0s autopkgtest [20:41:29]: starting date and time: 2024-11-14 20:41:29+0000 0s autopkgtest [20:41:29]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [20:41:29]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bq6qocvt/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-3.secgroup --name adt-plucky-ppc64el-tombo-20241114-204128-juju-7f2275-prod-proposed-migration-environment-20-c158da35-cfd6-48a1-91fd-049736acbe23 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 123s autopkgtest [20:43:32]: testbed dpkg architecture: ppc64el 123s autopkgtest [20:43:32]: testbed apt version: 2.9.8 123s autopkgtest [20:43:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 124s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 124s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.7 kB] 125s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1044 kB] 125s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 125s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 125s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [120 kB] 125s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [732 kB] 125s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [8632 B] 125s Fetched 2106 kB in 1s (1761 kB/s) 125s Reading package lists... 128s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s Calculating upgrade... 130s The following packages will be upgraded: 130s bpfcc-tools bpftrace libbpfcc libcap-ng0 libgnutls30t64 libjson-glib-1.0-0 130s libjson-glib-1.0-common libnewt0.52 libutempter0 pastebinit python3-bpfcc 130s python3-newt python3-systemd whiptail 130s 14 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Need to get 4678 kB of archives. 130s After this operation, 423 kB of additional disk space will be used. 130s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcap-ng0 ppc64el 0.8.5-3build1 [16.3 kB] 130s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 131s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 131s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 131s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 131s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 131s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 131s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 131s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 132s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 132s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 132s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 132s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el pastebinit all 1.7.1-1 [14.9 kB] 132s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-systemd ppc64el 235-1build5 [48.7 kB] 132s Fetched 4678 kB in 2s (2563 kB/s) 133s (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 ... 73767 files and directories currently installed.) 133s Preparing to unpack .../libcap-ng0_0.8.5-3build1_ppc64el.deb ... 133s Unpacking libcap-ng0:ppc64el (0.8.5-3build1) over (0.8.5-1) ... 133s Setting up libcap-ng0:ppc64el (0.8.5-3build1) ... 133s (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 ... 73767 files and directories currently installed.) 133s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 133s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 133s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 133s (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 ... 73767 files and directories currently installed.) 133s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 133s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 133s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 133s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 133s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 133s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 133s Preparing to unpack .../03-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 133s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 133s Preparing to unpack .../04-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 134s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 134s Preparing to unpack .../05-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 134s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 134s Preparing to unpack .../06-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 134s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 134s Preparing to unpack .../07-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 134s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 134s Preparing to unpack .../08-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 134s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 134s Preparing to unpack .../09-libutempter0_1.2.1-4_ppc64el.deb ... 134s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 134s Preparing to unpack .../10-pastebinit_1.7.1-1_all.deb ... 134s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 134s Preparing to unpack .../11-python3-systemd_235-1build5_ppc64el.deb ... 134s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 134s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 134s Setting up pastebinit (1.7.1-1) ... 134s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 134s Setting up libutempter0:ppc64el (1.2.1-4) ... 134s Setting up whiptail (0.52.24-2ubuntu4) ... 134s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 134s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 134s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 135s Setting up python3-systemd (235-1build5) ... 135s Setting up bpftrace (0.21.2-2ubuntu2) ... 135s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 135s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 135s Processing triggers for man-db (2.12.1-3) ... 137s Processing triggers for libc-bin (2.40-1ubuntu3) ... 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 138s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 138s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 138s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 140s Reading package lists... 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Calculating upgrade... 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s autopkgtest [20:43:53]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 145s autopkgtest [20:43:54]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 152s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (dsc) [2291 B] 152s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (tar) [22.3 MB] 152s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-6build1 (diff) [7100 B] 153s gpgv: Signature made Wed Apr 10 17:15:32 2024 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_1.5.1-6build1.dsc: no acceptable signature found 153s autopkgtest [20:44:02]: testing package tombo version 1.5.1-6build1 154s autopkgtest [20:44:03]: build not needed 155s autopkgtest [20:44:04]: test run-unit-test: preparing testbed 160s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s Starting pkgProblemResolver with broken count: 0 161s Starting 2 pkgProblemResolver with broken count: 0 161s Done 162s The following additional packages will be installed: 162s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 162s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 162s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 162s python3-decorator python3-h5py python3-h5py-serial python3-mappy 162s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 162s tombo-doc 162s Suggested packages: 162s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 162s gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 162s Recommended packages: 162s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 162s python3-rpy2 162s The following NEW packages will be installed: 162s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 162s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 162s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 162s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 162s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 162s tombo-doc 162s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 162s Need to get 65.0 MB/65.0 MB of archives. 162s After this operation, 229 MB of additional disk space will be used. 162s Get:1 /tmp/autopkgtest.ppkj4n/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 162s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-lato all 2.015-1 [2781 kB] 163s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 163s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 163s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libaec0 ppc64el 1.1.3-1 [30.1 kB] 163s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 163s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 163s Get:8 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libsz2 ppc64el 1.1.3-1 [5566 B] 163s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-4ubuntu3 [1387 kB] 163s Get:10 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-4ubuntu3 [71.2 kB] 163s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 163s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 163s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-sphinxdoc all 7.4.7-4 [158 kB] 163s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 164s Get:15 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 164s Get:16 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 164s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 164s Get:18 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11ubuntu1 [5148 kB] 164s Get:19 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py-serial ppc64el 3.11.0-5ubuntu1 [1159 kB] 164s Get:20 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py all 3.11.0-5ubuntu1 [7974 B] 164s Get:21 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mappy ppc64el 2.27+dfsg-1 [192 kB] 164s Get:22 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-tqdm all 4.67.0-1 [91.6 kB] 164s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 164s Get:24 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5 [18.3 MB] 165s Get:25 http://ftpmaster.internal/ubuntu plucky/universe ppc64el tombo ppc64el 1.5.1-6build1 [463 kB] 165s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 165s Get:27 http://ftpmaster.internal/ubuntu plucky/universe ppc64el tombo-doc all 1.5.1-6build1 [21.7 MB] 166s Fetched 65.0 MB in 4s (16.1 MB/s) 166s Selecting previously unselected package fonts-lato. 166s (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 ... 73773 files and directories currently installed.) 166s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 166s Unpacking fonts-lato (2.015-1) ... 167s Selecting previously unselected package fonts-font-awesome. 167s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 167s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 167s Selecting previously unselected package fonts-mathjax. 167s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 167s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 167s Selecting previously unselected package libaec0:ppc64el. 167s Preparing to unpack .../03-libaec0_1.1.3-1_ppc64el.deb ... 167s Unpacking libaec0:ppc64el (1.1.3-1) ... 167s Selecting previously unselected package libblas3:ppc64el. 167s Preparing to unpack .../04-libblas3_3.12.0-3build2_ppc64el.deb ... 