0s autopkgtest [20:01:44]: starting date and time: 2024-03-14 20:01:44+0000 0s autopkgtest [20:01:44]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [20:01:44]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.w3ids4ll/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:h5py,src:hdf5,src:openmpi,src:openssl,src:pmix --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=h5py/3.10.0-1ubuntu2 hdf5/1.10.10+repack-3.1ubuntu2 openmpi/4.1.6-5.1ubuntu3 openssl/3.0.13-0ubuntu1 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-ppc64el-20.secgroup --name adt-noble-ppc64el-tombo-20240314-200144-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 254s autopkgtest [20:05:58]: testbed dpkg architecture: ppc64el 257s autopkgtest [20:06:01]: testbed apt version: 2.7.12 257s autopkgtest [20:06:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 258s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 258s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3020 kB] 259s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 259s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [48.4 kB] 259s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [454 kB] 259s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [607 kB] 259s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 260s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 260s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 260s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [3317 kB] 260s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 260s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [42.8 kB] 260s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 263s Fetched 7625 kB in 3s (2240 kB/s) 263s Reading package lists... 266s Reading package lists... 266s Building dependency tree... 266s Reading state information... 267s Calculating upgrade... 267s The following packages will be REMOVED: 267s libssl3 267s The following NEW packages will be installed: 267s libssl3t64 267s The following packages will be upgraded: 267s openssl 267s 1 upgraded, 1 newly installed, 1 to remove and 0 not upgraded. 267s Need to get 3195 kB of archives. 267s After this operation, 6144 B of additional disk space will be used. 267s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu1 [1028 kB] 267s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu1 [2168 kB] 268s Fetched 3195 kB in 1s (3004 kB/s) 268s (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 ... 70095 files and directories currently installed.) 268s Preparing to unpack .../openssl_3.0.13-0ubuntu1_ppc64el.deb ... 268s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 268s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 268s wget depends on libssl3 (>= 3.0.0). 268s tnftp depends on libssl3 (>= 3.0.0). 268s tcpdump depends on libssl3 (>= 3.0.0). 268s systemd-resolved depends on libssl3 (>= 3.0.0). 268s systemd depends on libssl3 (>= 3.0.0). 268s sudo depends on libssl3 (>= 3.0.0). 268s rsync depends on libssl3 (>= 3.0.0). 268s python3-cryptography depends on libssl3 (>= 3.0.0). 268s openssh-server depends on libssl3 (>= 3.0.10). 268s openssh-client depends on libssl3 (>= 3.0.10). 268s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 268s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 268s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 268s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 268s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 268s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 268s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 268s libnvme1 depends on libssl3 (>= 3.0.0). 268s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 268s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 268s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 268s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 268s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 268s kmod depends on libssl3 (>= 3.0.0). 268s dhcpcd-base depends on libssl3 (>= 3.0.0). 268s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 268s 268s (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 ... 70095 files and directories currently installed.) 268s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 268s Selecting previously unselected package libssl3t64:ppc64el. 269s (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 ... 70084 files and directories currently installed.) 269s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_ppc64el.deb ... 269s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu1) ... 269s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu1) ... 269s Setting up openssl (3.0.13-0ubuntu1) ... 269s Processing triggers for man-db (2.12.0-3) ... 269s Processing triggers for libc-bin (2.39-0ubuntu2) ... 269s Reading package lists... 270s Building dependency tree... 270s Reading state information... 270s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 270s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 270s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 270s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 271s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 272s Reading package lists... 272s Reading package lists... 272s Building dependency tree... 272s Reading state information... 272s Calculating upgrade... 273s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 273s Reading package lists... 273s Building dependency tree... 273s Reading state information... 273s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 276s autopkgtest [20:06:20]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 276s autopkgtest [20:06:20]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 282s Get:1 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (dsc) [2292 B] 282s Get:2 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (tar) [22.3 MB] 282s Get:3 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (diff) [7024 B] 282s gpgv: Signature made Sun Dec 17 19:23:46 2023 UTC 282s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 282s gpgv: issuer "tille@debian.org" 282s gpgv: Can't check signature: No public key 282s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6.dsc: no acceptable signature found 283s autopkgtest [20:06:27]: testing package tombo version 1.5.1-6 283s autopkgtest [20:06:27]: build not needed 293s autopkgtest [20:06:37]: test run-unit-test: preparing testbed 295s Reading package lists... 295s Building dependency tree... 295s Reading state information... 295s Starting pkgProblemResolver with broken count: 0 295s Starting 2 pkgProblemResolver with broken count: 0 295s Done 296s The following additional packages will be installed: 296s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 296s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 296s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 296s python3-decorator python3-h5py python3-h5py-serial python3-mappy 296s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 296s tombo-doc 296s Suggested packages: 296s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 296s gfortran python3-dev python3-pytest python-scipy-doc 296s Recommended packages: 296s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 296s python3-rpy2 296s The following NEW packages will be installed: 296s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 296s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 296s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 296s libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy 296s python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo 296s tombo-doc 296s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 296s Need to get 68.5 MB/68.5 MB of archives. 296s After this operation, 268 MB of additional disk space will be used. 296s Get:1 /tmp/autopkgtest.QBy1fQ/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [708 B] 296s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-lato all 2.015-1 [2781 kB] 297s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 297s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 297s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libaec0 ppc64el 1.1.2-1 [29.9 kB] 297s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 297s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 297s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsz2 ppc64el 1.1.2-1 [5472 B] 297s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-3.1ubuntu2 [1395 kB] 297s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-3.1ubuntu2 [70.9 kB] 297s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 297s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 297s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-sphinxdoc all 7.2.6-4 [149 kB] 297s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 298s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1 [32.8 kB] 298s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 298s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 298s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 298s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-h5py-serial ppc64el 3.10.0-1ubuntu2 [955 kB] 298s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-h5py all 3.10.0-1ubuntu2 [7980 B] 298s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-mappy ppc64el 2.24+dfsg-3build2 [221 kB] 298s Get:22 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-tqdm all 4.64.1-2 [95.2 kB] 298s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] 298s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-scipy ppc64el 1.11.4-6 [21.4 MB] 300s Get:25 http://ftpmaster.internal/ubuntu noble/universe ppc64el tombo ppc64el 1.5.1-6 [514 kB] 300s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 300s Get:27 http://ftpmaster.internal/ubuntu noble/universe ppc64el tombo-doc all 1.5.1-6 [21.7 MB] 302s Fetched 68.5 MB in 6s (11.4 MB/s) 302s Selecting previously unselected package fonts-lato. 302s (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 ... 