SEQUENCES_FILENAME] 182s [--corrected-group CORRECTED_GROUP] 182s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 182s [--quiet] [--help] 182s 182s Required Arguments: 182s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 182s Directories containing fast5 files. 182s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 182s Set of directories containing fast5 files for control 182s reads, containing only canonical nucleotides. 182s 182s Overplotting Arguments: 182s --overplot-threshold OVERPLOT_THRESHOLD 182s Coverage level to trigger alternative plot type 182s instead of raw signal. Default: 50 182s --overplot-type {Downsample,Boxplot,Quantile,Density} 182s Plot type for regions with higher coverage. Default: 182s Downsample 182s 182s Plotting Region Arguments: 182s --num-regions NUM_REGIONS 182s Number of regions to plot. Default: 10 182s --num-bases NUM_BASES 182s Number of bases to plot/output. Default: 21 182s 182s Output Arguments: 182s --pdf-filename PDF_FILENAME 182s PDF filename to store plot(s). Default: 182s tombo_results.max_difference.pdf 182s --sequences-filename SEQUENCES_FILENAME 182s File for sequences from selected regions. Sequences 182s will be stored in FASTA format. Default: None. 182s 182s FAST5 Data Arguments: 182s --corrected-group CORRECTED_GROUP 182s FAST5 group created by resquiggle command. Default: 182s RawGenomeCorrected_000 182s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 182s FAST5 subgroup(s) (under /Analyses/[--basecall- 182s group]/) containing basecalls and created within 182s [--corrected-group] containing re-squiggle results. 182s Default: ['BaseCalled_template'] 182s 182s Miscellaneous Arguments: 182s --quiet, -q Don't print status information. 182s --help, -h Print this help message and exit 182s usage: tombo plot most_significant 182s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 182s --statistics-filename STATISTICS_FILENAME 182s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 182s [--plot-standard-model] 182s [--plot-alternate-model {dam,CpG,dcm,6mA,5mC}] 182s [--overplot-threshold OVERPLOT_THRESHOLD] 182s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 182s [--num-regions NUM_REGIONS] 182s [--num-bases NUM_BASES] 182s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 182s [--pdf-filename PDF_FILENAME] 182s [--sequences-filename SEQUENCES_FILENAME] 182s [--corrected-group CORRECTED_GROUP] 182s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 182s [--quiet] [--help] 182s 182s Required Arguments: 182s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 182s Directories containing fast5 files. 182s --statistics-filename STATISTICS_FILENAME 182s File to save/load genomic base anchored statistics. 182s 182s Comparison Arguments: 182s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 182s Set of directories containing fast5 files for control 182s reads, containing only canonical nucleotides. 182s --plot-standard-model 182s Add default standard model distribution to the plot. 182s --plot-alternate-model {dam,CpG,dcm,6mA,5mC} 182s Add alternative model distribution to the plot. 182s 182s Overplotting Arguments: 182s --overplot-threshold OVERPLOT_THRESHOLD 182s Coverage level to trigger alternative plot type 182s instead of raw signal. Default: 50 182s --overplot-type {Downsample,Boxplot,Quantile,Density} 182s Plot type for regions with higher coverage. Default: 182s Downsample 182s 182s Plotting Region Arguments: 182s --num-regions NUM_REGIONS 182s Number of regions to plot. Default: 10 182s --num-bases NUM_BASES 182s Number of bases to plot/output. Default: 21 182s 182s Statistical Argument: 182s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 182s Dampen fraction modified estimates for low coverage 182s sites. Two parameters are unmodified and modified 182s pseudo read counts. This is equivalent to a beta prior 182s on the fraction estimate. Set to "0 0" to disable 182s dampened fraction estimation. Default: [2, 0] 182s 182s Output Arguments: 182s --pdf-filename PDF_FILENAME 182s PDF filename to store plot(s). Default: 182s tombo_results.significant_difference.pdf 182s --sequences-filename SEQUENCES_FILENAME 182s File for sequences from selected regions. Sequences 182s will be stored in FASTA format. Default: None. 182s 182s FAST5 Data Arguments: 182s --corrected-group CORRECTED_GROUP 182s FAST5 group created by resquiggle command. Default: 182s RawGenomeCorrected_000 182s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 182s FAST5 subgroup(s) (under /Analyses/[--basecall- 182s group]/) containing basecalls and created within 182s [--corrected-group] containing re-squiggle results. 