167s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 167s Selecting previously unselected package libgfortran5:ppc64el. 167s Preparing to unpack .../05-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 167s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 167s Selecting previously unselected package libsz2:ppc64el. 167s Preparing to unpack .../06-libsz2_1.1.3-1_ppc64el.deb ... 167s Unpacking libsz2:ppc64el (1.1.3-1) ... 167s Selecting previously unselected package libhdf5-103-1t64:ppc64el. 167s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_ppc64el.deb ... 167s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ... 167s Selecting previously unselected package libhdf5-hl-100t64:ppc64el. 167s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_ppc64el.deb ... 167s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-4ubuntu3) ... 167s Selecting previously unselected package libjs-jquery. 167s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 167s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 167s Selecting previously unselected package libjs-underscore. 167s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 167s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 167s Selecting previously unselected package libjs-sphinxdoc. 167s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-4_all.deb ... 167s Unpacking libjs-sphinxdoc (7.4.7-4) ... 167s Selecting previously unselected package liblapack3:ppc64el. 167s Preparing to unpack .../12-liblapack3_3.12.0-3build2_ppc64el.deb ... 167s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 167s Selecting previously unselected package liblbfgsb0:ppc64el. 167s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 167s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 167s Selecting previously unselected package liblzf1:ppc64el. 167s Preparing to unpack .../14-liblzf1_3.6-4_ppc64el.deb ... 167s Unpacking liblzf1:ppc64el (3.6-4) ... 168s Selecting previously unselected package python3-decorator. 168s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 168s Unpacking python3-decorator (5.1.1-5) ... 168s Selecting previously unselected package python3-numpy. 168s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-11ubuntu1_ppc64el.deb ... 168s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 168s Selecting previously unselected package python3-h5py-serial. 168s Preparing to unpack .../17-python3-h5py-serial_3.11.0-5ubuntu1_ppc64el.deb ... 168s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 168s Selecting previously unselected package python3-h5py. 168s Preparing to unpack .../18-python3-h5py_3.11.0-5ubuntu1_all.deb ... 168s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 168s Selecting previously unselected package python3-mappy. 168s Preparing to unpack .../19-python3-mappy_2.27+dfsg-1_ppc64el.deb ... 168s Unpacking python3-mappy (2.27+dfsg-1) ... 168s Selecting previously unselected package python3-tqdm. 168s Preparing to unpack .../20-python3-tqdm_4.67.0-1_all.deb ... 168s Unpacking python3-tqdm (4.67.0-1) ... 168s Selecting previously unselected package sphinx-rtd-theme-common. 168s Preparing to unpack .../21-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 168s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 168s Selecting previously unselected package python3-scipy. 168s Preparing to unpack .../22-python3-scipy_1.13.1-5_ppc64el.deb ... 168s 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autopkgtest-satdep (0) ... 179s Processing triggers for man-db (2.12.1-3) ... 180s Processing triggers for libc-bin (2.40-1ubuntu3) ... 184s (Reading database ... 80995 files and directories currently installed.) 184s Removing autopkgtest-satdep (0) ... 185s autopkgtest [20:44:34]: test run-unit-test: [----------------------- 185s ********* Testing help commands ********** 185s usage: tombo [-h] [-v] 185s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 185s ... 185s 185s ********** Tombo ********* 185s 185s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 185s 185s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 185s 185s Tombo command groups (additional help available within each command group): 185s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 185s preprocess Pre-process nanopore reads for Tombo processing. 185s filter Apply filter to Tombo index file for specified criterion. 185s detect_modifications Perform statistical testing to detect non-standard nucleotides. 185s text_output Output Tombo results in text files. 185s build_model Create canonical and alternative base Tombo models. 185s plot Save plots to visualize raw nanopore signal or testing results. 185s 185s options: 185s -h, --help show this help message and exit 185s -v, --version show Tombo version and exit. 185s usage: tombo resquiggle [--dna] [--rna] 185s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 185s [--q-score Q_SCORE] 185s [--signal-matching-score SIGNAL_MATCHING_SCORE] 185s [--processes PROCESSES] 185s [--corrected-group CORRECTED_GROUP] 185s [--basecall-group BASECALL_GROUP] 185s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 185s [--overwrite] 185s [--failed-reads-filename FAILED_READS_FILENAME] 185s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 185s [--print-advanced-arguments] [--quiet] [--help] 185s fast5s_basedir reference 185s 185s Required Arguments: 185s fast5s_basedir Directory containing fast5 files. All files ending in 185s "fast5" found recursively within this base directory 185s will be processed. 185s reference Reference genome/transcriptome FASTA file or minimap2 185s index (with "map-ont" preset) for mapping. 185s 185s Model Parameters: 185s --dna Explicitly select canonical DNA model. Default: 185s Automatically determine from FAST5s 185s --rna Explicitly select canonical RNA model. Default: 185s Automatically determine from FAST5s 185s 185s Read Filtering Argument: 185s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 185s Filter reads based on observations per base percentile 185s thresholds. Format thresholds as "percentile:thresh 185s [pctl2:thresh2 ...]". For example to filter reads with 185s 99th pctl > 200 obs/base or max > 5k obs/base use 185s "99:200 100:5000". 185s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 185s Default: 0.000000 185s --signal-matching-score SIGNAL_MATCHING_SCORE 185s Observed to expected signal matching score (higher 185s score indicates poor matching). Sample type defaults: 185s RNA : 2 || DNA : 1.1 185s 185s Multiprocessing Arguments: 185s --processes PROCESSES 185s Number of processes. Default: 1 185s 185s FAST5 Data Arguments: 185s --corrected-group CORRECTED_GROUP 185s FAST5 group created by resquiggle command. Default: 185s RawGenomeCorrected_000 185s --basecall-group BASECALL_GROUP 185s FAST5 group obtain original basecalls (under Analyses 185s group). Default: Basecall_1D_000 185s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 185s FAST5 subgroup(s) (under /Analyses/[--basecall- 185s group]/) containing basecalls and created within 185s [--corrected-group] containing re-squiggle results. 185s Default: ['BaseCalled_template'] 185s --overwrite Overwrite previous corrected group in FAST5 files. 185s Note: only effects --corrected-group or --new- 185s corrected-group. 185s 185s Input/Output Arguments: 185s --failed-reads-filename FAILED_READS_FILENAME 185s Output failed read filenames with assoicated error. 185s Default: Do not store failed reads. 185s --num-most-common-errors NUM_MOST_COMMON_ERRORS 185s Dynamically show this many most common errors so far 185s through run. Default: 0; Just show progress 185s 185s Advanced Arguments: 185s --print-advanced-arguments 185s Print advanced re-squiggle arguments and exit. 185s 185s Miscellaneous Arguments: 185s --quiet, -q Don't print status information. 185s --help, -h Print this help message and exit 185s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 185s --fastq-filenames 185s FASTQ_FILENAMES 185s [FASTQ_FILENAMES ...] 185s [--basecall-group BASECALL_GROUP] 185s [--basecall-subgroup BASECALL_SUBGROUP] 185s [--overwrite] 185s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 185s [--processes PROCESSES] 185s [--quiet] [--help] 185s 185s Required Arguments: 185s --fast5-basedir FAST5_BASEDIR 185s Directory containing fast5 files. 185s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 185s FASTQ filenames containing basecalls to be added to 185s raw FAST5 files. 185s 185s FAST5 Data Arguments: 185s --basecall-group BASECALL_GROUP 185s FAST5 group obtain original basecalls (under Analyses 185s group). Default: Basecall_1D_000 185s --basecall-subgroup BASECALL_SUBGROUP 185s FAST5 subgroup (under /Analyses/[--basecall-group]/) 185s under which to store basecalls from FASTQs. Default: 185s BaseCalled_template 185s --overwrite Overwrite previous corrected group in FAST5 files. 185s Note: only effects --corrected-group or --new- 185s corrected-group. 185s 185s Sequencing Summary Argument: 185s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 185s Sequencing summary filenames produced by albacore. 185s These can make annotation of raw FAST5 files with 185s FASTQ sequence much faster. 185s 185s Multiprocessing Argument: 185s --processes PROCESSES 185s Number of processes. Default: 1 185s 185s Miscellaneous Arguments: 185s --quiet, -q Don't print status information. 185s --help, -h Print this help message and exit 186s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 186s [FAST5_BASEDIRS ...] 186s [--corrected-group CORRECTED_GROUP] 186s [--quiet] [--help] 186s 186s Required Argument: 186s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 186s Directories containing fast5 files. 186s 186s FAST5 Data Argument: 186s --corrected-group CORRECTED_GROUP 186s FAST5 group created by resquiggle command. Default: 186s RawGenomeCorrected_000 186s 186s Miscellaneous Arguments: 186s --quiet, -q Don't print status information. 186s --help, -h Print this help message and exit 186s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 186s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 186s [--corrected-group CORRECTED_GROUP] [--quiet] 186s [--help] 186s 186s Required Argument: 186s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 186s Directories containing fast5 files. 186s 186s Read Filtering Argument: 186s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 186s Filter reads based on observations per base percentile 186s thresholds. Format thresholds as "percentile:thresh 186s [pctl2:thresh2 ...]". For example to filter reads with 186s 99th pctl > 200 obs/base or max > 5k obs/base use 186s "99:200 100:5000". 186s 186s FAST5 Data Argument: 186s --corrected-group CORRECTED_GROUP 186s FAST5 group created by resquiggle command. Default: 186s RawGenomeCorrected_000 186s 186s Miscellaneous Arguments: 186s --quiet, -q Don't print status information. 186s --help, -h Print this help message and exit 186s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 186s [FAST5_BASEDIRS ...] 186s [--percent-to-filter PERCENT_TO_FILTER] 186s [--corrected-group CORRECTED_GROUP] 186s [--quiet] [--help] 186s 186s Required Arguments: 186s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 186s Directories containing fast5 files. 