70097 files and directories currently installed.) 302s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 302s Unpacking fonts-lato (2.015-1) ... 302s Selecting previously unselected package fonts-font-awesome. 302s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 302s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 303s Selecting previously unselected package fonts-mathjax. 303s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 303s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 303s Selecting previously unselected package libaec0:ppc64el. 303s Preparing to unpack .../03-libaec0_1.1.2-1_ppc64el.deb ... 303s Unpacking libaec0:ppc64el (1.1.2-1) ... 303s Selecting previously unselected package libblas3:ppc64el. 303s Preparing to unpack .../04-libblas3_3.12.0-3_ppc64el.deb ... 303s Unpacking libblas3:ppc64el (3.12.0-3) ... 303s Selecting previously unselected package libgfortran5:ppc64el. 303s Preparing to unpack .../05-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 303s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 303s Selecting previously unselected package libsz2:ppc64el. 303s Preparing to unpack .../06-libsz2_1.1.2-1_ppc64el.deb ... 303s Unpacking libsz2:ppc64el (1.1.2-1) ... 303s Selecting previously unselected package libhdf5-103-1t64:ppc64el. 303s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu2_ppc64el.deb ... 303s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-3.1ubuntu2) ... 303s Selecting previously unselected package libhdf5-hl-100t64:ppc64el. 303s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu2_ppc64el.deb ... 303s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-3.1ubuntu2) ... 303s Selecting previously unselected package libjs-jquery. 303s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 303s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 303s Selecting previously unselected package libjs-underscore. 303s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 303s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 303s Selecting previously unselected package libjs-sphinxdoc. 303s Preparing to unpack .../11-libjs-sphinxdoc_7.2.6-4_all.deb ... 303s Unpacking libjs-sphinxdoc (7.2.6-4) ... 303s Selecting previously unselected package liblapack3:ppc64el. 303s Preparing to unpack .../12-liblapack3_3.12.0-3_ppc64el.deb ... 303s Unpacking liblapack3:ppc64el (3.12.0-3) ... 303s Selecting previously unselected package liblbfgsb0:ppc64el. 303s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1_ppc64el.deb ... 303s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 303s Selecting previously unselected package liblzf1:ppc64el. 303s Preparing to unpack .../14-liblzf1_3.6-4_ppc64el.deb ... 303s Unpacking liblzf1:ppc64el (3.6-4) ... 303s Selecting previously unselected package python3-decorator. 303s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ... 303s Unpacking python3-decorator (5.1.1-5) ... 303s Selecting previously unselected package python3-numpy. 303s Preparing to unpack .../16-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 303s Unpacking python3-numpy (1:1.24.2-2) ... 304s Selecting previously unselected package python3-h5py-serial. 304s Preparing to unpack .../17-python3-h5py-serial_3.10.0-1ubuntu2_ppc64el.deb ... 304s Unpacking python3-h5py-serial (3.10.0-1ubuntu2) ... 304s Selecting previously unselected package python3-h5py. 304s Preparing to unpack .../18-python3-h5py_3.10.0-1ubuntu2_all.deb ... 304s Unpacking python3-h5py (3.10.0-1ubuntu2) ... 304s Selecting previously unselected package python3-mappy. 304s Preparing to unpack .../19-python3-mappy_2.24+dfsg-3build2_ppc64el.deb ... 304s Unpacking python3-mappy (2.24+dfsg-3build2) ... 304s Selecting previously unselected package python3-tqdm. 304s Preparing to unpack .../20-python3-tqdm_4.64.1-2_all.deb ... 304s Unpacking python3-tqdm (4.64.1-2) ... 304s Selecting previously unselected package sphinx-rtd-theme-common. 304s Preparing to unpack .../21-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... 304s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 304s Selecting previously unselected package python3-scipy. 304s Preparing to unpack .../22-python3-scipy_1.11.4-6_ppc64el.deb ... 304s Unpacking python3-scipy (1.11.4-6) ... 305s Selecting previously unselected package tombo. 305s Preparing to unpack .../23-tombo_1.5.1-6_ppc64el.deb ... 305s Unpacking tombo (1.5.1-6) ... 305s Selecting previously unselected package libjs-mathjax. 305s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 305s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 306s Selecting previously unselected package tombo-doc. 306s Preparing to unpack .../25-tombo-doc_1.5.1-6_all.deb ... 306s Unpacking tombo-doc (1.5.1-6) ... 306s Selecting previously unselected package autopkgtest-satdep. 306s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 306s Unpacking autopkgtest-satdep (0) ... 306s Setting up fonts-lato (2.015-1) ... 306s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 306s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 306s Setting up python3-tqdm (4.64.1-2) ... 307s Setting up python3-mappy (2.24+dfsg-3build2) ... 307s Setting up libaec0:ppc64el (1.1.2-1) ... 307s Setting up python3-decorator (5.1.1-5) ... 307s Setting up libblas3:ppc64el (3.12.0-3) ... 307s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 307s Setting up liblzf1:ppc64el (3.6-4) ... 307s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 307s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 307s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 307s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 307s Setting up libsz2:ppc64el (1.1.2-1) ... 307s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 307s Setting up liblapack3:ppc64el (3.12.0-3) ... 307s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 307s Setting up python3-numpy (1:1.24.2-2) ... 309s Setting up libjs-sphinxdoc (7.2.6-4) ... 309s Setting up tombo-doc (1.5.1-6) ... 309s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-3.1ubuntu2) ... 309s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 309s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-3.1ubuntu2) ... 309s Setting up python3-scipy (1.11.4-6) ... 313s Setting up python3-h5py-serial (3.10.0-1ubuntu2) ... 313s Setting up python3-h5py (3.10.0-1ubuntu2) ... 313s Setting up tombo (1.5.1-6) ... 313s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 313s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 313s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 313s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 313s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 313s re.match('\+', fastq_rec[2]) is None): 314s Setting up autopkgtest-satdep (0) ... 314s Processing triggers for man-db (2.12.0-3) ... 314s Processing triggers for libc-bin (2.39-0ubuntu2) ... 319s (Reading database ... 77475 files and directories currently installed.) 319s Removing autopkgtest-satdep (0) ... 319s autopkgtest [20:07:03]: test run-unit-test: [----------------------- 320s ********* Testing help commands ********** 320s usage: tombo [-h] [-v] 320s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 320s ... 320s 320s ********** Tombo ********* 320s 320s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 320s 320s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 320s 320s Tombo command groups (additional help available within each command group): 320s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 320s preprocess Pre-process nanopore reads for Tombo processing. 320s filter Apply filter to Tombo index file for specified criterion. 320s detect_modifications Perform statistical testing to detect non-standard nucleotides. 320s text_output Output Tombo results in text files. 320s build_model Create canonical and alternative base Tombo models. 320s plot Save plots to visualize raw nanopore signal or testing results. 320s 320s options: 320s -h, --help show this help message and exit 320s -v, --version show Tombo version and exit. 320s usage: tombo resquiggle [--dna] [--rna] 320s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 320s [--q-score Q_SCORE] 320s [--signal-matching-score SIGNAL_MATCHING_SCORE] 320s [--processes PROCESSES] 320s [--corrected-group CORRECTED_GROUP] 320s [--basecall-group BASECALL_GROUP] 320s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 320s [--overwrite] 320s [--failed-reads-filename FAILED_READS_FILENAME] 320s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 320s [--print-advanced-arguments] [--quiet] [--help] 320s fast5s_basedir reference 320s 320s Required Arguments: 320s fast5s_basedir Directory containing fast5 files. All files ending in 320s "fast5" found recursively within this base directory 320s will be processed. 320s reference Reference genome/transcriptome FASTA file or minimap2 320s index (with "map-ont" preset) for mapping. 