182s Default: ['BaseCalled_template'] 182s 182s Miscellaneous Arguments: 182s --quiet, -q Don't print status information. 182s --help, -h Print this help message and exit 182s usage: tombo plot motif_with_stats 182s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 182s --motif MOTIF 182s --statistics-filename STATISTICS_FILENAME 182s --genome-fasta GENOME_FASTA 182s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 182s [--plot-standard-model] 182s [--plot-alternate-model {6mA,dam,dcm,CpG,5mC}] 182s [--overplot-threshold OVERPLOT_THRESHOLD] 182s [--num-regions NUM_REGIONS] 182s [--num-context NUM_CONTEXT] 182s [--num-statistics NUM_STATISTICS] 182s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 182s [--pdf-filename PDF_FILENAME] 182s [--corrected-group CORRECTED_GROUP] 182s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 182s [--quiet] [--help] 182s 182s Required Arguments: 182s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 182s Directories containing fast5 files. 182s --motif MOTIF Motif of interest at which to plot signal and 182s statsitics. Supports IUPAC single letter codes (use T 182s for RNA). 182s --statistics-filename STATISTICS_FILENAME 182s File to save/load genomic base anchored statistics. 182s --genome-fasta GENOME_FASTA 182s FASTA file used to re-squiggle. For faster sequence 182s access. 182s 182s Comparison Arguments: 182s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 182s Set of directories containing fast5 files for control 182s reads, containing only canonical nucleotides. 182s --plot-standard-model 182s Add default standard model distribution to the plot. 182s --plot-alternate-model {6mA,dam,dcm,CpG,5mC} 182s Add alternative model distribution to the plot. 182s 182s Overplotting Argument: 182s --overplot-threshold OVERPLOT_THRESHOLD 182s Coverage level to trigger alternative plot type 182s instead of raw signal. Default: 50 182s 182s Plotting Region Arguments: 182s --num-regions NUM_REGIONS 182s Number of regions to plot. Default: 3 182s --num-context NUM_CONTEXT 182s Number of context bases around motif. Default: 5 182s --num-statistics NUM_STATISTICS 182s Number of motif centered regions to include in 182s statistic distributions. Default: 200 182s 182s Statistical Argument: 182s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 182s Dampen fraction modified estimates for low coverage 182s sites. Two parameters are unmodified and modified 182s pseudo read counts. This is equivalent to a beta prior 182s on the fraction estimate. Set to "0 0" to disable 182s dampened fraction estimation. Default: [2, 0] 182s 182s Output Argument: 182s --pdf-filename PDF_FILENAME 182s PDF filename to store plot(s). Default: 182s tombo_results.motif_statistics.pdf 182s 182s FAST5 Data Arguments: 182s --corrected-group CORRECTED_GROUP 182s FAST5 group created by resquiggle command. Default: 182s RawGenomeCorrected_000 182s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 182s FAST5 subgroup(s) (under /Analyses/[--basecall- 182s group]/) containing basecalls and created within 182s [--corrected-group] containing re-squiggle results. 182s Default: ['BaseCalled_template'] 182s 182s Miscellaneous Arguments: 182s --quiet, -q Don't print status information. 182s --help, -h Print this help message and exit 183s usage: tombo plot per_read 183s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 183s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 183s [--genome-fasta GENOME_FASTA] 183s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 183s [--num-reads NUM_READS] [--num-bases NUM_BASES] 183s [--box-center] [--pdf-filename PDF_FILENAME] 183s [--corrected-group CORRECTED_GROUP] 183s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 183s [--quiet] [--help] 183s 183s Required Arguments: 183s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 183s Genomic locations at which to plot signal. Format 183s locations as "chrm:position[:strand] 183s [chrm2:position2[:strand2] ...]" (strand not 183s applicable for all applications) 183s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 183s Binary file containing per-read statistics from 183s statistical testing. 