186s 186s Read Filtering Argument: 186s --percent-to-filter PERCENT_TO_FILTER 186s Percentage of all reads to filter. Reads are randomly 186s selected weighted according to the approximate 186s coverage at the mapped genomic location. This can be 186s useful in modeling and testing. Default: 10.000000 186s 186s FAST5 Data Arguments: 186s --corrected-group CORRECTED_GROUP 186s FAST5 group created by resquiggle command. Default: 186s RawGenomeCorrected_000 186s 186s Miscellaneous Arguments: 186s --quiet, -q Don't print status information. 186s --help, -h Print this help message and exit 186s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 186s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 186s [--corrected-group CORRECTED_GROUP] 186s [--basecall-group BASECALL_GROUP] [--quiet] 186s [--help] 186s 186s Required Arguments: 186s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 186s Directories containing fast5 files. 186s 186s Read Filtering Argument: 186s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 186s Default: 7.000000 186s 186s FAST5 Data Arguments: 186s --corrected-group CORRECTED_GROUP 186s FAST5 group created by resquiggle command. Default: 186s RawGenomeCorrected_000 186s --basecall-group BASECALL_GROUP 186s FAST5 group obtain original basecalls (under Analyses 186s group). Default: Basecall_1D_000 186s 186s Miscellaneous Arguments: 186s --quiet, -q Don't print status information. 186s --help, -h Print this help message and exit 186s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 186s [FAST5_BASEDIRS ...] 186s --signal-matching-score 186s SIGNAL_MATCHING_SCORE 186s [--corrected-group CORRECTED_GROUP] 186s [--quiet] [--help] 186s 186s Required Arguments: 186s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 186s Directories containing fast5 files. 186s --signal-matching-score SIGNAL_MATCHING_SCORE 186s Observed to expected signal matching score (higher 186s score indicates poor matching). Sample type defaults: 186s RNA : 2 || DNA : 1.1 186s 186s FAST5 Data Arguments: 186s --corrected-group CORRECTED_GROUP 186s FAST5 group created by resquiggle command. Default: 186s RawGenomeCorrected_000 186s 186s Miscellaneous Arguments: 186s --quiet, -q Don't print status information. 186s --help, -h Print this help message and exit 186s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 186s [FAST5_BASEDIRS ...] 186s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 186s [--include-partial-overlap] 186s [--corrected-group CORRECTED_GROUP] 186s [--quiet] [--help] 186s 186s Required Arguments: 186s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 186s Directories containing fast5 files. 186s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 186s Filter out reads not falling completely within include 186s regions. Omit start and end coordinates to include an 186s entire chromosome/sequence record. Format regions as 186s "chrm[:start-end] [chrm2[:start2-end2] ...]". 186s 186s Filter Argument: 186s --include-partial-overlap 186s Include reads that partially overlap the specified 186s region. Default: Only include reads completely 186s contained in a specified region 186s 186s FAST5 Data Argument: 186s --corrected-group CORRECTED_GROUP 186s FAST5 group created by resquiggle command. Default: 186s RawGenomeCorrected_000 186s 186s Miscellaneous Arguments: 186s --quiet, -q Don't print status information. 186s --help, -h Print this help message and exit 187s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 187s [FAST5_BASEDIRS ...] 187s --statistics-file-basename 187s STATISTICS_FILE_BASENAME [--dna] 187s [--rna] 187s [--fishers-method-context FISHERS_METHOD_CONTEXT] 187s [--minimum-test-reads MINIMUM_TEST_READS] 187s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 187s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 187s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 187s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 187s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 187s [--processes PROCESSES] 187s [--corrected-group CORRECTED_GROUP] 187s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 187s [--quiet] [--help] 187s 187s Required Argument: 187s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 187s Directories containing fast5 files. 187s --statistics-file-basename STATISTICS_FILE_BASENAME 187s File base name to save base by base statistics from 187s testing. Filenames will be [--statistics-file- 187s basename].[--alternate-bases]?.tombo.stats 187s 187s Comparison Model Arguments: 187s --dna Explicitly select canonical DNA model. Default: 187s Automatically determine from FAST5s 187s --rna Explicitly select canonical RNA model. Default: 187s Automatically determine from FAST5s 187s 187s Significance Test Arguments: 187s --fishers-method-context FISHERS_METHOD_CONTEXT 187s Number of context bases up and downstream over which 187s to compute Fisher's method combined p-values. Note: 187s Not applicable for alternative model likelihood ratio 187s tests. Default: 1. 187s --minimum-test-reads MINIMUM_TEST_READS 187s Number of reads required at a position to perform 187s significance testing or contribute to model 187s estimation. Default: 1 187s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 187s P-value threshold when computing fraction of 187s significant reads at each genomic position. If two 187s values are provided, statistics between these values 187s are not considered. Default thresholds: DNA:0.15-0.5 , 187s RNA:0.05-0.4 187s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 187s Dampen fraction modified estimates for low coverage 187s sites. Two parameters are unmodified and modified 187s pseudo read counts. This is equivalent to a beta prior 187s on the fraction estimate. Set to "0 0" to disable 187s dampened fraction estimation. Default: [2, 0] 187s 187s Output Argument: 187s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 187s Base for binary files containing per-read statistics 187s from statistical testing. Filenames will be [--per- 187s read-statistics-basename].[--alternate- 187s bases]?.tombo.per_read_stats 187s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 187s Number of the most significant sites to store for 187s faster access. If a longer list of most significant 187s sites is required the list must be re-computed from 187s all batches. Very large values can increase RAM usage. 187s Default: 100000 187s 187s Multiprocessing Arguments: 187s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 187s Size of regions over which to multiprocesses statistic 187s computation. For very deep samples a smaller value is 187s recommmended in order to control memory consumption. 187s Default: 10000 187s --processes PROCESSES 187s Number of processes. Default: 1 187s 187s FAST5 Data Arguments: 187s --corrected-group CORRECTED_GROUP 187s FAST5 group created by resquiggle command. Default: 187s RawGenomeCorrected_000 187s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 187s FAST5 subgroup(s) (under /Analyses/[--basecall- 187s group]/) containing basecalls and created within 187s [--corrected-group] containing re-squiggle results. 187s Default: ['BaseCalled_template'] 187s 187s Miscellaneous Arguments: 187s --quiet, -q Don't print status information. 187s --help, -h Print this help message and exit 187s usage: tombo detect_modifications alternative_model 187s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 187s [--statistics-file-basename STATISTICS_FILE_BASENAME] 187s [--alternate-bases {5mC,6mA,CpG,dcm,dam} [{5mC,6mA,CpG,dcm,dam} ...]] 187s [--print-available-models] 187s [--dna] [--rna] 187s [--minimum-test-reads MINIMUM_TEST_READS] 187s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 187s [--standard-log-likelihood-ratio] 187s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 187s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 187s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 187s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 187s [--processes PROCESSES] 187s [--corrected-group CORRECTED_GROUP] 187s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 187s [--quiet] [--help] 187s 187s Required Argument: 187s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 187s Directories containing fast5 files. 187s --statistics-file-basename STATISTICS_FILE_BASENAME 187s File base name to save base by base statistics from 187s testing. Filenames will be [--statistics-file- 187s basename].[--alternate-bases]?.tombo.stats 187s --alternate-bases {5mC,6mA,CpG,dcm,dam} [{5mC,6mA,CpG,dcm,dam} ...] 187s Default non-standard base model for testing (not 187s required if user created --alternate-model-filenames 187s is provided). 187s 187s Comparison Arguments: 187s --print-available-models 187s Print available alternative models and exit. 187s --dna Explicitly select canonical DNA model. Default: 187s Automatically determine from FAST5s 187s --rna Explicitly select canonical RNA model. Default: 187s Automatically determine from FAST5s 187s 187s Significance Test Arguments: 187s --minimum-test-reads MINIMUM_TEST_READS 187s Number of reads required at a position to perform 187s significance testing or contribute to model 187s estimation. Default: 1 187s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 187s Log likelihood ratio threshold when computing fraction 187s of significant reads at each genomic position. If two 187s values are provided, statistics between these values 187s are not considered. Default thresholds: DNA:-1.5-2.5 , 187s RNA:-2.5-2.5 187s --standard-log-likelihood-ratio 187s Use a standard log likelihood ratio (LLR) statistic. 187s Default is to use an outlier-robust LLR-like 187s statistic. Detail in full online documentation. 187s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 187s Dampen fraction modified estimates for low coverage 187s sites. Two parameters are unmodified and modified 187s pseudo read counts. This is equivalent to a beta prior 187s on the fraction estimate. Set to "0 0" to disable 187s dampened fraction estimation. Default: [2, 0] 187s 187s Output Argument: 187s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 187s Base for binary files containing per-read statistics 187s from statistical testing. Filenames will be [--per- 187s read-statistics-basename].[--alternate- 187s bases]?.tombo.per_read_stats 187s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 187s Number of the most significant sites to store for 187s faster access. If a longer list of most significant 187s sites is required the list must be re-computed from 187s all batches. Very large values can increase RAM usage. 187s Default: 100000 187s 187s Multiprocessing Arguments: 187s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 187s Size of regions over which to multiprocesses statistic 187s computation. For very deep samples a smaller value is 187s recommmended in order to control memory consumption. 187s Default: 10000 187s --processes PROCESSES 187s Number of processes. Default: 1 187s 187s FAST5 Data Arguments: 187s --corrected-group CORRECTED_GROUP 187s FAST5 group created by resquiggle command. Default: 187s RawGenomeCorrected_000 187s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 187s FAST5 subgroup(s) (under /Analyses/[--basecall- 187s group]/) containing basecalls and created within 187s [--corrected-group] containing re-squiggle results. 