320s 320s Model Parameters: 320s --dna Explicitly select canonical DNA model. Default: 320s Automatically determine from FAST5s 320s --rna Explicitly select canonical RNA model. Default: 320s Automatically determine from FAST5s 320s 320s Read Filtering Argument: 320s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 320s Filter reads based on observations per base percentile 320s thresholds. Format thresholds as "percentile:thresh 320s [pctl2:thresh2 ...]". For example to filter reads with 320s 99th pctl > 200 obs/base or max > 5k obs/base use 320s "99:200 100:5000". 320s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 320s Default: 0.000000 320s --signal-matching-score SIGNAL_MATCHING_SCORE 320s Observed to expected signal matching score (higher 320s score indicates poor matching). Sample type defaults: 320s RNA : 2 || DNA : 1.1 320s 320s Multiprocessing Arguments: 320s --processes PROCESSES 320s Number of processes. Default: 1 320s 320s FAST5 Data Arguments: 320s --corrected-group CORRECTED_GROUP 320s FAST5 group created by resquiggle command. Default: 320s RawGenomeCorrected_000 320s --basecall-group BASECALL_GROUP 320s FAST5 group obtain original basecalls (under Analyses 320s group). Default: Basecall_1D_000 320s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 320s FAST5 subgroup(s) (under /Analyses/[--basecall- 320s group]/) containing basecalls and created within 320s [--corrected-group] containing re-squiggle results. 320s Default: ['BaseCalled_template'] 320s --overwrite Overwrite previous corrected group in FAST5 files. 320s Note: only effects --corrected-group or --new- 320s corrected-group. 320s 320s Input/Output Arguments: 320s --failed-reads-filename FAILED_READS_FILENAME 320s Output failed read filenames with assoicated error. 320s Default: Do not store failed reads. 320s --num-most-common-errors NUM_MOST_COMMON_ERRORS 320s Dynamically show this many most common errors so far 320s through run. Default: 0; Just show progress 320s 320s Advanced Arguments: 320s --print-advanced-arguments 320s Print advanced re-squiggle arguments and exit. 320s 320s Miscellaneous Arguments: 320s --quiet, -q Don't print status information. 320s --help, -h Print this help message and exit 320s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 320s --fastq-filenames 320s FASTQ_FILENAMES 320s [FASTQ_FILENAMES ...] 320s [--basecall-group BASECALL_GROUP] 320s [--basecall-subgroup BASECALL_SUBGROUP] 320s [--overwrite] 320s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 320s [--processes PROCESSES] 320s [--quiet] [--help] 320s 320s Required Arguments: 320s --fast5-basedir FAST5_BASEDIR 320s Directory containing fast5 files. 320s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 320s FASTQ filenames containing basecalls to be added to 320s raw FAST5 files. 320s 320s FAST5 Data Arguments: 320s --basecall-group BASECALL_GROUP 320s FAST5 group obtain original basecalls (under Analyses 320s group). Default: Basecall_1D_000 320s --basecall-subgroup BASECALL_SUBGROUP 320s FAST5 subgroup (under /Analyses/[--basecall-group]/) 320s under which to store basecalls from FASTQs. Default: 320s BaseCalled_template 320s --overwrite Overwrite previous corrected group in FAST5 files. 320s Note: only effects --corrected-group or --new- 320s corrected-group. 320s 320s Sequencing Summary Argument: 320s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 320s Sequencing summary filenames produced by albacore. 320s These can make annotation of raw FAST5 files with 320s FASTQ sequence much faster. 320s 320s Multiprocessing Argument: 320s --processes PROCESSES 320s Number of processes. Default: 1 320s 320s Miscellaneous Arguments: 320s --quiet, -q Don't print status information. 320s --help, -h Print this help message and exit 320s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 320s [FAST5_BASEDIRS ...] 320s [--corrected-group CORRECTED_GROUP] 320s [--quiet] [--help] 320s 320s Required Argument: 320s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 320s Directories containing fast5 files. 320s 320s FAST5 Data Argument: 320s --corrected-group CORRECTED_GROUP 320s FAST5 group created by resquiggle command. Default: 320s RawGenomeCorrected_000 320s 320s Miscellaneous Arguments: 320s --quiet, -q Don't print status information. 320s --help, -h Print this help message and exit 320s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 320s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 320s [--corrected-group CORRECTED_GROUP] [--quiet] 320s [--help] 320s 320s Required Argument: 320s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 320s Directories containing fast5 files. 320s 320s Read Filtering Argument: 320s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 320s Filter reads based on observations per base percentile 320s thresholds. Format thresholds as "percentile:thresh 320s [pctl2:thresh2 ...]". For example to filter reads with 320s 99th pctl > 200 obs/base or max > 5k obs/base use 320s "99:200 100:5000". 320s 320s FAST5 Data Argument: 320s --corrected-group CORRECTED_GROUP 320s FAST5 group created by resquiggle command. Default: 320s RawGenomeCorrected_000 320s 320s Miscellaneous Arguments: 320s --quiet, -q Don't print status information. 320s --help, -h Print this help message and exit 320s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 320s [FAST5_BASEDIRS ...] 320s [--percent-to-filter PERCENT_TO_FILTER] 320s [--corrected-group CORRECTED_GROUP] 320s [--quiet] [--help] 320s 320s Required Arguments: 320s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 320s Directories containing fast5 files. 320s 320s Read Filtering Argument: 320s --percent-to-filter PERCENT_TO_FILTER 320s Percentage of all reads to filter. Reads are randomly 320s selected weighted according to the approximate 320s coverage at the mapped genomic location. This can be 320s useful in modeling and testing. Default: 10.000000 320s 320s FAST5 Data Arguments: 320s --corrected-group CORRECTED_GROUP 320s FAST5 group created by resquiggle command. Default: 320s RawGenomeCorrected_000 320s 320s Miscellaneous Arguments: 320s --quiet, -q Don't print status information. 320s --help, -h Print this help message and exit 320s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 320s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 320s [--corrected-group CORRECTED_GROUP] 320s [--basecall-group BASECALL_GROUP] [--quiet] 320s [--help] 320s 320s Required Arguments: 320s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 320s Directories containing fast5 files. 320s 320s Read Filtering Argument: 320s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 320s Default: 7.000000 320s 320s FAST5 Data Arguments: 320s --corrected-group CORRECTED_GROUP 320s FAST5 group created by resquiggle command. Default: 320s RawGenomeCorrected_000 320s --basecall-group BASECALL_GROUP 320s FAST5 group obtain original basecalls (under Analyses 320s group). Default: Basecall_1D_000 320s 320s Miscellaneous Arguments: 320s --quiet, -q Don't print status information. 320s --help, -h Print this help message and exit 320s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 320s [FAST5_BASEDIRS ...] 320s --signal-matching-score 320s SIGNAL_MATCHING_SCORE 320s [--corrected-group CORRECTED_GROUP] 320s [--quiet] [--help] 320s 320s Required Arguments: 320s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 320s Directories containing fast5 files. 320s --signal-matching-score SIGNAL_MATCHING_SCORE 320s Observed to expected signal matching score (higher 320s score indicates poor matching). Sample type defaults: 320s RNA : 2 || DNA : 1.1 320s 320s FAST5 Data Arguments: 320s --corrected-group CORRECTED_GROUP 320s FAST5 group created by resquiggle command. Default: 320s RawGenomeCorrected_000 320s 320s Miscellaneous Arguments: 320s --quiet, -q Don't print status information. 320s --help, -h Print this help message and exit 321s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 321s [FAST5_BASEDIRS ...] 321s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 321s [--include-partial-overlap] 321s [--corrected-group CORRECTED_GROUP] 321s [--quiet] [--help] 321s 321s Required Arguments: 321s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 321s Directories containing fast5 files. 321s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 321s Filter out reads not falling completely within include 321s regions. Omit start and end coordinates to include an 321s entire chromosome/sequence record. Format regions as 321s "chrm[:start-end] [chrm2[:start2-end2] ...]". 321s 321s Filter Argument: 321s --include-partial-overlap 321s Include reads that partially overlap the specified 321s region. Default: Only include reads completely 321s contained in a specified region 321s 321s FAST5 Data Argument: 321s --corrected-group CORRECTED_GROUP 321s FAST5 group created by resquiggle command. Default: 321s RawGenomeCorrected_000 321s 321s Miscellaneous Arguments: 321s --quiet, -q Don't print status information. 321s --help, -h Print this help message and exit 321s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 321s [FAST5_BASEDIRS ...] 321s --statistics-file-basename 321s STATISTICS_FILE_BASENAME [--dna] 321s [--rna] 321s [--fishers-method-context FISHERS_METHOD_CONTEXT] 321s [--minimum-test-reads MINIMUM_TEST_READS] 321s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 321s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 321s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 321s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 321s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 321s [--processes PROCESSES] 321s [--corrected-group CORRECTED_GROUP] 321s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 321s [--quiet] [--help] 321s 321s Required Argument: 321s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 321s Directories containing fast5 files. 