183s 183s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 183s --genome-fasta GENOME_FASTA 183s FASTA file used to re-squiggle. For faster sequence 183s access. 183s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 183s Directories containing fast5 files. 183s 183s Plotting Region Arguments: 183s --num-reads NUM_READS 183s Number of reads to plot. Default: 100 183s --num-bases NUM_BASES 183s Number of bases to plot/output. Default: 51 183s --box-center Plot a box around the central base. 183s 183s Output Argument: 183s --pdf-filename PDF_FILENAME 183s PDF filename to store plot(s). Default: 183s tombo_results.per_read_stats.pdf 183s 183s FAST5 Data Arguments: 183s --corrected-group CORRECTED_GROUP 183s FAST5 group created by resquiggle command. Default: 183s RawGenomeCorrected_000 183s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 183s FAST5 subgroup(s) (under /Analyses/[--basecall- 183s group]/) containing basecalls and created within 183s [--corrected-group] containing re-squiggle results. 183s Default: ['BaseCalled_template'] 183s 183s Miscellaneous Arguments: 183s --quiet, -q Don't print status information. 183s --help, -h Print this help message and exit 183s usage: tombo plot roc 183s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 183s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 183s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 183s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 183s [--genome-fasta GENOME_FASTA] 183s [--pdf-filename PDF_FILENAME] 183s [--statistics-per-block STATISTICS_PER_BLOCK] 183s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 183s [--quiet] [--help] 183s 183s Required Argument: 183s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 183s Files to load genomic base anchored statistics. 183s 183s Ground Truth Arguments (provide bed files or motifs): 183s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 183s Modification description and bed format files 183s containing single base locations of ground truth 183s modified sites. Bed files should contain 6 fields 183s including strand. Format descriptions as 183s "mod_name:locs.bed". Example: "CpG 183s bisulfite":bisulfite_locs.bed 183s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 183s Bed format files containing single base locations of 183s ground truth unmodified sites. Bed files should 183s contain 6 fields including strand. 183s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 183s Ground truth, motif centered, modified base 183s descriptions for computing ROC and PR curves. Each 183s statistics file is associated with a set of motif 183s descriptions. Format descriptions as: 183s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 183s mod_pos indicates the alternate-base within the motif 183s (1-based index). Example: CCWGG:2:"dcm 183s 5mC"::GATC:2:"dam 6mA" would assess the performance of 183s a single Tombo statistics file for identification of 183s E. coli dam and dcm methylation. 183s --genome-fasta GENOME_FASTA 183s FASTA file used to re-squiggle. For faster sequence 183s access. 183s 183s Output Arguments: 183s --pdf-filename PDF_FILENAME 183s PDF filename to store plot(s). Default: 183s tombo_results.roc.pdf 183s 183s Down-sampling Arguments: 183s --statistics-per-block STATISTICS_PER_BLOCK 183s Number of randomly selected per-read, per-base 183s statistics to extract from each genomic block for 183s plotting. Default: Include all stats 183s --total-statistics-limit TOTAL_STATISTICS_LIMIT 183s Total per-read statistics to be extracted for 183s plotting. Avoids memory overflow for large runs. 183s Default: 5000000 183s 183s Miscellaneous Arguments: 183s --quiet, -q Don't print status information. 