187s Default: ['BaseCalled_template'] 187s 187s Miscellaneous Arguments: 187s --quiet, -q Don't print status information. 187s --help, -h Print this help message and exit 187s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 187s FAST5_BASEDIRS 187s [FAST5_BASEDIRS ...] 187s --statistics-file-basename 187s STATISTICS_FILE_BASENAME 187s --control-fast5-basedirs 187s CONTROL_FAST5_BASEDIRS 187s [CONTROL_FAST5_BASEDIRS ...] 187s [--sample-only-estimates] 187s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 187s [--dna] [--rna] 187s [--fishers-method-context FISHERS_METHOD_CONTEXT] 187s [--minimum-test-reads MINIMUM_TEST_READS] 187s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 187s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 187s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 187s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 187s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 187s [--processes PROCESSES] 187s [--corrected-group CORRECTED_GROUP] 187s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 187s [--quiet] [--help] 187s 187s Required Argument: 187s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 187s Directories containing fast5 files. 187s --statistics-file-basename STATISTICS_FILE_BASENAME 187s File base name to save base by base statistics from 187s testing. Filenames will be [--statistics-file- 187s basename].[--alternate-bases]?.tombo.stats 187s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 187s Set of directories containing fast5 files for control 187s reads, containing only canonical nucleotides. 187s 187s Model Prior Arguments: 187s --sample-only-estimates 187s Only use canonical sample to estimate expected signal 187s level and spread. Default: Use canonical model to 187s improve estimtates (esp. for low coverage regions) 187s using baysian posterior estimates. 187s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 187s Prior weights (one each for mean and spread) applied 187s to canonical base model for estimating posterior model 187s parameters for sample comparison. Default: [5, 40] 187s --dna Explicitly select canonical DNA model. Default: 187s Automatically determine from FAST5s 187s --rna Explicitly select canonical RNA model. Default: 187s Automatically determine from FAST5s 187s 187s Significance Test Arguments: 187s --fishers-method-context FISHERS_METHOD_CONTEXT 187s Number of context bases up and downstream over which 187s to compute Fisher's method combined p-values. Note: 187s Not applicable for alternative model likelihood ratio 187s tests. Default: 1. 187s --minimum-test-reads MINIMUM_TEST_READS 187s Number of reads required at a position to perform 187s significance testing or contribute to model 187s estimation. Default: 1 187s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 187s P-value threshold when computing fraction of 187s significant reads at each genomic position. If two 187s values are provided, statistics between these values 187s are not considered. Default thresholds: DNA:0.15-0.5 , 187s RNA:0.05-0.4 187s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 187s Dampen fraction modified estimates for low coverage 187s sites. Two parameters are unmodified and modified 187s pseudo read counts. This is equivalent to a beta prior 187s on the fraction estimate. Set to "0 0" to disable 187s dampened fraction estimation. Default: [2, 0] 187s 187s Output Argument: 187s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 187s Base for binary files containing per-read statistics 187s from statistical testing. Filenames will be [--per- 187s read-statistics-basename].[--alternate- 187s bases]?.tombo.per_read_stats 187s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 187s Number of the most significant sites to store for 187s faster access. If a longer list of most significant 187s sites is required the list must be re-computed from 187s all batches. Very large values can increase RAM usage. 187s Default: 100000 187s 187s Multiprocessing Arguments: 187s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 187s Size of regions over which to multiprocesses statistic 187s computation. For very deep samples a smaller value is 187s recommmended in order to control memory consumption. 187s Default: 10000 187s --processes PROCESSES 187s Number of processes. Default: 1 187s 187s FAST5 Data Arguments: 187s --corrected-group CORRECTED_GROUP 187s FAST5 group created by resquiggle command. Default: 187s RawGenomeCorrected_000 187s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 187s FAST5 subgroup(s) (under /Analyses/[--basecall- 187s group]/) containing basecalls and created within 187s [--corrected-group] containing re-squiggle results. 187s Default: ['BaseCalled_template'] 187s 187s Miscellaneous Arguments: 187s --quiet, -q Don't print status information. 187s --help, -h Print this help message and exit 187s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 187s FAST5_BASEDIRS 187s [FAST5_BASEDIRS ...] 187s --statistics-file-basename 187s STATISTICS_FILE_BASENAME 187s --alternate-fast5-basedirs 187s ALTERNATE_FAST5_BASEDIRS 187s [ALTERNATE_FAST5_BASEDIRS ...] 187s [--fishers-method-context FISHERS_METHOD_CONTEXT] 187s [--minimum-test-reads MINIMUM_TEST_READS] 187s [--statistic-type {ks,u,t}] 187s [--store-p-value] 187s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 187s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 187s [--processes PROCESSES] 187s [--corrected-group CORRECTED_GROUP] 187s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 187s [--quiet] [--help] 187s 187s Required Argument: 187s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 187s Directories containing fast5 files. 187s --statistics-file-basename STATISTICS_FILE_BASENAME 187s File base name to save base by base statistics from 187s testing. Filenames will be [--statistics-file- 187s basename].[--alternate-bases]?.tombo.stats 187s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 187s Set of directories containing fast5 files for 187s alternate set of reads. 187s 187s Significance Test Arguments: 187s --fishers-method-context FISHERS_METHOD_CONTEXT 187s Number of context bases up and downstream over which 187s to compute Fisher's method combined p-values. Note: 187s Not applicable for alternative model likelihood ratio 187s tests. Default: 1. 187s --minimum-test-reads MINIMUM_TEST_READS 187s Number of reads required at a position to perform 187s significance testing or contribute to model 187s estimation. Default: 50 187s --statistic-type {ks,u,t} 187s Type of statistical test to apply. Default: "ks" 187s --store-p-value Store p-value instead of effect-size statistic. 187s Statistics are D-statistic (KS-test), deviation from 187s even common language effect size (u-test), and Cohen's 187s D (t-test). 187s 187s Output Argument: 187s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 187s Number of the most significant sites to store for 187s faster access. If a longer list of most significant 187s sites is required the list must be re-computed from 187s all batches. Very large values can increase RAM usage. 187s Default: 100000 187s 187s Multiprocessing Arguments: 187s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 187s Size of regions over which to multiprocesses statistic 187s computation. For very deep samples a smaller value is 187s recommmended in order to control memory consumption. 187s Default: 10000 187s --processes PROCESSES 187s Number of processes. Default: 1 187s 187s FAST5 Data Arguments: 187s --corrected-group CORRECTED_GROUP 187s FAST5 group created by resquiggle command. Default: 187s RawGenomeCorrected_000 187s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 187s FAST5 subgroup(s) (under /Analyses/[--basecall- 187s group]/) containing basecalls and created within 187s [--corrected-group] containing re-squiggle results. 187s Default: ['BaseCalled_template'] 187s 187s Miscellaneous Arguments: 187s --quiet, -q Don't print status information. 187s --help, -h Print this help message and exit 187s usage: tombo detect_modifications aggregate_per_read_stats 187s --per-read-statistics-filename 187s PER_READ_STATISTICS_FILENAME 187s --statistics-filename 187s STATISTICS_FILENAME 187s --single-read-threshold 187s SINGLE_READ_THRESHOLD 187s [SINGLE_READ_THRESHOLD ...] 187s [--minimum-test-reads MINIMUM_TEST_READS] 187s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 187s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 187s [--processes PROCESSES] 187s [--corrected-group CORRECTED_GROUP] 187s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 187s [--quiet] [--help] 187s 187s Required Argument: 187s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 187s Binary file containing per-read statistics from 187s statistical testing. 187s --statistics-filename STATISTICS_FILENAME 187s File to save/load genomic base anchored statistics. 187s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 187s P-value or log likelihood ratio threshold when 187s computing fraction of significant reads at each 187s genomic position. If two values are provided, 187s statistics between these values are not considered. 187s 187s Significance Test Arguments: 187s --minimum-test-reads MINIMUM_TEST_READS 187s Number of reads required at a position to perform 187s significance testing or contribute to model 187s estimation. Default: 1 187s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 187s Dampen fraction modified estimates for low coverage 187s sites. Two parameters are unmodified and modified 187s pseudo read counts. This is equivalent to a beta prior 187s on the fraction estimate. Set to "0 0" to disable 187s dampened fraction estimation. Default: [2, 0] 187s 187s Output Argument: 187s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 187s Number of the most significant sites to store for 187s faster access. If a longer list of most significant 187s sites is required the list must be re-computed from 187s all batches. Very large values can increase RAM usage. 187s Default: 100000 187s 187s Multiprocessing Arguments: 187s --processes PROCESSES 187s Number of processes. Default: 1 187s 187s FAST5 Data Arguments: 187s --corrected-group CORRECTED_GROUP 187s FAST5 group created by resquiggle command. Default: 187s RawGenomeCorrected_000 187s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 187s FAST5 subgroup(s) (under /Analyses/[--basecall- 187s group]/) containing basecalls and created within 187s [--corrected-group] containing re-squiggle results. 187s Default: ['BaseCalled_template'] 187s 187s Miscellaneous Arguments: 187s --quiet, -q Don't print status information. 187s --help, -h Print this help message and exit 187s usage: tombo text_output browser_files 187s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 187s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 187s [--statistics-filename STATISTICS_FILENAME] 187s [--genome-fasta GENOME_FASTA] 187s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 187s [--browser-file-basename BROWSER_FILE_BASENAME] 187s [--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} ...]] 