321s --statistics-file-basename STATISTICS_FILE_BASENAME 321s File base name to save base by base statistics from 321s testing. Filenames will be [--statistics-file- 321s basename].[--alternate-bases]?.tombo.stats 321s 321s Comparison Model Arguments: 321s --dna Explicitly select canonical DNA model. Default: 321s Automatically determine from FAST5s 321s --rna Explicitly select canonical RNA model. Default: 321s Automatically determine from FAST5s 321s 321s Significance Test Arguments: 321s --fishers-method-context FISHERS_METHOD_CONTEXT 321s Number of context bases up and downstream over which 321s to compute Fisher's method combined p-values. Note: 321s Not applicable for alternative model likelihood ratio 321s tests. Default: 1. 321s --minimum-test-reads MINIMUM_TEST_READS 321s Number of reads required at a position to perform 321s significance testing or contribute to model 321s estimation. Default: 1 321s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 321s P-value threshold when computing fraction of 321s significant reads at each genomic position. If two 321s values are provided, statistics between these values 321s are not considered. Default thresholds: DNA:0.15-0.5 , 321s RNA:0.05-0.4 321s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 321s Dampen fraction modified estimates for low coverage 321s sites. Two parameters are unmodified and modified 321s pseudo read counts. This is equivalent to a beta prior 321s on the fraction estimate. Set to "0 0" to disable 321s dampened fraction estimation. Default: [2, 0] 321s 321s Output Argument: 321s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 321s Base for binary files containing per-read statistics 321s from statistical testing. Filenames will be [--per- 321s read-statistics-basename].[--alternate- 321s bases]?.tombo.per_read_stats 321s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 321s Number of the most significant sites to store for 321s faster access. If a longer list of most significant 321s sites is required the list must be re-computed from 321s all batches. Very large values can increase RAM usage. 321s Default: 100000 321s 321s Multiprocessing Arguments: 321s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 321s Size of regions over which to multiprocesses statistic 321s computation. For very deep samples a smaller value is 321s recommmended in order to control memory consumption. 321s Default: 10000 321s --processes PROCESSES 321s Number of processes. Default: 1 321s 321s FAST5 Data Arguments: 321s --corrected-group CORRECTED_GROUP 321s FAST5 group created by resquiggle command. Default: 321s RawGenomeCorrected_000 321s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 321s FAST5 subgroup(s) (under /Analyses/[--basecall- 321s group]/) containing basecalls and created within 321s [--corrected-group] containing re-squiggle results. 321s Default: ['BaseCalled_template'] 321s 321s Miscellaneous Arguments: 321s --quiet, -q Don't print status information. 321s --help, -h Print this help message and exit 321s usage: tombo detect_modifications alternative_model 321s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 321s [--statistics-file-basename STATISTICS_FILE_BASENAME] 321s [--alternate-bases {dcm,5mC,dam,6mA,CpG} [{dcm,5mC,dam,6mA,CpG} ...]] 321s [--print-available-models] 321s [--dna] [--rna] 321s [--minimum-test-reads MINIMUM_TEST_READS] 321s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 321s [--standard-log-likelihood-ratio] 321s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 321s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 321s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 321s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 321s [--processes PROCESSES] 321s [--corrected-group CORRECTED_GROUP] 321s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 321s [--quiet] [--help] 321s 321s Required Argument: 321s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 321s Directories containing fast5 files. 321s --statistics-file-basename STATISTICS_FILE_BASENAME 321s File base name to save base by base statistics from 321s testing. Filenames will be [--statistics-file- 321s basename].[--alternate-bases]?.tombo.stats 321s --alternate-bases {dcm,5mC,dam,6mA,CpG} [{dcm,5mC,dam,6mA,CpG} ...] 321s Default non-standard base model for testing (not 321s required if user created --alternate-model-filenames 321s is provided). 321s 321s Comparison Arguments: 321s --print-available-models 321s Print available alternative models and exit. 321s --dna Explicitly select canonical DNA model. Default: 321s Automatically determine from FAST5s 321s --rna Explicitly select canonical RNA model. Default: 321s Automatically determine from FAST5s 321s 321s Significance Test Arguments: 321s --minimum-test-reads MINIMUM_TEST_READS 321s Number of reads required at a position to perform 321s significance testing or contribute to model 321s estimation. Default: 1 321s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 321s Log likelihood ratio threshold when computing fraction 321s of significant reads at each genomic position. If two 321s values are provided, statistics between these values 321s are not considered. Default thresholds: DNA:-1.5-2.5 , 321s RNA:-2.5-2.5 321s --standard-log-likelihood-ratio 321s Use a standard log likelihood ratio (LLR) statistic. 321s Default is to use an outlier-robust LLR-like 321s statistic. Detail in full online documentation. 321s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 321s Dampen fraction modified estimates for low coverage 321s sites. Two parameters are unmodified and modified 321s pseudo read counts. This is equivalent to a beta prior 321s on the fraction estimate. Set to "0 0" to disable 321s dampened fraction estimation. Default: [2, 0] 321s 321s Output Argument: 321s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 321s Base for binary files containing per-read statistics 321s from statistical testing. Filenames will be [--per- 321s read-statistics-basename].[--alternate- 321s bases]?.tombo.per_read_stats 321s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 321s Number of the most significant sites to store for 321s faster access. If a longer list of most significant 321s sites is required the list must be re-computed from 321s all batches. Very large values can increase RAM usage. 321s Default: 100000 321s 321s Multiprocessing Arguments: 321s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 321s Size of regions over which to multiprocesses statistic 321s computation. For very deep samples a smaller value is 321s recommmended in order to control memory consumption. 321s Default: 10000 321s --processes PROCESSES 321s Number of processes. Default: 1 321s 321s FAST5 Data Arguments: 321s --corrected-group CORRECTED_GROUP 321s FAST5 group created by resquiggle command. Default: 321s RawGenomeCorrected_000 321s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 321s FAST5 subgroup(s) (under /Analyses/[--basecall- 321s group]/) containing basecalls and created within 321s [--corrected-group] containing re-squiggle results. 321s Default: ['BaseCalled_template'] 321s 321s Miscellaneous Arguments: 321s --quiet, -q Don't print status information. 321s --help, -h Print this help message and exit 321s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 321s FAST5_BASEDIRS 321s [FAST5_BASEDIRS ...] 321s --statistics-file-basename 321s STATISTICS_FILE_BASENAME 321s --control-fast5-basedirs 321s CONTROL_FAST5_BASEDIRS 321s [CONTROL_FAST5_BASEDIRS ...] 321s [--sample-only-estimates] 321s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 321s [--dna] [--rna] 321s [--fishers-method-context FISHERS_METHOD_CONTEXT] 321s [--minimum-test-reads MINIMUM_TEST_READS] 321s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 321s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 321s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 321s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 321s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 321s [--processes PROCESSES] 321s [--corrected-group CORRECTED_GROUP] 321s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 321s [--quiet] [--help] 321s 321s Required Argument: 321s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 321s Directories containing fast5 files. 321s --statistics-file-basename STATISTICS_FILE_BASENAME 321s File base name to save base by base statistics from 321s testing. Filenames will be [--statistics-file- 321s basename].[--alternate-bases]?.tombo.stats 321s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 321s Set of directories containing fast5 files for control 321s reads, containing only canonical nucleotides. 321s 321s Model Prior Arguments: 321s --sample-only-estimates 321s Only use canonical sample to estimate expected signal 321s level and spread. Default: Use canonical model to 321s improve estimtates (esp. for low coverage regions) 321s using baysian posterior estimates. 321s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 321s Prior weights (one each for mean and spread) applied 321s to canonical base model for estimating posterior model 321s parameters for sample comparison. Default: [5, 40] 321s --dna Explicitly select canonical DNA model. Default: 321s Automatically determine from FAST5s 321s --rna Explicitly select canonical RNA model. Default: 321s Automatically determine from FAST5s 321s 321s Significance Test Arguments: 321s --fishers-method-context FISHERS_METHOD_CONTEXT 321s Number of context bases up and downstream over which 321s to compute Fisher's method combined p-values. Note: 321s Not applicable for alternative model likelihood ratio 321s tests. Default: 1. 