183s --help, -h Print this help message and exit 183s usage: tombo plot per_read_roc 183s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 183s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 183s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 183s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 183s [--genome-fasta GENOME_FASTA] 183s [--statistics-per-block STATISTICS_PER_BLOCK] 183s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 183s [--pdf-filename PDF_FILENAME] [--quiet] 183s [--help] 183s 183s Required Argument: 183s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 183s Binary files containing per-read statistics from 183s statistical testing. 183s 183s Ground Truth Arguments (provide bed files or motifs): 183s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 183s Modification description and bed format files 183s containing single base locations of ground truth 183s modified sites. Bed files should contain 6 fields 183s including strand. Format descriptions as 183s "mod_name:locs.bed". Example: "CpG 183s bisulfite":bisulfite_locs.bed 183s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 183s Bed format files containing single base locations of 183s ground truth unmodified sites. Bed files should 183s contain 6 fields including strand. 183s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 183s Ground truth, motif centered, modified base 183s descriptions for computing ROC and PR curves. Each 183s statistics file is associated with a set of motif 183s descriptions. Format descriptions as: 183s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 183s mod_pos indicates the alternate-base within the motif 183s (1-based index). Example: CCWGG:2:"dcm 183s 5mC"::GATC:2:"dam 6mA" would assess the performance of 183s a single Tombo statistics file for identification of 183s E. coli dam and dcm methylation. 183s --genome-fasta GENOME_FASTA 183s FASTA file used to re-squiggle. For faster sequence 183s access. 183s 183s Down-sampling Arguments: 183s --statistics-per-block STATISTICS_PER_BLOCK 183s Number of randomly selected per-read, per-base 183s statistics to extract from each genomic block for 183s plotting. Default: 100000 183s --total-statistics-limit TOTAL_STATISTICS_LIMIT 183s Total per-read statistics to be extracted for 183s plotting. Avoids memory overflow for large runs. 183s Default: 5000000 183s 183s Output Arguments: 183s --pdf-filename PDF_FILENAME 183s PDF filename to store plot(s). Default: 183s tombo_results.per_reads_roc.pdf 183s 183s Miscellaneous Arguments: 183s --quiet, -q Don't print status information. 183s --help, -h Print this help message and exit 183s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 183s [--upstream-bases {0,1,2,3,4}] 183s [--downstream-bases {0,1,2,3,4}] [--read-mean] 183s [--num-kmer-threshold NUM_KMER_THRESHOLD] 183s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 183s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 183s [--corrected-group CORRECTED_GROUP] 183s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 183s [--quiet] [--help] 183s 183s Required Argument: 183s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 183s Directories containing fast5 files. 183s 183s Data Processing Arguments: 183s --upstream-bases {0,1,2,3,4} 183s Upstream bases in k-mer. Default: 1 183s --downstream-bases {0,1,2,3,4} 183s Downstream bases in k-mer. Default: 2 183s --read-mean Plot k-mer means across whole reads as opposed to 183s individual k-mer event levels. 183s --num-kmer-threshold NUM_KMER_THRESHOLD 183s Observations of each k-mer required to include a read 183s in read level averages. Default: 1 183s 183s Plotting Region Arguments: 183s --num-reads NUM_READS 183s Number of reads to plot. Default: 100 183s 183s Output Arguments: 183s --pdf-filename PDF_FILENAME 183s PDF filename to store plot(s). Default: 183s tombo_results.kmer_distribution.pdf 183s --r-data-filename R_DATA_FILENAME 183s Filename to save R data structure. Default: Don't save 183s --dont-plot Don't plot result. Useful to produce only R data file. 183s 183s FAST5 Data Arguments: 183s --corrected-group CORRECTED_GROUP 183s FAST5 group created by resquiggle command. Default: 183s RawGenomeCorrected_000 183s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 183s FAST5 subgroup(s) (under /Analyses/[--basecall- 183s group]/) containing basecalls and created within 183s [--corrected-group] containing re-squiggle results. 