187s [--corrected-group CORRECTED_GROUP] 187s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 187s [--quiet] [--help] 187s 187s Data Arguments: 187s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 187s Directories containing fast5 files. 187s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 187s Set of directories containing fast5 files for control 187s reads, containing only canonical nucleotides. 187s --statistics-filename STATISTICS_FILENAME 187s File to save/load genomic base anchored statistics. 187s 187s Statistic Motif Filter Arguments: 187s --genome-fasta GENOME_FASTA 187s FASTA file used to re-squiggle. For faster sequence 187s access. 187s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 187s Ground truth, motif centered, modified base 187s descriptions for output filtering. Format descriptions 187s as: "motif:mod_pos:name". The mod_pos indicates the 187s modified base within the motif (1-based index). 187s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 187s output for identification of E. coli dam and dcm 187s methylation. 187s 187s Output Arguments: 187s --browser-file-basename BROWSER_FILE_BASENAME 187s Basename for output browser files. Two files (plus and 187s minus strand) will be produced for each --file-types 187s supplied. Filenames formatted as "[browser-file- 187s basename].[file- 187s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 187s Default: tombo_results 187s --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} ...] 187s Data types of genome browser files to produce. 187s Produced coverage files are in bedGraph format, while 187s all other file types will be in wiggle format 187s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 187s Default: "coverage" 187s 187s FAST5 Data Arguments: 187s --corrected-group CORRECTED_GROUP 187s FAST5 group created by resquiggle command. Default: 187s RawGenomeCorrected_000 187s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 187s FAST5 subgroup(s) (under /Analyses/[--basecall- 187s group]/) containing basecalls and created within 187s [--corrected-group] containing re-squiggle results. 187s Default: ['BaseCalled_template'] 187s 187s Miscellaneous Arguments: 187s --quiet, -q Don't print status information. 187s --help, -h Print this help message and exit 187s usage: tombo text_output signif_sequence_context --statistics-filename 187s STATISTICS_FILENAME 187s [--genome-fasta GENOME_FASTA] 187s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 187s [--num-regions NUM_REGIONS] 187s [--num-bases NUM_BASES] 187s [--sequences-filename SEQUENCES_FILENAME] 187s [--corrected-group CORRECTED_GROUP] 187s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 187s [--quiet] [--help] 187s 187s Required Argument: 187s --statistics-filename STATISTICS_FILENAME 187s File to save/load genomic base anchored statistics. 187s 187s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 187s --genome-fasta GENOME_FASTA 187s FASTA file used to re-squiggle. For faster sequence 187s access. 187s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 187s Directories containing fast5 files. 187s 187s Region Selection Arguments: 187s --num-regions NUM_REGIONS 187s Number of regions to plot. Default: 100 187s --num-bases NUM_BASES 187s Number of bases to plot/output. Default: 15 187s 187s Output Arguments: 187s --sequences-filename SEQUENCES_FILENAME 187s File for sequences from selected regions. Sequences 187s will be stored in FASTA format. Default: 187s tombo_results.significant_regions.fasta. 187s 187s FAST5 Data Arguments: 187s --corrected-group CORRECTED_GROUP 187s FAST5 group created by resquiggle command. Default: 187s RawGenomeCorrected_000 187s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 187s FAST5 subgroup(s) (under /Analyses/[--basecall- 187s group]/) containing basecalls and created within 187s [--corrected-group] containing re-squiggle results. 187s Default: ['BaseCalled_template'] 187s 187s Miscellaneous Arguments: 187s --quiet, -q Don't print status information. 187s --help, -h Print this help message and exit 188s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 188s [FAST5_BASEDIRS ...] 188s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 188s [--plot-standard-model] 188s [--plot-alternate-model {5mC,dcm,dam,6mA,CpG}] 188s [--overplot-threshold OVERPLOT_THRESHOLD] 188s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 188s [--num-regions NUM_REGIONS] 188s [--num-bases NUM_BASES] 188s [--pdf-filename PDF_FILENAME] 188s [--corrected-group CORRECTED_GROUP] 188s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 188s [--quiet] [--help] 188s 188s Required Argument: 188s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 188s Directories containing fast5 files. 188s 188s Comparison Arguments: 188s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 188s Set of directories containing fast5 files for control 188s reads, containing only canonical nucleotides. 188s --plot-standard-model 188s Add default standard model distribution to the plot. 188s --plot-alternate-model {5mC,dcm,dam,6mA,CpG} 188s Add alternative model distribution to the plot. 188s 188s Overplotting Arguments: 188s --overplot-threshold OVERPLOT_THRESHOLD 188s Coverage level to trigger alternative plot type 188s instead of raw signal. Default: 50 188s --overplot-type {Downsample,Boxplot,Quantile,Density} 188s Plot type for regions with higher coverage. Default: 188s Downsample 188s 188s Plotting Region Arguments: 188s --num-regions NUM_REGIONS 188s Number of regions to plot. Default: 10 188s --num-bases NUM_BASES 188s Number of bases to plot/output. Default: 21 188s 188s Output Argument: 188s --pdf-filename PDF_FILENAME 188s PDF filename to store plot(s). Default: 188s tombo_results.max_coverage.pdf 188s 188s FAST5 Data Arguments: 188s --corrected-group CORRECTED_GROUP 188s FAST5 group created by resquiggle command. Default: 188s RawGenomeCorrected_000 188s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 188s FAST5 subgroup(s) (under /Analyses/[--basecall- 188s group]/) containing basecalls and created within 188s [--corrected-group] containing re-squiggle results. 188s Default: ['BaseCalled_template'] 188s 188s Miscellaneous Arguments: 188s --quiet, -q Don't print status information. 188s --help, -h Print this help message and exit 188s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 188s [FAST5_BASEDIRS ...] --genome-locations 188s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 188s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 188s [--plot-standard-model] 188s [--plot-alternate-model {dcm,6mA,5mC,CpG,dam}] 188s [--overplot-threshold OVERPLOT_THRESHOLD] 188s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 188s [--num-bases NUM_BASES] 188s [--pdf-filename PDF_FILENAME] 188s [--corrected-group CORRECTED_GROUP] 188s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 188s [--quiet] [--help] 188s 188s Required Arguments: 188s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 188s Directories containing fast5 files. 188s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 188s Genomic locations at which to plot signal. Format 188s locations as "chrm:position[:strand] 188s [chrm2:position2[:strand2] ...]" (strand not 188s applicable for all applications) 188s 188s Comparison Arguments: 188s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 188s Set of directories containing fast5 files for control 188s reads, containing only canonical nucleotides. 188s --plot-standard-model 188s Add default standard model distribution to the plot. 188s --plot-alternate-model {dcm,6mA,5mC,CpG,dam} 188s Add alternative model distribution to the plot. 188s 188s Overplotting Arguments: 188s --overplot-threshold OVERPLOT_THRESHOLD 188s Coverage level to trigger alternative plot type 188s instead of raw signal. Default: 50 188s --overplot-type {Downsample,Boxplot,Quantile,Density} 188s Plot type for regions with higher coverage. Default: 188s Downsample 188s 188s Plotting Region Argument: 188s --num-bases NUM_BASES 188s Number of bases to plot/output. Default: 21 188s 188s Output Argument: 188s --pdf-filename PDF_FILENAME 188s PDF filename to store plot(s). Default: 188s tombo_results.genome_locations.pdf 188s 188s FAST5 Data Arguments: 188s --corrected-group CORRECTED_GROUP 188s FAST5 group created by resquiggle command. Default: 188s RawGenomeCorrected_000 188s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 188s FAST5 subgroup(s) (under /Analyses/[--basecall- 188s group]/) containing basecalls and created within 188s [--corrected-group] containing re-squiggle results. 188s Default: ['BaseCalled_template'] 188s 188s Miscellaneous Arguments: 188s --quiet, -q Don't print status information. 188s --help, -h Print this help message and exit 188s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 188s [FAST5_BASEDIRS ...] --motif MOTIF 188s --genome-fasta GENOME_FASTA 188s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 188s [--plot-standard-model] 188s [--plot-alternate-model {6mA,CpG,dam,5mC,dcm}] 188s [--overplot-threshold OVERPLOT_THRESHOLD] 188s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 188s [--num-regions NUM_REGIONS] 188s [--num-bases NUM_BASES] [--deepest-coverage] 188s [--pdf-filename PDF_FILENAME] 188s [--corrected-group CORRECTED_GROUP] 188s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 188s [--quiet] [--help] 188s 188s Required Arguments: 188s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 188s Directories containing fast5 files. 188s --motif MOTIF Motif of interest at which to plot signal and 188s statsitics. Supports IUPAC single letter codes (use T 188s for RNA). 188s --genome-fasta GENOME_FASTA 188s FASTA file used to re-squiggle. For faster sequence 188s access. 188s 188s Comparison Arguments: 188s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 188s Set of directories containing fast5 files for control 188s reads, containing only canonical nucleotides. 188s --plot-standard-model 188s Add default standard model distribution to the plot. 188s --plot-alternate-model {6mA,CpG,dam,5mC,dcm} 188s Add alternative model distribution to the plot. 188s 188s Overplotting Arguments: 188s --overplot-threshold OVERPLOT_THRESHOLD 188s Coverage level to trigger alternative plot type 188s instead of raw signal. Default: 50 188s --overplot-type {Downsample,Boxplot,Quantile,Density} 188s Plot type for regions with higher coverage. Default: 188s Downsample 188s 188s Plotting Region Arguments: 188s --num-regions NUM_REGIONS 188s Number of regions to plot. Default: 10 188s --num-bases NUM_BASES 188s Number of bases to plot/output. Default: 21 188s --deepest-coverage Plot the deepest coverage regions. 188s 188s Output Argument: 188s --pdf-filename PDF_FILENAME 188s PDF filename to store plot(s). Default: 188s tombo_results.motif_centered.pdf 188s 188s FAST5 Data Arguments: 188s --corrected-group CORRECTED_GROUP 188s FAST5 group created by resquiggle command. Default: 188s RawGenomeCorrected_000 188s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 188s FAST5 subgroup(s) (under /Analyses/[--basecall- 188s group]/) containing basecalls and created within 188s [--corrected-group] containing re-squiggle results. 188s Default: ['BaseCalled_template'] 188s 188s Miscellaneous Arguments: 188s --quiet, -q Don't print status information. 