321s --minimum-test-reads MINIMUM_TEST_READS 321s Number of reads required at a position to perform 321s significance testing or contribute to model 321s estimation. Default: 1 321s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 321s P-value threshold when computing fraction of 321s significant reads at each genomic position. If two 321s values are provided, statistics between these values 321s are not considered. Default thresholds: DNA:0.15-0.5 , 321s RNA:0.05-0.4 321s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 321s Dampen fraction modified estimates for low coverage 321s sites. Two parameters are unmodified and modified 321s pseudo read counts. This is equivalent to a beta prior 321s on the fraction estimate. Set to "0 0" to disable 321s dampened fraction estimation. Default: [2, 0] 321s 321s Output Argument: 321s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 321s Base for binary files containing per-read statistics 321s from statistical testing. Filenames will be [--per- 321s read-statistics-basename].[--alternate- 321s bases]?.tombo.per_read_stats 321s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 321s Number of the most significant sites to store for 321s faster access. If a longer list of most significant 321s sites is required the list must be re-computed from 321s all batches. Very large values can increase RAM usage. 321s Default: 100000 321s 321s Multiprocessing Arguments: 321s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 321s Size of regions over which to multiprocesses statistic 321s computation. For very deep samples a smaller value is 321s recommmended in order to control memory consumption. 321s Default: 10000 321s --processes PROCESSES 321s Number of processes. Default: 1 321s 321s FAST5 Data Arguments: 321s --corrected-group CORRECTED_GROUP 321s FAST5 group created by resquiggle command. Default: 321s RawGenomeCorrected_000 321s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 321s FAST5 subgroup(s) (under /Analyses/[--basecall- 321s group]/) containing basecalls and created within 321s [--corrected-group] containing re-squiggle results. 321s Default: ['BaseCalled_template'] 321s 321s Miscellaneous Arguments: 321s --quiet, -q Don't print status information. 321s --help, -h Print this help message and exit 321s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 321s FAST5_BASEDIRS 321s [FAST5_BASEDIRS ...] 321s --statistics-file-basename 321s STATISTICS_FILE_BASENAME 321s --alternate-fast5-basedirs 321s ALTERNATE_FAST5_BASEDIRS 321s [ALTERNATE_FAST5_BASEDIRS ...] 321s [--fishers-method-context FISHERS_METHOD_CONTEXT] 321s [--minimum-test-reads MINIMUM_TEST_READS] 321s [--statistic-type {ks,u,t}] 321s [--store-p-value] 321s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 321s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 321s [--processes PROCESSES] 321s [--corrected-group CORRECTED_GROUP] 321s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 321s [--quiet] [--help] 321s 321s Required Argument: 321s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 321s Directories containing fast5 files. 321s --statistics-file-basename STATISTICS_FILE_BASENAME 321s File base name to save base by base statistics from 321s testing. Filenames will be [--statistics-file- 321s basename].[--alternate-bases]?.tombo.stats 321s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 321s Set of directories containing fast5 files for 321s alternate set of reads. 321s 321s Significance Test Arguments: 321s --fishers-method-context FISHERS_METHOD_CONTEXT 321s Number of context bases up and downstream over which 321s to compute Fisher's method combined p-values. Note: 321s Not applicable for alternative model likelihood ratio 321s tests. Default: 1. 321s --minimum-test-reads MINIMUM_TEST_READS 321s Number of reads required at a position to perform 321s significance testing or contribute to model 321s estimation. Default: 50 321s --statistic-type {ks,u,t} 321s Type of statistical test to apply. Default: "ks" 321s --store-p-value Store p-value instead of effect-size statistic. 321s Statistics are D-statistic (KS-test), deviation from 321s even common language effect size (u-test), and Cohen's 321s D (t-test). 321s 321s Output Argument: 321s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 321s Number of the most significant sites to store for 321s faster access. If a longer list of most significant 321s sites is required the list must be re-computed from 321s all batches. Very large values can increase RAM usage. 321s Default: 100000 321s 321s Multiprocessing Arguments: 321s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 321s Size of regions over which to multiprocesses statistic 321s computation. For very deep samples a smaller value is 321s recommmended in order to control memory consumption. 321s Default: 10000 321s --processes PROCESSES 321s Number of processes. Default: 1 321s 321s FAST5 Data Arguments: 321s --corrected-group CORRECTED_GROUP 321s FAST5 group created by resquiggle command. Default: 321s RawGenomeCorrected_000 321s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 321s FAST5 subgroup(s) (under /Analyses/[--basecall- 321s group]/) containing basecalls and created within 321s [--corrected-group] containing re-squiggle results. 321s Default: ['BaseCalled_template'] 321s 321s Miscellaneous Arguments: 321s --quiet, -q Don't print status information. 321s --help, -h Print this help message and exit 321s usage: tombo detect_modifications aggregate_per_read_stats 321s --per-read-statistics-filename 321s PER_READ_STATISTICS_FILENAME 321s --statistics-filename 321s STATISTICS_FILENAME 321s --single-read-threshold 321s SINGLE_READ_THRESHOLD 321s [SINGLE_READ_THRESHOLD ...] 321s [--minimum-test-reads MINIMUM_TEST_READS] 321s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 321s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 321s [--processes PROCESSES] 321s [--corrected-group CORRECTED_GROUP] 321s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 321s [--quiet] [--help] 321s 321s Required Argument: 321s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 321s Binary file containing per-read statistics from 321s statistical testing. 321s --statistics-filename STATISTICS_FILENAME 321s File to save/load genomic base anchored statistics. 321s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 321s P-value or log likelihood ratio threshold when 321s computing fraction of significant reads at each 321s genomic position. If two values are provided, 321s statistics between these values are not considered. 321s 321s Significance Test Arguments: 321s --minimum-test-reads MINIMUM_TEST_READS 321s Number of reads required at a position to perform 321s significance testing or contribute to model 321s estimation. Default: 1 321s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 321s Dampen fraction modified estimates for low coverage 321s sites. Two parameters are unmodified and modified 321s pseudo read counts. This is equivalent to a beta prior 321s on the fraction estimate. Set to "0 0" to disable 321s dampened fraction estimation. Default: [2, 0] 321s 321s Output Argument: 321s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 321s Number of the most significant sites to store for 321s faster access. If a longer list of most significant 321s sites is required the list must be re-computed from 321s all batches. Very large values can increase RAM usage. 321s Default: 100000 321s 321s Multiprocessing Arguments: 321s --processes PROCESSES 321s Number of processes. Default: 1 321s 321s FAST5 Data Arguments: 321s --corrected-group CORRECTED_GROUP 321s FAST5 group created by resquiggle command. Default: 321s RawGenomeCorrected_000 321s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 321s FAST5 subgroup(s) (under /Analyses/[--basecall- 321s group]/) containing basecalls and created within 321s [--corrected-group] containing re-squiggle results. 321s Default: ['BaseCalled_template'] 321s 321s Miscellaneous Arguments: 321s --quiet, -q Don't print status information. 321s --help, -h Print this help message and exit 321s usage: tombo text_output browser_files 321s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 321s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 321s [--statistics-filename STATISTICS_FILENAME] 321s [--genome-fasta GENOME_FASTA] 321s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 321s [--browser-file-basename BROWSER_FILE_BASENAME] 321s [--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} ...]] 321s [--corrected-group CORRECTED_GROUP] 321s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 321s [--quiet] [--help] 321s 321s Data Arguments: 321s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 321s Directories containing fast5 files. 321s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 321s Set of directories containing fast5 files for control 321s reads, containing only canonical nucleotides. 321s --statistics-filename STATISTICS_FILENAME 321s File to save/load genomic base anchored statistics. 321s 321s Statistic Motif Filter Arguments: 321s --genome-fasta GENOME_FASTA 321s FASTA file used to re-squiggle. For faster sequence 321s access. 