183s Default: ['BaseCalled_template'] 183s 183s Miscellaneous Arguments: 183s --quiet, -q Don't print status information. 183s --help, -h Print this help message and exit 183s usage: tombo plot cluster_most_significant 183s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 183s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 183s --statistics-filename STATISTICS_FILENAME 183s [--genome-fasta GENOME_FASTA] 183s [--processes PROCESSES] 183s [--num-regions NUM_REGIONS] 183s [--num-bases NUM_BASES] 183s [--slide-span SLIDE_SPAN] 183s [--pdf-filename PDF_FILENAME] 183s [--r-data-filename R_DATA_FILENAME] 183s [--corrected-group CORRECTED_GROUP] 183s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 183s [--quiet] [--help] 183s 183s Required Arguments: 183s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 183s Directories containing fast5 files. 183s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 183s Set of directories containing fast5 files for control 183s reads, containing only canonical nucleotides. 183s --statistics-filename STATISTICS_FILENAME 183s File to save/load genomic base anchored statistics. 183s 183s FASTA Sequence Argument: 183s --genome-fasta GENOME_FASTA 183s FASTA file used to re-squiggle. For faster sequence 183s access. 183s 183s Multiprocessing Argument: 183s --processes PROCESSES 183s Number of processes. Default: 1 183s 183s Plotting Region Arguments: 183s --num-regions NUM_REGIONS 183s Number of regions to plot. Default: 10 183s --num-bases NUM_BASES 183s Number of bases to plot/output. Default: 21 183s --slide-span SLIDE_SPAN 183s Number of bases offset over which to search when 183s computing distances for signal cluster plotting. 183s Default: 0 (exact position) 183s 183s Output Arguments: 183s --pdf-filename PDF_FILENAME 183s PDF filename to store plot(s). Default: 183s tombo_results.signal_clusters.pdf 183s --r-data-filename R_DATA_FILENAME 183s Filename to save R data structure. Default: Don't save 183s 183s FAST5 Data Arguments: 183s --corrected-group CORRECTED_GROUP 183s FAST5 group created by resquiggle command. Default: 183s RawGenomeCorrected_000 183s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 183s FAST5 subgroup(s) (under /Analyses/[--basecall- 183s group]/) containing basecalls and created within 183s [--corrected-group] containing re-squiggle results. 183s Default: ['BaseCalled_template'] 183s 183s Miscellaneous Arguments: 183s --quiet, -q Don't print status information. 183s --help, -h Print this help message and exit 184s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 184s 184s Required Arguments: 184s fast5s_basedir Directory containing fast5 files. All files ending in 184s "fast5" found recursively within this base directory will be 184s processed. 184s 184s Miscellaneous Arguments: 184s --quiet, -q Don't print status information. 184s --help, -h Print this help message and exit 184s usage: tombo build_model event_resquiggle 184s [--minimap2-executable MINIMAP2_EXECUTABLE] 184s [--minimap2-index MINIMAP2_INDEX] 184s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 184s [--graphmap-executable GRAPHMAP_EXECUTABLE] 184s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 184s [--normalization-type {median,pA,pA_raw,none}] 184s [--pore-model-filename PORE_MODEL_FILENAME] 184s [--outlier-threshold OUTLIER_THRESHOLD] 184s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 184s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 184s [--timeout TIMEOUT] 184s [--cpts-limit CPTS_LIMIT] 184s [--skip-index] [--overwrite] 184s [--failed-reads-filename FAILED_READS_FILENAME] 184s [--include-event-stdev] 184s [--corrected-group CORRECTED_GROUP] 184s [--basecall-group BASECALL_GROUP] 184s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 184s [--processes PROCESSES] 184s [--align-processes ALIGN_PROCESSES] 184s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 184s [--resquiggle-processes RESQUIGGLE_PROCESSES] 184s [--quiet] [--help] 184s fast5s_basedir reference_fasta 184s 184s Required Arguments: 184s fast5s_basedir Directory containing fast5 files. All files ending in 184s "fast5" found recursively within this base directory 184s will be processed. 