188s --help, -h Print this help message and exit 188s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 188s [FAST5_BASEDIRS ...] --control-fast5-basedirs 188s CONTROL_FAST5_BASEDIRS 188s [CONTROL_FAST5_BASEDIRS ...] 188s [--overplot-threshold OVERPLOT_THRESHOLD] 188s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 188s [--num-regions NUM_REGIONS] 188s [--num-bases NUM_BASES] 188s [--pdf-filename PDF_FILENAME] 188s [--sequences-filename SEQUENCES_FILENAME] 188s [--corrected-group CORRECTED_GROUP] 188s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 188s [--quiet] [--help] 188s 188s Required Arguments: 188s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 188s Directories containing fast5 files. 188s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 188s Set of directories containing fast5 files for control 188s reads, containing only canonical nucleotides. 188s 188s Overplotting Arguments: 188s --overplot-threshold OVERPLOT_THRESHOLD 188s Coverage level to trigger alternative plot type 188s instead of raw signal. Default: 50 188s --overplot-type {Downsample,Boxplot,Quantile,Density} 188s Plot type for regions with higher coverage. Default: 188s Downsample 188s 188s Plotting Region Arguments: 188s --num-regions NUM_REGIONS 188s Number of regions to plot. Default: 10 188s --num-bases NUM_BASES 188s Number of bases to plot/output. Default: 21 188s 188s Output Arguments: 188s --pdf-filename PDF_FILENAME 188s PDF filename to store plot(s). Default: 188s tombo_results.max_difference.pdf 188s --sequences-filename SEQUENCES_FILENAME 188s File for sequences from selected regions. Sequences 188s will be stored in FASTA format. Default: None. 188s 188s FAST5 Data Arguments: 188s --corrected-group CORRECTED_GROUP 188s FAST5 group created by resquiggle command. Default: 188s RawGenomeCorrected_000 188s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 188s FAST5 subgroup(s) (under /Analyses/[--basecall- 188s group]/) containing basecalls and created within 188s [--corrected-group] containing re-squiggle results. 188s Default: ['BaseCalled_template'] 188s 188s Miscellaneous Arguments: 188s --quiet, -q Don't print status information. 188s --help, -h Print this help message and exit 188s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 188s [FAST5_BASEDIRS ...] --statistics-filename 188s STATISTICS_FILENAME 188s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 188s [--plot-standard-model] 188s [--plot-alternate-model {CpG,dcm,5mC,dam,6mA}] 188s [--overplot-threshold OVERPLOT_THRESHOLD] 188s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 188s [--num-regions NUM_REGIONS] 188s [--num-bases NUM_BASES] 188s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 188s [--pdf-filename PDF_FILENAME] 188s [--sequences-filename SEQUENCES_FILENAME] 188s [--corrected-group CORRECTED_GROUP] 188s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 188s [--quiet] [--help] 188s 188s Required Arguments: 188s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 188s Directories containing fast5 files. 188s --statistics-filename STATISTICS_FILENAME 188s File to save/load genomic base anchored statistics. 188s 188s Comparison Arguments: 188s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 188s Set of directories containing fast5 files for control 188s reads, containing only canonical nucleotides. 188s --plot-standard-model 188s Add default standard model distribution to the plot. 188s --plot-alternate-model {CpG,dcm,5mC,dam,6mA} 188s Add alternative model distribution to the plot. 188s 188s Overplotting Arguments: 188s --overplot-threshold OVERPLOT_THRESHOLD 188s Coverage level to trigger alternative plot type 188s instead of raw signal. Default: 50 188s --overplot-type {Downsample,Boxplot,Quantile,Density} 188s Plot type for regions with higher coverage. Default: 188s Downsample 188s 188s Plotting Region Arguments: 188s --num-regions NUM_REGIONS 188s Number of regions to plot. Default: 10 188s --num-bases NUM_BASES 188s Number of bases to plot/output. Default: 21 188s 188s Statistical Argument: 188s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 188s Dampen fraction modified estimates for low coverage 188s sites. Two parameters are unmodified and modified 188s pseudo read counts. This is equivalent to a beta prior 188s on the fraction estimate. Set to "0 0" to disable 188s dampened fraction estimation. Default: [2, 0] 188s 188s Output Arguments: 188s --pdf-filename PDF_FILENAME 188s PDF filename to store plot(s). Default: 188s tombo_results.significant_difference.pdf 188s --sequences-filename SEQUENCES_FILENAME 188s File for sequences from selected regions. Sequences 188s will be stored in FASTA format. Default: None. 188s 188s FAST5 Data Arguments: 188s --corrected-group CORRECTED_GROUP 188s FAST5 group created by resquiggle command. Default: 188s RawGenomeCorrected_000 188s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 188s FAST5 subgroup(s) (under /Analyses/[--basecall- 188s group]/) containing basecalls and created within 188s [--corrected-group] containing re-squiggle results. 188s Default: ['BaseCalled_template'] 188s 188s Miscellaneous Arguments: 188s --quiet, -q Don't print status information. 188s --help, -h Print this help message and exit 189s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 189s [FAST5_BASEDIRS ...] --motif MOTIF 189s --statistics-filename STATISTICS_FILENAME 189s --genome-fasta GENOME_FASTA 189s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 189s [--plot-standard-model] 189s [--plot-alternate-model {6mA,5mC,dam,dcm,CpG}] 189s [--overplot-threshold OVERPLOT_THRESHOLD] 189s [--num-regions NUM_REGIONS] 189s [--num-context NUM_CONTEXT] 189s [--num-statistics NUM_STATISTICS] 189s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 189s [--pdf-filename PDF_FILENAME] 189s [--corrected-group CORRECTED_GROUP] 189s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 189s [--quiet] [--help] 189s 189s Required Arguments: 189s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 189s Directories containing fast5 files. 189s --motif MOTIF Motif of interest at which to plot signal and 189s statsitics. Supports IUPAC single letter codes (use T 189s for RNA). 189s --statistics-filename STATISTICS_FILENAME 189s File to save/load genomic base anchored statistics. 189s --genome-fasta GENOME_FASTA 189s FASTA file used to re-squiggle. For faster sequence 189s access. 189s 189s Comparison Arguments: 189s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 189s Set of directories containing fast5 files for control 189s reads, containing only canonical nucleotides. 189s --plot-standard-model 189s Add default standard model distribution to the plot. 189s --plot-alternate-model {6mA,5mC,dam,dcm,CpG} 189s Add alternative model distribution to the plot. 189s 189s Overplotting Argument: 189s --overplot-threshold OVERPLOT_THRESHOLD 189s Coverage level to trigger alternative plot type 189s instead of raw signal. Default: 50 189s 189s Plotting Region Arguments: 189s --num-regions NUM_REGIONS 189s Number of regions to plot. Default: 3 189s --num-context NUM_CONTEXT 189s Number of context bases around motif. Default: 5 189s --num-statistics NUM_STATISTICS 189s Number of motif centered regions to include in 189s statistic distributions. Default: 200 189s 189s Statistical Argument: 189s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 189s Dampen fraction modified estimates for low coverage 189s sites. Two parameters are unmodified and modified 189s pseudo read counts. This is equivalent to a beta prior 189s on the fraction estimate. Set to "0 0" to disable 189s dampened fraction estimation. Default: [2, 0] 189s 189s Output Argument: 189s --pdf-filename PDF_FILENAME 189s PDF filename to store plot(s). Default: 189s tombo_results.motif_statistics.pdf 189s 189s FAST5 Data Arguments: 189s --corrected-group CORRECTED_GROUP 189s FAST5 group created by resquiggle command. Default: 189s RawGenomeCorrected_000 189s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 189s FAST5 subgroup(s) (under /Analyses/[--basecall- 189s group]/) containing basecalls and created within 189s [--corrected-group] containing re-squiggle results. 189s Default: ['BaseCalled_template'] 189s 189s Miscellaneous Arguments: 189s --quiet, -q Don't print status information. 189s --help, -h Print this help message and exit 189s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 189s [GENOME_LOCATIONS ...] 189s --per-read-statistics-filename 189s PER_READ_STATISTICS_FILENAME 189s [--genome-fasta GENOME_FASTA] 189s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 189s [--num-reads NUM_READS] [--num-bases NUM_BASES] 189s [--box-center] [--pdf-filename PDF_FILENAME] 189s [--corrected-group CORRECTED_GROUP] 189s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 189s [--quiet] [--help] 189s 189s Required Arguments: 189s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 189s Genomic locations at which to plot signal. Format 189s locations as "chrm:position[:strand] 189s [chrm2:position2[:strand2] ...]" (strand not 189s applicable for all applications) 189s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 189s Binary file containing per-read statistics from 189s statistical testing. 189s 189s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 189s --genome-fasta GENOME_FASTA 189s FASTA file used to re-squiggle. For faster sequence 189s access. 189s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 189s Directories containing fast5 files. 189s 189s Plotting Region Arguments: 189s --num-reads NUM_READS 189s Number of reads to plot. Default: 100 189s --num-bases NUM_BASES 189s Number of bases to plot/output. Default: 51 189s --box-center Plot a box around the central base. 189s 189s Output Argument: 189s --pdf-filename PDF_FILENAME 189s PDF filename to store plot(s). Default: 189s tombo_results.per_read_stats.pdf 189s 189s FAST5 Data Arguments: 189s --corrected-group CORRECTED_GROUP 189s FAST5 group created by resquiggle command. Default: 189s RawGenomeCorrected_000 189s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 189s FAST5 subgroup(s) (under /Analyses/[--basecall- 189s group]/) containing basecalls and created within 189s [--corrected-group] containing re-squiggle results. 189s Default: ['BaseCalled_template'] 189s 189s Miscellaneous Arguments: 189s --quiet, -q Don't print status information. 189s --help, -h Print this help message and exit 189s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 189s [STATISTICS_FILENAMES ...] 189s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 189s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 189s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 189s [--genome-fasta GENOME_FASTA] 189s [--pdf-filename PDF_FILENAME] 189s [--statistics-per-block STATISTICS_PER_BLOCK] 189s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 189s [--quiet] [--help] 189s 189s Required Argument: 189s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 189s Files to load genomic base anchored statistics. 