321s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 321s Ground truth, motif centered, modified base 321s descriptions for output filtering. Format descriptions 321s as: "motif:mod_pos:name". The mod_pos indicates the 321s modified base within the motif (1-based index). 321s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 321s output for identification of E. coli dam and dcm 321s methylation. 321s 321s Output Arguments: 321s --browser-file-basename BROWSER_FILE_BASENAME 321s Basename for output browser files. Two files (plus and 321s minus strand) will be produced for each --file-types 321s supplied. Filenames formatted as "[browser-file- 321s basename].[file- 321s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 321s Default: tombo_results 321s --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} ...] 321s Data types of genome browser files to produce. 321s Produced coverage files are in bedGraph format, while 321s all other file types will be in wiggle format 321s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 321s Default: "coverage" 321s 321s FAST5 Data Arguments: 321s --corrected-group CORRECTED_GROUP 321s FAST5 group created by resquiggle command. Default: 321s RawGenomeCorrected_000 321s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 321s FAST5 subgroup(s) (under /Analyses/[--basecall- 321s group]/) containing basecalls and created within 321s [--corrected-group] containing re-squiggle results. 321s Default: ['BaseCalled_template'] 321s 321s Miscellaneous Arguments: 321s --quiet, -q Don't print status information. 321s --help, -h Print this help message and exit 321s usage: tombo text_output signif_sequence_context --statistics-filename 321s STATISTICS_FILENAME 321s [--genome-fasta GENOME_FASTA] 321s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 321s [--num-regions NUM_REGIONS] 321s [--num-bases NUM_BASES] 321s [--sequences-filename SEQUENCES_FILENAME] 321s [--corrected-group CORRECTED_GROUP] 321s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 321s [--quiet] [--help] 321s 321s Required Argument: 321s --statistics-filename STATISTICS_FILENAME 321s File to save/load genomic base anchored statistics. 321s 321s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 321s --genome-fasta GENOME_FASTA 321s FASTA file used to re-squiggle. For faster sequence 321s access. 321s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 321s Directories containing fast5 files. 321s 321s Region Selection Arguments: 321s --num-regions NUM_REGIONS 321s Number of regions to plot. Default: 100 321s --num-bases NUM_BASES 321s Number of bases to plot/output. Default: 15 321s 321s Output Arguments: 321s --sequences-filename SEQUENCES_FILENAME 321s File for sequences from selected regions. Sequences 321s will be stored in FASTA format. Default: 321s tombo_results.significant_regions.fasta. 321s 321s FAST5 Data Arguments: 321s --corrected-group CORRECTED_GROUP 321s FAST5 group created by resquiggle command. Default: 321s RawGenomeCorrected_000 321s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 321s FAST5 subgroup(s) (under /Analyses/[--basecall- 321s group]/) containing basecalls and created within 321s [--corrected-group] containing re-squiggle results. 321s Default: ['BaseCalled_template'] 321s 321s Miscellaneous Arguments: 321s --quiet, -q Don't print status information. 321s --help, -h Print this help message and exit 321s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 321s [FAST5_BASEDIRS ...] 321s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 321s [--plot-standard-model] 321s [--plot-alternate-model {CpG,5mC,dam,dcm,6mA}] 321s [--overplot-threshold OVERPLOT_THRESHOLD] 321s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 321s [--num-regions NUM_REGIONS] 321s [--num-bases NUM_BASES] 321s [--pdf-filename PDF_FILENAME] 321s [--corrected-group CORRECTED_GROUP] 321s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 321s [--quiet] [--help] 321s 321s Required Argument: 321s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 321s Directories containing fast5 files. 321s 321s Comparison Arguments: 321s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 321s Set of directories containing fast5 files for control 321s reads, containing only canonical nucleotides. 321s --plot-standard-model 321s Add default standard model distribution to the plot. 321s --plot-alternate-model {CpG,5mC,dam,dcm,6mA} 321s Add alternative model distribution to the plot. 321s 321s Overplotting Arguments: 321s --overplot-threshold OVERPLOT_THRESHOLD 321s Coverage level to trigger alternative plot type 321s instead of raw signal. Default: 50 321s --overplot-type {Downsample,Boxplot,Quantile,Density} 321s Plot type for regions with higher coverage. Default: 321s Downsample 321s 321s Plotting Region Arguments: 321s --num-regions NUM_REGIONS 321s Number of regions to plot. Default: 10 321s --num-bases NUM_BASES 321s Number of bases to plot/output. Default: 21 321s 321s Output Argument: 321s --pdf-filename PDF_FILENAME 321s PDF filename to store plot(s). Default: 321s tombo_results.max_coverage.pdf 321s 321s FAST5 Data Arguments: 321s --corrected-group CORRECTED_GROUP 321s FAST5 group created by resquiggle command. Default: 321s RawGenomeCorrected_000 321s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 321s FAST5 subgroup(s) (under /Analyses/[--basecall- 321s group]/) containing basecalls and created within 321s [--corrected-group] containing re-squiggle results. 321s Default: ['BaseCalled_template'] 321s 321s Miscellaneous Arguments: 321s --quiet, -q Don't print status information. 321s --help, -h Print this help message and exit 322s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 322s [FAST5_BASEDIRS ...] --genome-locations 322s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 322s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 322s [--plot-standard-model] 322s [--plot-alternate-model {6mA,dcm,dam,CpG,5mC}] 322s [--overplot-threshold OVERPLOT_THRESHOLD] 322s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 322s [--num-bases NUM_BASES] 322s [--pdf-filename PDF_FILENAME] 322s [--corrected-group CORRECTED_GROUP] 322s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 322s [--quiet] [--help] 322s 322s Required Arguments: 322s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 322s Directories containing fast5 files. 322s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 322s Genomic locations at which to plot signal. Format 322s locations as "chrm:position[:strand] 322s [chrm2:position2[:strand2] ...]" (strand not 322s applicable for all applications) 322s 322s Comparison Arguments: 322s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 322s Set of directories containing fast5 files for control 322s reads, containing only canonical nucleotides. 322s --plot-standard-model 322s Add default standard model distribution to the plot. 322s --plot-alternate-model {6mA,dcm,dam,CpG,5mC} 322s Add alternative model distribution to the plot. 322s 322s Overplotting Arguments: 322s --overplot-threshold OVERPLOT_THRESHOLD 322s Coverage level to trigger alternative plot type 322s instead of raw signal. Default: 50 322s --overplot-type {Downsample,Boxplot,Quantile,Density} 322s Plot type for regions with higher coverage. Default: 322s Downsample 322s 322s Plotting Region Argument: 322s --num-bases NUM_BASES 322s Number of bases to plot/output. Default: 21 322s 322s Output Argument: 322s --pdf-filename PDF_FILENAME 322s PDF filename to store plot(s). Default: 322s tombo_results.genome_locations.pdf 322s 322s FAST5 Data Arguments: 322s --corrected-group CORRECTED_GROUP 322s FAST5 group created by resquiggle command. Default: 322s RawGenomeCorrected_000 322s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 322s FAST5 subgroup(s) (under /Analyses/[--basecall- 322s group]/) containing basecalls and created within 322s [--corrected-group] containing re-squiggle results. 322s Default: ['BaseCalled_template'] 322s 322s Miscellaneous Arguments: 322s --quiet, -q Don't print status information. 322s --help, -h Print this help message and exit 322s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 322s [FAST5_BASEDIRS ...] --motif MOTIF 322s --genome-fasta GENOME_FASTA 322s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 322s [--plot-standard-model] 322s [--plot-alternate-model {dam,6mA,5mC,dcm,CpG}] 322s [--overplot-threshold OVERPLOT_THRESHOLD] 322s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 322s [--num-regions NUM_REGIONS] 322s [--num-bases NUM_BASES] [--deepest-coverage] 322s [--pdf-filename PDF_FILENAME] 322s [--corrected-group CORRECTED_GROUP] 322s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 322s [--quiet] [--help] 322s 322s Required Arguments: 322s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 322s Directories containing fast5 files. 322s --motif MOTIF Motif of interest at which to plot signal and 322s statsitics. Supports IUPAC single letter codes (use T 322s for RNA). 322s --genome-fasta GENOME_FASTA 322s FASTA file used to re-squiggle. For faster sequence 322s access. 322s 322s Comparison Arguments: 322s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 322s Set of directories containing fast5 files for control 322s reads, containing only canonical nucleotides. 