184s reference_fasta Reference genome/transcriptome FASTA file for mapping. 184s 184s Mapper Arguments (One mapper is required): 184s --minimap2-executable MINIMAP2_EXECUTABLE 184s Path to minimap2 executable. 184s --minimap2-index MINIMAP2_INDEX 184s Path to minimap2 index (with map-ont preset) file 184s corresponding to the [genome_fasta] provided. 184s --bwa-mem-executable BWA_MEM_EXECUTABLE 184s Path to bwa-mem executable. 184s --graphmap-executable GRAPHMAP_EXECUTABLE 184s Path to graphmap executable. 184s --alignment-batch-size ALIGNMENT_BATCH_SIZE 184s Number of reads included in each alignment call. Note: 184s A new system mapping call is made for each batch 184s (including loading of the genome), so it is advised to 184s use larger values for larger genomes. Default: 1000 184s 184s Signal Processing Arguments: 184s --normalization-type {median,pA,pA_raw,none} 184s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 184s as in the ONT events (using offset, range and 184s digitization), "pA": k-mer-based correction for pA 184s drift as in nanopolish (requires [--pore-model- 184s filename]), "median": median and MAD from raw signal. 184s Default: median 184s --pore-model-filename PORE_MODEL_FILENAME 184s File containing kmer model parameters (level_mean and 184s level_stdv) used in order to compute kmer-based 184s corrected pA values. E.g. https://github.com/jts/nanop 184s olish/blob/master/etc/r9- 184s models/template_median68pA.5mers.model 184s --outlier-threshold OUTLIER_THRESHOLD 184s Windosrize the signal at this number of scale values. 184s Negative value disables outlier clipping. Default: 184s 5.000000 184s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 184s Specify the 2 parameters for segmentation 1) running 184s neighboring windows width 2) minimum raw observations 184s per genomic base. Sample type defaults: RNA : 12 6 || 184s DNA : 5 3 184s 184s Read Filtering Arguments: 184s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 184s Filter reads based on observations per base percentile 184s thresholds. Format thresholds as "percentile:thresh 184s [pctl2:thresh2 ...]". For example to filter reads with 184s 99th pctl > 200 obs/base or max > 5k obs/base use 184s "99:200 100:5000". 184s --timeout TIMEOUT Timeout in seconds for processing a single read. 184s Default: No timeout. 184s --cpts-limit CPTS_LIMIT 184s Maximum number of changepoints to find within a single 184s indel group. Default: No limit. 184s 184s Input/Output Arguments: 184s --skip-index Skip creation of tombo index. This drastically slows 184s downstream tombo commands. Default stores tombo index 184s named ".[--fast5-basedir].[--corrected- 184s group].tombo.index" to be loaded automatically for 184s downstream commands. 184s --overwrite Overwrite previous corrected group in FAST5 files. 184s Note: only effects --corrected-group or --new- 184s corrected-group. 184s --failed-reads-filename FAILED_READS_FILENAME 184s Output failed read filenames with assoicated error. 184s Default: Do not store failed reads. 184s --include-event-stdev 184s Include corrected event standard deviation in output 184s FAST5 data. 184s 184s FAST5 Data Arguments: 184s --corrected-group CORRECTED_GROUP 184s FAST5 group created by resquiggle command. Default: 184s RawGenomeCorrected_000 184s --basecall-group BASECALL_GROUP 184s FAST5 group obtain original basecalls (under Analyses 184s group). Default: Basecall_1D_000 184s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 184s FAST5 subgroup(s) (under /Analyses/[--basecall- 184s group]/) containing basecalls and created within 184s [--corrected-group] containing re-squiggle results. 