189s 189s Ground Truth Arguments (provide bed files or motifs): 189s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 189s Modification description and bed format files 189s containing single base locations of ground truth 189s modified sites. Bed files should contain 6 fields 189s including strand. Format descriptions as 189s "mod_name:locs.bed". Example: "CpG 189s bisulfite":bisulfite_locs.bed 189s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 189s Bed format files containing single base locations of 189s ground truth unmodified sites. Bed files should 189s contain 6 fields including strand. 189s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 189s Ground truth, motif centered, modified base 189s descriptions for computing ROC and PR curves. Each 189s statistics file is associated with a set of motif 189s descriptions. Format descriptions as: 189s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 189s mod_pos indicates the alternate-base within the motif 189s (1-based index). Example: CCWGG:2:"dcm 189s 5mC"::GATC:2:"dam 6mA" would assess the performance of 189s a single Tombo statistics file for identification of 189s E. coli dam and dcm methylation. 189s --genome-fasta GENOME_FASTA 189s FASTA file used to re-squiggle. For faster sequence 189s access. 189s 189s Output Arguments: 189s --pdf-filename PDF_FILENAME 189s PDF filename to store plot(s). Default: 189s tombo_results.roc.pdf 189s 189s Down-sampling Arguments: 189s --statistics-per-block STATISTICS_PER_BLOCK 189s Number of randomly selected per-read, per-base 189s statistics to extract from each genomic block for 189s plotting. Default: Include all stats 189s --total-statistics-limit TOTAL_STATISTICS_LIMIT 189s Total per-read statistics to be extracted for 189s plotting. Avoids memory overflow for large runs. 189s Default: 5000000 189s 189s Miscellaneous Arguments: 189s --quiet, -q Don't print status information. 189s --help, -h Print this help message and exit 189s usage: tombo plot per_read_roc --per-read-statistics-filenames 189s PER_READ_STATISTICS_FILENAMES 189s [PER_READ_STATISTICS_FILENAMES ...] 189s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 189s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 189s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 189s [--genome-fasta GENOME_FASTA] 189s [--statistics-per-block STATISTICS_PER_BLOCK] 189s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 189s [--pdf-filename PDF_FILENAME] [--quiet] 189s [--help] 189s 189s Required Argument: 189s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 189s Binary files containing per-read statistics from 189s statistical testing. 189s 189s Ground Truth Arguments (provide bed files or motifs): 189s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 189s Modification description and bed format files 189s containing single base locations of ground truth 189s modified sites. Bed files should contain 6 fields 189s including strand. Format descriptions as 189s "mod_name:locs.bed". Example: "CpG 189s bisulfite":bisulfite_locs.bed 189s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 189s Bed format files containing single base locations of 189s ground truth unmodified sites. Bed files should 189s contain 6 fields including strand. 189s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 189s Ground truth, motif centered, modified base 189s descriptions for computing ROC and PR curves. Each 189s statistics file is associated with a set of motif 189s descriptions. Format descriptions as: 189s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 189s mod_pos indicates the alternate-base within the motif 189s (1-based index). Example: CCWGG:2:"dcm 189s 5mC"::GATC:2:"dam 6mA" would assess the performance of 189s a single Tombo statistics file for identification of 189s E. coli dam and dcm methylation. 189s --genome-fasta GENOME_FASTA 189s FASTA file used to re-squiggle. For faster sequence 189s access. 189s 189s Down-sampling Arguments: 189s --statistics-per-block STATISTICS_PER_BLOCK 189s Number of randomly selected per-read, per-base 189s statistics to extract from each genomic block for 189s plotting. Default: 100000 189s --total-statistics-limit TOTAL_STATISTICS_LIMIT 189s Total per-read statistics to be extracted for 189s plotting. Avoids memory overflow for large runs. 189s Default: 5000000 189s 189s Output Arguments: 189s --pdf-filename PDF_FILENAME 189s PDF filename to store plot(s). Default: 189s tombo_results.per_reads_roc.pdf 189s 189s Miscellaneous Arguments: 189s --quiet, -q Don't print status information. 189s --help, -h Print this help message and exit 189s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 189s [--upstream-bases {0,1,2,3,4}] 189s [--downstream-bases {0,1,2,3,4}] [--read-mean] 189s [--num-kmer-threshold NUM_KMER_THRESHOLD] 189s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 189s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 189s [--corrected-group CORRECTED_GROUP] 189s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 189s [--quiet] [--help] 189s 189s Required Argument: 189s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 189s Directories containing fast5 files. 189s 189s Data Processing Arguments: 189s --upstream-bases {0,1,2,3,4} 189s Upstream bases in k-mer. Default: 1 189s --downstream-bases {0,1,2,3,4} 189s Downstream bases in k-mer. Default: 2 189s --read-mean Plot k-mer means across whole reads as opposed to 189s individual k-mer event levels. 189s --num-kmer-threshold NUM_KMER_THRESHOLD 189s Observations of each k-mer required to include a read 189s in read level averages. Default: 1 189s 189s Plotting Region Arguments: 189s --num-reads NUM_READS 189s Number of reads to plot. Default: 100 189s 189s Output Arguments: 189s --pdf-filename PDF_FILENAME 189s PDF filename to store plot(s). Default: 189s tombo_results.kmer_distribution.pdf 189s --r-data-filename R_DATA_FILENAME 189s Filename to save R data structure. Default: Don't save 189s --dont-plot Don't plot result. Useful to produce only R data file. 189s 189s FAST5 Data Arguments: 189s --corrected-group CORRECTED_GROUP 189s FAST5 group created by resquiggle command. Default: 189s RawGenomeCorrected_000 189s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 189s FAST5 subgroup(s) (under /Analyses/[--basecall- 189s group]/) containing basecalls and created within 189s [--corrected-group] containing re-squiggle results. 189s Default: ['BaseCalled_template'] 189s 189s Miscellaneous Arguments: 189s --quiet, -q Don't print status information. 189s --help, -h Print this help message and exit 189s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 189s [FAST5_BASEDIRS ...] 189s --control-fast5-basedirs 189s CONTROL_FAST5_BASEDIRS 189s [CONTROL_FAST5_BASEDIRS ...] 189s --statistics-filename 189s STATISTICS_FILENAME 189s [--genome-fasta GENOME_FASTA] 189s [--processes PROCESSES] 189s [--num-regions NUM_REGIONS] 189s [--num-bases NUM_BASES] 189s [--slide-span SLIDE_SPAN] 189s [--pdf-filename PDF_FILENAME] 189s [--r-data-filename R_DATA_FILENAME] 189s [--corrected-group CORRECTED_GROUP] 189s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 189s [--quiet] [--help] 189s 189s Required Arguments: 189s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 189s Directories containing fast5 files. 189s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 189s Set of directories containing fast5 files for control 189s reads, containing only canonical nucleotides. 189s --statistics-filename STATISTICS_FILENAME 189s File to save/load genomic base anchored statistics. 189s 189s FASTA Sequence Argument: 189s --genome-fasta GENOME_FASTA 189s FASTA file used to re-squiggle. For faster sequence 189s access. 189s 189s Multiprocessing Argument: 189s --processes PROCESSES 189s Number of processes. Default: 1 189s 189s Plotting Region Arguments: 189s --num-regions NUM_REGIONS 189s Number of regions to plot. Default: 10 189s --num-bases NUM_BASES 189s Number of bases to plot/output. Default: 21 189s --slide-span SLIDE_SPAN 189s Number of bases offset over which to search when 189s computing distances for signal cluster plotting. 189s Default: 0 (exact position) 189s 189s Output Arguments: 189s --pdf-filename PDF_FILENAME 189s PDF filename to store plot(s). Default: 189s tombo_results.signal_clusters.pdf 189s --r-data-filename R_DATA_FILENAME 189s Filename to save R data structure. Default: Don't save 189s 189s FAST5 Data Arguments: 189s --corrected-group CORRECTED_GROUP 189s FAST5 group created by resquiggle command. Default: 189s RawGenomeCorrected_000 189s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 189s FAST5 subgroup(s) (under /Analyses/[--basecall- 189s group]/) containing basecalls and created within 189s [--corrected-group] containing re-squiggle results. 189s Default: ['BaseCalled_template'] 189s 189s Miscellaneous Arguments: 189s --quiet, -q Don't print status information. 189s --help, -h Print this help message and exit 190s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 190s 190s Required Arguments: 190s fast5s_basedir Directory containing fast5 files. All files ending in 190s "fast5" found recursively within this base directory will be 190s processed. 190s 190s Miscellaneous Arguments: 190s --quiet, -q Don't print status information. 190s --help, -h Print this help message and exit 190s usage: tombo build_model event_resquiggle 190s [--minimap2-executable MINIMAP2_EXECUTABLE] 190s [--minimap2-index MINIMAP2_INDEX] 190s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 190s [--graphmap-executable GRAPHMAP_EXECUTABLE] 190s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 190s [--normalization-type {median,pA,pA_raw,none}] 190s [--pore-model-filename PORE_MODEL_FILENAME] 190s [--outlier-threshold OUTLIER_THRESHOLD] 190s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 190s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 190s [--timeout TIMEOUT] 190s [--cpts-limit CPTS_LIMIT] 190s [--skip-index] [--overwrite] 190s [--failed-reads-filename FAILED_READS_FILENAME] 190s [--include-event-stdev] 190s [--corrected-group CORRECTED_GROUP] 190s [--basecall-group BASECALL_GROUP] 190s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 190s [--processes PROCESSES] 190s [--align-processes ALIGN_PROCESSES] 190s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 190s [--resquiggle-processes RESQUIGGLE_PROCESSES] 190s [--quiet] [--help] 190s fast5s_basedir reference_fasta 190s 190s Required Arguments: 190s fast5s_basedir Directory containing fast5 files. All files ending in 190s "fast5" found recursively within this base directory 190s will be processed. 190s reference_fasta Reference genome/transcriptome FASTA file for mapping. 190s 190s Mapper Arguments (One mapper is required): 190s --minimap2-executable MINIMAP2_EXECUTABLE 190s Path to minimap2 executable. 190s --minimap2-index MINIMAP2_INDEX 190s Path to minimap2 index (with map-ont preset) file 190s corresponding to the [genome_fasta] provided. 190s --bwa-mem-executable BWA_MEM_EXECUTABLE 190s Path to bwa-mem executable. 190s --graphmap-executable GRAPHMAP_EXECUTABLE 190s Path to graphmap executable. 190s --alignment-batch-size ALIGNMENT_BATCH_SIZE 190s Number of reads included in each alignment call. Note: 190s A new system mapping call is made for each batch 190s (including loading of the genome), so it is advised to 190s use larger values for larger genomes. Default: 1000 190s 190s Signal Processing Arguments: 190s --normalization-type {median,pA,pA_raw,none} 190s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 190s as in the ONT events (using offset, range and 190s digitization), "pA": k-mer-based correction for pA 190s drift as in nanopolish (requires [--pore-model- 190s filename]), "median": median and MAD from raw signal. 