322s --plot-standard-model 322s Add default standard model distribution to the plot. 322s --plot-alternate-model {dam,6mA,5mC,dcm,CpG} 322s Add alternative model distribution to the plot. 322s 322s Overplotting Arguments: 322s --overplot-threshold OVERPLOT_THRESHOLD 322s Coverage level to trigger alternative plot type 322s instead of raw signal. Default: 50 322s --overplot-type {Downsample,Boxplot,Quantile,Density} 322s Plot type for regions with higher coverage. Default: 322s Downsample 322s 322s Plotting Region Arguments: 322s --num-regions NUM_REGIONS 322s Number of regions to plot. Default: 10 322s --num-bases NUM_BASES 322s Number of bases to plot/output. Default: 21 322s --deepest-coverage Plot the deepest coverage regions. 322s 322s Output Argument: 322s --pdf-filename PDF_FILENAME 322s PDF filename to store plot(s). Default: 322s tombo_results.motif_centered.pdf 322s 322s FAST5 Data Arguments: 322s --corrected-group CORRECTED_GROUP 322s FAST5 group created by resquiggle command. Default: 322s RawGenomeCorrected_000 322s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 322s FAST5 subgroup(s) (under /Analyses/[--basecall- 322s group]/) containing basecalls and created within 322s [--corrected-group] containing re-squiggle results. 322s Default: ['BaseCalled_template'] 322s 322s Miscellaneous Arguments: 322s --quiet, -q Don't print status information. 322s --help, -h Print this help message and exit 322s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 322s [FAST5_BASEDIRS ...] --control-fast5-basedirs 322s CONTROL_FAST5_BASEDIRS 322s [CONTROL_FAST5_BASEDIRS ...] 322s [--overplot-threshold OVERPLOT_THRESHOLD] 322s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 322s [--num-regions NUM_REGIONS] 322s [--num-bases NUM_BASES] 322s [--pdf-filename PDF_FILENAME] 322s [--sequences-filename SEQUENCES_FILENAME] 322s [--corrected-group CORRECTED_GROUP] 322s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 322s [--quiet] [--help] 322s 322s Required Arguments: 322s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 322s Directories containing fast5 files. 322s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 322s Set of directories containing fast5 files for control 322s reads, containing only canonical nucleotides. 322s 322s Overplotting Arguments: 322s --overplot-threshold OVERPLOT_THRESHOLD 322s Coverage level to trigger alternative plot type 322s instead of raw signal. Default: 50 322s --overplot-type {Downsample,Boxplot,Quantile,Density} 322s Plot type for regions with higher coverage. Default: 322s Downsample 322s 322s Plotting Region Arguments: 322s --num-regions NUM_REGIONS 322s Number of regions to plot. Default: 10 322s --num-bases NUM_BASES 322s Number of bases to plot/output. Default: 21 322s 322s Output Arguments: 322s --pdf-filename PDF_FILENAME 322s PDF filename to store plot(s). Default: 322s tombo_results.max_difference.pdf 322s --sequences-filename SEQUENCES_FILENAME 322s File for sequences from selected regions. Sequences 322s will be stored in FASTA format. Default: None. 322s 322s FAST5 Data Arguments: 322s --corrected-group CORRECTED_GROUP 322s FAST5 group created by resquiggle command. Default: 322s RawGenomeCorrected_000 322s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 322s FAST5 subgroup(s) (under /Analyses/[--basecall- 322s group]/) containing basecalls and created within 322s [--corrected-group] containing re-squiggle results. 322s Default: ['BaseCalled_template'] 322s 322s Miscellaneous Arguments: 322s --quiet, -q Don't print status information. 322s --help, -h Print this help message and exit 322s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 322s [FAST5_BASEDIRS ...] --statistics-filename 322s STATISTICS_FILENAME 322s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 322s [--plot-standard-model] 322s [--plot-alternate-model {6mA,5mC,CpG,dcm,dam}] 322s [--overplot-threshold OVERPLOT_THRESHOLD] 322s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 322s [--num-regions NUM_REGIONS] 322s [--num-bases NUM_BASES] 322s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 322s [--pdf-filename PDF_FILENAME] 322s [--sequences-filename SEQUENCES_FILENAME] 322s [--corrected-group CORRECTED_GROUP] 322s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 322s [--quiet] [--help] 322s 322s Required Arguments: 322s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 322s Directories containing fast5 files. 322s --statistics-filename STATISTICS_FILENAME 322s File to save/load genomic base anchored statistics. 322s 322s Comparison Arguments: 322s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 322s Set of directories containing fast5 files for control 322s reads, containing only canonical nucleotides. 322s --plot-standard-model 322s Add default standard model distribution to the plot. 322s --plot-alternate-model {6mA,5mC,CpG,dcm,dam} 322s Add alternative model distribution to the plot. 322s 322s Overplotting Arguments: 322s --overplot-threshold OVERPLOT_THRESHOLD 322s Coverage level to trigger alternative plot type 322s instead of raw signal. Default: 50 322s --overplot-type {Downsample,Boxplot,Quantile,Density} 322s Plot type for regions with higher coverage. Default: 322s Downsample 322s 322s Plotting Region Arguments: 322s --num-regions NUM_REGIONS 322s Number of regions to plot. Default: 10 322s --num-bases NUM_BASES 322s Number of bases to plot/output. Default: 21 322s 322s Statistical Argument: 322s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 322s Dampen fraction modified estimates for low coverage 322s sites. Two parameters are unmodified and modified 322s pseudo read counts. This is equivalent to a beta prior 322s on the fraction estimate. Set to "0 0" to disable 322s dampened fraction estimation. Default: [2, 0] 322s 322s Output Arguments: 322s --pdf-filename PDF_FILENAME 322s PDF filename to store plot(s). Default: 322s tombo_results.significant_difference.pdf 322s --sequences-filename SEQUENCES_FILENAME 322s File for sequences from selected regions. Sequences 322s will be stored in FASTA format. Default: None. 322s 322s FAST5 Data Arguments: 322s --corrected-group CORRECTED_GROUP 322s FAST5 group created by resquiggle command. Default: 322s RawGenomeCorrected_000 322s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 322s FAST5 subgroup(s) (under /Analyses/[--basecall- 322s group]/) containing basecalls and created within 322s [--corrected-group] containing re-squiggle results. 322s Default: ['BaseCalled_template'] 322s 322s Miscellaneous Arguments: 322s --quiet, -q Don't print status information. 322s --help, -h Print this help message and exit 322s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 322s [FAST5_BASEDIRS ...] --motif MOTIF 322s --statistics-filename STATISTICS_FILENAME 322s --genome-fasta GENOME_FASTA 322s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 322s [--plot-standard-model] 322s [--plot-alternate-model {CpG,5mC,6mA,dam,dcm}] 322s [--overplot-threshold OVERPLOT_THRESHOLD] 322s [--num-regions NUM_REGIONS] 322s [--num-context NUM_CONTEXT] 322s [--num-statistics NUM_STATISTICS] 322s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 322s [--pdf-filename PDF_FILENAME] 322s [--corrected-group CORRECTED_GROUP] 322s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 322s [--quiet] [--help] 322s 322s Required Arguments: 322s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 322s Directories containing fast5 files. 322s --motif MOTIF Motif of interest at which to plot signal and 322s statsitics. Supports IUPAC single letter codes (use T 322s for RNA). 322s --statistics-filename STATISTICS_FILENAME 322s File to save/load genomic base anchored statistics. 322s --genome-fasta GENOME_FASTA 322s FASTA file used to re-squiggle. For faster sequence 322s access. 322s 322s Comparison Arguments: 322s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 322s Set of directories containing fast5 files for control 322s reads, containing only canonical nucleotides. 322s --plot-standard-model 322s Add default standard model distribution to the plot. 322s --plot-alternate-model {CpG,5mC,6mA,dam,dcm} 322s Add alternative model distribution to the plot. 322s 322s Overplotting Argument: 322s --overplot-threshold OVERPLOT_THRESHOLD 322s Coverage level to trigger alternative plot type 322s instead of raw signal. Default: 50 322s 322s Plotting Region Arguments: 322s --num-regions NUM_REGIONS 322s Number of regions to plot. Default: 3 322s --num-context NUM_CONTEXT 322s Number of context bases around motif. Default: 5 322s --num-statistics NUM_STATISTICS 322s Number of motif centered regions to include in 322s statistic distributions. Default: 200 322s 322s Statistical Argument: 322s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 322s Dampen fraction modified estimates for low coverage 322s sites. Two parameters are unmodified and modified 322s pseudo read counts. This is equivalent to a beta prior 322s on the fraction estimate. Set to "0 0" to disable 322s dampened fraction estimation. Default: [2, 0] 322s 322s Output Argument: 322s --pdf-filename PDF_FILENAME 322s PDF filename to store plot(s). Default: 322s tombo_results.motif_statistics.pdf 322s 322s FAST5 Data Arguments: 322s --corrected-group CORRECTED_GROUP 322s FAST5 group created by resquiggle command. Default: 322s RawGenomeCorrected_000 322s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 322s FAST5 subgroup(s) (under /Analyses/[--basecall- 322s group]/) containing basecalls and created within 322s [--corrected-group] containing re-squiggle results. 322s Default: ['BaseCalled_template'] 322s 322s Miscellaneous Arguments: 322s --quiet, -q Don't print status information. 322s --help, -h Print this help message and exit 322s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 322s [GENOME_LOCATIONS ...] 