184s Default: ['BaseCalled_template'] 184s 184s Multiprocessing Arguments: 184s --processes PROCESSES 184s Number of processes. Default: 2 184s --align-processes ALIGN_PROCESSES 184s Number of processes to use for parsing and aligning 184s original basecalls. Each process will independently 184s load the genome into memory, so use caution with 184s larger genomes (e.g. human). Default: 1 184s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 184s Number of threads to use for aligner system call. 184s Default: [--processes] / (2 * [--align-processes)] 184s --resquiggle-processes RESQUIGGLE_PROCESSES 184s Number of processes to use for resquiggle algorithm. 184s Default: [--processes] / 2 184s 184s Miscellaneous Arguments: 184s --quiet, -q Don't print status information. 184s --help, -h Print this help message and exit 184s usage: tombo build_model estimate_reference 184s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 184s --tombo-model-filename TOMBO_MODEL_FILENAME 184s [--estimate-mean] 184s [--kmer-specific-sd] 184s [--upstream-bases {0,1,2,3,4}] 184s [--downstream-bases {0,1,2,3,4}] 184s [--minimum-test-reads MINIMUM_TEST_READS] 184s [--coverage-threshold COVERAGE_THRESHOLD] 184s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 184s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 184s [--processes PROCESSES] 184s [--corrected-group CORRECTED_GROUP] 184s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 184s [--quiet] [--help] 184s 184s Required Arguments: 184s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 184s Directories containing fast5 files. 184s --tombo-model-filename TOMBO_MODEL_FILENAME 184s Filename to save Tombo model. 184s 184s Modeling Arguments: 184s --estimate-mean Use the mean instead of median for model level 184s estimation. Note: This can cause poor fits due to 184s outliers 184s --kmer-specific-sd Estimate standard deviation for each k-mers 184s individually. 184s --upstream-bases {0,1,2,3,4} 184s Upstream bases in k-mer. Default: 1 184s --downstream-bases {0,1,2,3,4} 184s Downstream bases in k-mer. Default: 2 184s 184s Filtering Arguments: 184s --minimum-test-reads MINIMUM_TEST_READS 184s Number of reads required at a position to perform 184s significance testing or contribute to model 184s estimation. Default: 10 184s --coverage-threshold COVERAGE_THRESHOLD 184s Maximum mean coverage per region when estimating k-mer 184s model (limits compute time for deep samples). Default: 184s 100 184s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 184s Number of each k-mer observations required in order to 184s produce a reference (genomic locations for standard 184s reference and per-read for alternative reference). 184s Default: 5 184s 184s Multiprocessing Arguments: 184s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 184s Size of regions over which to multiprocesses statistic 184s computation. For very deep samples a smaller value is 184s recommmended in order to control memory consumption. 184s Default: 10000 184s --processes PROCESSES 184s Number of processes. Default: 1 184s 184s FAST5 Data Arguments: 184s --corrected-group CORRECTED_GROUP 184s FAST5 group created by resquiggle command. Default: 184s RawGenomeCorrected_000 184s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 184s FAST5 subgroup(s) (under /Analyses/[--basecall- 184s group]/) containing basecalls and created within 184s [--corrected-group] containing re-squiggle results. 184s Default: ['BaseCalled_template'] 184s 184s Miscellaneous Arguments: 184s --quiet, -q Don't print status information. 184s --help, -h Print this help message and exit 184s usage: tombo build_model estimate_alt_reference 184s --alternate-model-filename ALTERNATE_MODEL_FILENAME 184s --alternate-model-name ALTERNATE_MODEL_NAME 184s --alternate-model-base {A,C,G,T} 184s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 184s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 184s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 184s [--control-density-filename CONTROL_DENSITY_FILENAME] 184s [--dna] [--rna] 184s [--tombo-model-filename TOMBO_MODEL_FILENAME] 184s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 184s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 184s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 184s [--save-density-basename SAVE_DENSITY_BASENAME] 184s [--processes PROCESSES] 184s [--corrected-group CORRECTED_GROUP] 184s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 184s [--quiet] [--help] 184s 184s Required Arguments: 184s --alternate-model-filename ALTERNATE_MODEL_FILENAME 184s Tombo model for alternative likelihood ratio 184s significance testing. 