190s Default: median 190s --pore-model-filename PORE_MODEL_FILENAME 190s File containing kmer model parameters (level_mean and 190s level_stdv) used in order to compute kmer-based 190s corrected pA values. E.g. https://github.com/jts/nanop 190s olish/blob/master/etc/r9- 190s models/template_median68pA.5mers.model 190s --outlier-threshold OUTLIER_THRESHOLD 190s Windosrize the signal at this number of scale values. 190s Negative value disables outlier clipping. Default: 190s 5.000000 190s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 190s Specify the 2 parameters for segmentation 1) running 190s neighboring windows width 2) minimum raw observations 190s per genomic base. Sample type defaults: RNA : 12 6 || 190s DNA : 5 3 190s 190s Read Filtering Arguments: 190s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 190s Filter reads based on observations per base percentile 190s thresholds. Format thresholds as "percentile:thresh 190s [pctl2:thresh2 ...]". For example to filter reads with 190s 99th pctl > 200 obs/base or max > 5k obs/base use 190s "99:200 100:5000". 190s --timeout TIMEOUT Timeout in seconds for processing a single read. 190s Default: No timeout. 190s --cpts-limit CPTS_LIMIT 190s Maximum number of changepoints to find within a single 190s indel group. Default: No limit. 190s 190s Input/Output Arguments: 190s --skip-index Skip creation of tombo index. This drastically slows 190s downstream tombo commands. Default stores tombo index 190s named ".[--fast5-basedir].[--corrected- 190s group].tombo.index" to be loaded automatically for 190s downstream commands. 190s --overwrite Overwrite previous corrected group in FAST5 files. 190s Note: only effects --corrected-group or --new- 190s corrected-group. 190s --failed-reads-filename FAILED_READS_FILENAME 190s Output failed read filenames with assoicated error. 190s Default: Do not store failed reads. 190s --include-event-stdev 190s Include corrected event standard deviation in output 190s FAST5 data. 190s 190s FAST5 Data Arguments: 190s --corrected-group CORRECTED_GROUP 190s FAST5 group created by resquiggle command. Default: 190s RawGenomeCorrected_000 190s --basecall-group BASECALL_GROUP 190s FAST5 group obtain original basecalls (under Analyses 190s group). Default: Basecall_1D_000 190s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 190s FAST5 subgroup(s) (under /Analyses/[--basecall- 190s group]/) containing basecalls and created within 190s [--corrected-group] containing re-squiggle results. 190s Default: ['BaseCalled_template'] 190s 190s Multiprocessing Arguments: 190s --processes PROCESSES 190s Number of processes. Default: 2 190s --align-processes ALIGN_PROCESSES 190s Number of processes to use for parsing and aligning 190s original basecalls. Each process will independently 190s load the genome into memory, so use caution with 190s larger genomes (e.g. human). Default: 1 190s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 190s Number of threads to use for aligner system call. 190s Default: [--processes] / (2 * [--align-processes)] 190s --resquiggle-processes RESQUIGGLE_PROCESSES 190s Number of processes to use for resquiggle algorithm. 190s Default: [--processes] / 2 190s 190s Miscellaneous Arguments: 190s --quiet, -q Don't print status information. 190s --help, -h Print this help message and exit 190s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 190s [FAST5_BASEDIRS ...] 190s --tombo-model-filename 190s TOMBO_MODEL_FILENAME 190s [--estimate-mean] 190s [--kmer-specific-sd] 190s [--upstream-bases {0,1,2,3,4}] 190s [--downstream-bases {0,1,2,3,4}] 190s [--minimum-test-reads MINIMUM_TEST_READS] 190s [--coverage-threshold COVERAGE_THRESHOLD] 190s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 190s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 190s [--processes PROCESSES] 190s [--corrected-group CORRECTED_GROUP] 190s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 190s [--quiet] [--help] 190s 190s Required Arguments: 190s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 190s Directories containing fast5 files. 190s --tombo-model-filename TOMBO_MODEL_FILENAME 190s Filename to save Tombo model. 190s 190s Modeling Arguments: 190s --estimate-mean Use the mean instead of median for model level 190s estimation. Note: This can cause poor fits due to 190s outliers 190s --kmer-specific-sd Estimate standard deviation for each k-mers 190s individually. 190s --upstream-bases {0,1,2,3,4} 190s Upstream bases in k-mer. Default: 1 190s --downstream-bases {0,1,2,3,4} 190s Downstream bases in k-mer. Default: 2 190s 190s Filtering Arguments: 190s --minimum-test-reads MINIMUM_TEST_READS 190s Number of reads required at a position to perform 190s significance testing or contribute to model 190s estimation. Default: 10 190s --coverage-threshold COVERAGE_THRESHOLD 190s Maximum mean coverage per region when estimating k-mer 190s model (limits compute time for deep samples). Default: 190s 100 190s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 190s Number of each k-mer observations required in order to 190s produce a reference (genomic locations for standard 190s reference and per-read for alternative reference). 190s Default: 5 190s 190s Multiprocessing Arguments: 190s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 190s Size of regions over which to multiprocesses statistic 190s computation. For very deep samples a smaller value is 190s recommmended in order to control memory consumption. 190s Default: 10000 190s --processes PROCESSES 190s Number of processes. Default: 1 190s 190s FAST5 Data Arguments: 190s --corrected-group CORRECTED_GROUP 190s FAST5 group created by resquiggle command. Default: 190s RawGenomeCorrected_000 190s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 190s FAST5 subgroup(s) (under /Analyses/[--basecall- 190s group]/) containing basecalls and created within 190s [--corrected-group] containing re-squiggle results. 190s Default: ['BaseCalled_template'] 190s 190s Miscellaneous Arguments: 190s --quiet, -q Don't print status information. 190s --help, -h Print this help message and exit 190s usage: tombo build_model estimate_alt_reference --alternate-model-filename 190s ALTERNATE_MODEL_FILENAME 190s --alternate-model-name 190s ALTERNATE_MODEL_NAME 190s --alternate-model-base 190s {A,C,G,T} 190s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 190s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 190s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 190s [--control-density-filename CONTROL_DENSITY_FILENAME] 190s [--dna] [--rna] 190s [--tombo-model-filename TOMBO_MODEL_FILENAME] 190s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 190s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 190s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 190s [--save-density-basename SAVE_DENSITY_BASENAME] 190s [--processes PROCESSES] 190s [--corrected-group CORRECTED_GROUP] 190s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 190s [--quiet] [--help] 190s 190s Required Arguments: 190s --alternate-model-filename ALTERNATE_MODEL_FILENAME 190s Tombo model for alternative likelihood ratio 190s significance testing. 190s --alternate-model-name ALTERNATE_MODEL_NAME 190s A short name to associate with this alternate model 190s (e.g. 5mC, 6mA, etc.). This text will be included in 190s output filenames when this model is used for testing. 190s --alternate-model-base {A,C,G,T} 190s Non-standard base is an alternative to this base. 190s 190s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 190s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 190s Directories containing fast5 files. 190s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 190s Set of directories containing fast5 files for control 190s reads, containing only canonical nucleotides. 190s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 190s File containing k-mer level kernel density estimates 190s for the alternative sample saved using --save-density- 190s basename. 190s --control-density-filename CONTROL_DENSITY_FILENAME 190s File containing k-mer level kernel density estimates 190s for the control sample saved using --save-density- 190s basename. 190s 190s Standard Model Arguments: 190s --dna Explicitly select canonical DNA model. Default: 190s Automatically determine from FAST5s 190s --rna Explicitly select canonical RNA model. Default: 190s Automatically determine from FAST5s 190s --tombo-model-filename TOMBO_MODEL_FILENAME 190s Tombo model filename. If no file is provided, the 190s default DNA or RNA Tombo model will be used. 190s 190s Model Fitting Arguments: 190s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 190s When esitmating the alternative base incorporation 190s rate, this percent of k-mers are assumed to have 190s significantly shifted signal so the alternative 190s distribution minimally overlaps the standard base 190s distribution. Default: 5.000000 190s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 190s Bandwidth applied when performing Gaussian kernal 190s density esitmation on standard and alternative base 190s signal distributions. Default: 0.050000 190s 190s Filtering Argument: 190s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 190s Number of each k-mer observations required in order to 190s produce a reference (genomic locations for standard 190s reference and per-read for alternative reference). 190s Default: 1000 190s 190s Output Argument: 190s --save-density-basename SAVE_DENSITY_BASENAME 190s Basename to save alternative model estimation density 190s estimation information. See scripts/debug_est_alt.R 190s for info use example. Default: Don't save. 190s 190s Multiprocessing Arguments: 190s --processes PROCESSES 190s Number of processes. Default: 1 190s 190s FAST5 Data Arguments: 190s --corrected-group CORRECTED_GROUP 190s FAST5 group created by resquiggle command. Default: 190s RawGenomeCorrected_000 190s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 190s FAST5 subgroup(s) (under /Analyses/[--basecall- 190s group]/) containing basecalls and created within 190s [--corrected-group] containing re-squiggle results. 190s Default: ['BaseCalled_template'] 190s 190s Miscellaneous Arguments: 190s --quiet, -q Don't print status information. 190s --help, -h Print this help message and exit 190s This test only tests the help system 190s There is an extensive test in 190s 190s tombo/tests/shell_tests.sh 190s 190s but this requires to download larger data 190s sets which is not done for the moment. 191s autopkgtest [20:44:40]: test run-unit-test: -----------------------] 191s autopkgtest [20:44:40]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 191s run-unit-test PASS 192s autopkgtest [20:44:41]: @@@@@@@@@@@@@@@@@@@@ summary 192s run-unit-test PASS 196s nova [W] Using flock in prodstack6-ppc64el 196s Creating nova instance adt-plucky-ppc64el-tombo-20241114-204128-juju-7f2275-prod-proposed-migration-environment-20-c158da35-cfd6-48a1-91fd-049736acbe23 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...