184s --alternate-model-name ALTERNATE_MODEL_NAME 184s A short name to associate with this alternate model 184s (e.g. 5mC, 6mA, etc.). This text will be included in 184s output filenames when this model is used for testing. 184s --alternate-model-base {A,C,G,T} 184s Non-standard base is an alternative to this base. 184s 184s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 184s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 184s Directories containing fast5 files. 184s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 184s Set of directories containing fast5 files for control 184s reads, containing only canonical nucleotides. 184s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 184s File containing k-mer level kernel density estimates 184s for the alternative sample saved using --save-density- 184s basename. 184s --control-density-filename CONTROL_DENSITY_FILENAME 184s File containing k-mer level kernel density estimates 184s for the control sample saved using --save-density- 184s basename. 184s 184s Standard Model Arguments: 184s --dna Explicitly select canonical DNA model. Default: 184s Automatically determine from FAST5s 184s --rna Explicitly select canonical RNA model. Default: 184s Automatically determine from FAST5s 184s --tombo-model-filename TOMBO_MODEL_FILENAME 184s Tombo model filename. If no file is provided, the 184s default DNA or RNA Tombo model will be used. 184s 184s Model Fitting Arguments: 184s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 184s When esitmating the alternative base incorporation 184s rate, this percent of k-mers are assumed to have 184s significantly shifted signal so the alternative 184s distribution minimally overlaps the standard base 184s distribution. Default: 5.000000 184s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 184s Bandwidth applied when performing Gaussian kernal 184s density esitmation on standard and alternative base 184s signal distributions. Default: 0.050000 184s 184s Filtering Argument: 184s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 184s Number of each k-mer observations required in order to 184s produce a reference (genomic locations for standard 184s reference and per-read for alternative reference). 184s Default: 1000 184s 184s Output Argument: 184s --save-density-basename SAVE_DENSITY_BASENAME 184s Basename to save alternative model estimation density 184s estimation information. See scripts/debug_est_alt.R 184s for info use example. Default: Don't save. 184s 184s Multiprocessing Arguments: 184s --processes PROCESSES 184s Number of processes. Default: 1 184s 184s FAST5 Data Arguments: 184s --corrected-group CORRECTED_GROUP 184s FAST5 group created by resquiggle command. Default: 184s RawGenomeCorrected_000 184s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 184s FAST5 subgroup(s) (under /Analyses/[--basecall- 184s group]/) containing basecalls and created within 184s [--corrected-group] containing re-squiggle results. 184s Default: ['BaseCalled_template'] 184s 184s Miscellaneous Arguments: 184s --quiet, -q Don't print status information. 184s --help, -h Print this help message and exit 184s This test only tests the help system 184s There is an extensive test in 184s 184s tombo/tests/shell_tests.sh 184s 184s but this requires to download larger data 184s sets which is not done for the moment. 185s autopkgtest [00:48:44]: test run-unit-test: -----------------------] 185s autopkgtest [00:48:44]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 185s run-unit-test PASS 186s autopkgtest [00:48:45]: @@@@@@@@@@@@@@@@@@@@ summary 186s run-unit-test PASS 190s nova [W] Using flock in prodstack6-ppc64el 190s Creating nova instance adt-plucky-ppc64el-tombo-20250220-004539-juju-7f2275-prod-proposed-migration-environment-15-11177a40-ec92-4bf4-bca8-41e248e30f09 from image adt/ubuntu-plucky-ppc64el-server-20250219.img (UUID 54e7bc81-8a85-40fa-b450-97b95b386f53)... 190s nova [W] Timed out waiting for bb7b1643-dcb9-4e29-a5d5-c332e2adc68c to get deleted.