322s --per-read-statistics-filename 322s PER_READ_STATISTICS_FILENAME 322s [--genome-fasta GENOME_FASTA] 322s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 322s [--num-reads NUM_READS] [--num-bases NUM_BASES] 322s [--box-center] [--pdf-filename PDF_FILENAME] 322s [--corrected-group CORRECTED_GROUP] 322s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 322s [--quiet] [--help] 322s 322s Required Arguments: 322s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 322s Genomic locations at which to plot signal. Format 322s locations as "chrm:position[:strand] 322s [chrm2:position2[:strand2] ...]" (strand not 322s applicable for all applications) 322s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 322s Binary file containing per-read statistics from 322s statistical testing. 322s 322s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 322s --genome-fasta GENOME_FASTA 322s FASTA file used to re-squiggle. For faster sequence 322s access. 322s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 322s Directories containing fast5 files. 322s 322s Plotting Region Arguments: 322s --num-reads NUM_READS 322s Number of reads to plot. Default: 100 322s --num-bases NUM_BASES 322s Number of bases to plot/output. Default: 51 322s --box-center Plot a box around the central base. 322s 322s Output Argument: 322s --pdf-filename PDF_FILENAME 322s PDF filename to store plot(s). Default: 322s tombo_results.per_read_stats.pdf 322s 322s FAST5 Data Arguments: 322s --corrected-group CORRECTED_GROUP 322s FAST5 group created by resquiggle command. Default: 322s RawGenomeCorrected_000 322s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 322s FAST5 subgroup(s) (under /Analyses/[--basecall- 322s group]/) containing basecalls and created within 322s [--corrected-group] containing re-squiggle results. 322s Default: ['BaseCalled_template'] 322s 322s Miscellaneous Arguments: 322s --quiet, -q Don't print status information. 322s --help, -h Print this help message and exit 322s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 322s [STATISTICS_FILENAMES ...] 322s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 322s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 322s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 322s [--genome-fasta GENOME_FASTA] 322s [--pdf-filename PDF_FILENAME] 322s [--statistics-per-block STATISTICS_PER_BLOCK] 322s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 322s [--quiet] [--help] 322s 322s Required Argument: 322s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 322s Files to load genomic base anchored statistics. 322s 322s Ground Truth Arguments (provide bed files or motifs): 322s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 322s Modification description and bed format files 322s containing single base locations of ground truth 322s modified sites. Bed files should contain 6 fields 322s including strand. Format descriptions as 322s "mod_name:locs.bed". Example: "CpG 322s bisulfite":bisulfite_locs.bed 322s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 322s Bed format files containing single base locations of 322s ground truth unmodified sites. Bed files should 322s contain 6 fields including strand. 322s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 322s Ground truth, motif centered, modified base 322s descriptions for computing ROC and PR curves. Each 322s statistics file is associated with a set of motif 322s descriptions. Format descriptions as: 322s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 322s mod_pos indicates the alternate-base within the motif 322s (1-based index). Example: CCWGG:2:"dcm 322s 5mC"::GATC:2:"dam 6mA" would assess the performance of 322s a single Tombo statistics file for identification of 322s E. coli dam and dcm methylation. 322s --genome-fasta GENOME_FASTA 322s FASTA file used to re-squiggle. For faster sequence 322s access. 322s 322s Output Arguments: 322s --pdf-filename PDF_FILENAME 322s PDF filename to store plot(s). Default: 322s tombo_results.roc.pdf 322s 322s Down-sampling Arguments: 322s --statistics-per-block STATISTICS_PER_BLOCK 322s Number of randomly selected per-read, per-base 322s statistics to extract from each genomic block for 322s plotting. Default: Include all stats 322s --total-statistics-limit TOTAL_STATISTICS_LIMIT 322s Total per-read statistics to be extracted for 322s plotting. Avoids memory overflow for large runs. 322s Default: 5000000 322s 322s Miscellaneous Arguments: 322s --quiet, -q Don't print status information. 322s --help, -h Print this help message and exit 322s usage: tombo plot per_read_roc --per-read-statistics-filenames 322s PER_READ_STATISTICS_FILENAMES 322s [PER_READ_STATISTICS_FILENAMES ...] 322s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 322s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 322s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 322s [--genome-fasta GENOME_FASTA] 322s [--statistics-per-block STATISTICS_PER_BLOCK] 322s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 322s [--pdf-filename PDF_FILENAME] [--quiet] 322s [--help] 322s 322s Required Argument: 322s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 322s Binary files containing per-read statistics from 322s statistical testing. 322s 322s Ground Truth Arguments (provide bed files or motifs): 322s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 322s Modification description and bed format files 322s containing single base locations of ground truth 322s modified sites. Bed files should contain 6 fields 322s including strand. Format descriptions as 322s "mod_name:locs.bed". Example: "CpG 322s bisulfite":bisulfite_locs.bed 322s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 322s Bed format files containing single base locations of 322s ground truth unmodified sites. Bed files should 322s contain 6 fields including strand. 322s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 322s Ground truth, motif centered, modified base 322s descriptions for computing ROC and PR curves. Each 322s statistics file is associated with a set of motif 322s descriptions. Format descriptions as: 322s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 322s mod_pos indicates the alternate-base within the motif 322s (1-based index). Example: CCWGG:2:"dcm 322s 5mC"::GATC:2:"dam 6mA" would assess the performance of 322s a single Tombo statistics file for identification of 322s E. coli dam and dcm methylation. 322s --genome-fasta GENOME_FASTA 322s FASTA file used to re-squiggle. For faster sequence 322s access. 322s 322s Down-sampling Arguments: 322s --statistics-per-block STATISTICS_PER_BLOCK 322s Number of randomly selected per-read, per-base 322s statistics to extract from each genomic block for 322s plotting. Default: 100000 322s --total-statistics-limit TOTAL_STATISTICS_LIMIT 322s Total per-read statistics to be extracted for 322s plotting. Avoids memory overflow for large runs. 322s Default: 5000000 322s 322s Output Arguments: 322s --pdf-filename PDF_FILENAME 322s PDF filename to store plot(s). Default: 322s tombo_results.per_reads_roc.pdf 322s 322s Miscellaneous Arguments: 322s --quiet, -q Don't print status information. 322s --help, -h Print this help message and exit 322s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 322s [--upstream-bases {0,1,2,3,4}] 322s [--downstream-bases {0,1,2,3,4}] [--read-mean] 322s [--num-kmer-threshold NUM_KMER_THRESHOLD] 322s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 322s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 322s [--corrected-group CORRECTED_GROUP] 322s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 322s [--quiet] [--help] 322s 322s Required Argument: 322s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 322s Directories containing fast5 files. 322s 322s Data Processing Arguments: 322s --upstream-bases {0,1,2,3,4} 322s Upstream bases in k-mer. Default: 1 322s --downstream-bases {0,1,2,3,4} 322s Downstream bases in k-mer. Default: 2 322s --read-mean Plot k-mer means across whole reads as opposed to 322s individual k-mer event levels. 322s --num-kmer-threshold NUM_KMER_THRESHOLD 322s Observations of each k-mer required to include a read 322s in read level averages. Default: 1 322s 322s Plotting Region Arguments: 322s --num-reads NUM_READS 322s Number of reads to plot. Default: 100 322s 322s Output Arguments: 322s --pdf-filename PDF_FILENAME 322s PDF filename to store plot(s). Default: 322s tombo_results.kmer_distribution.pdf 322s --r-data-filename R_DATA_FILENAME 322s Filename to save R data structure. Default: Don't save 322s --dont-plot Don't plot result. Useful to produce only R data file. 322s 322s FAST5 Data Arguments: 322s --corrected-group CORRECTED_GROUP 322s FAST5 group created by resquiggle command. Default: 322s RawGenomeCorrected_000 322s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 322s FAST5 subgroup(s) (under /Analyses/[--basecall- 322s group]/) containing basecalls and created within 322s [--corrected-group] containing re-squiggle results. 322s Default: ['BaseCalled_template'] 322s 322s Miscellaneous Arguments: 322s --quiet, -q Don't print status information. 322s --help, -h Print this help message and exit 323s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 323s [FAST5_BASEDIRS ...] 323s --control-fast5-basedirs 323s CONTROL_FAST5_BASEDIRS 323s [CONTROL_FAST5_BASEDIRS ...] 323s --statistics-filename 323s STATISTICS_FILENAME 323s [--genome-fasta GENOME_FASTA] 323s [--processes PROCESSES] 323s [--num-regions NUM_REGIONS] 323s [--num-bases NUM_BASES] 323s [--slide-span SLIDE_SPAN] 323s [--pdf-filename PDF_FILENAME] 323s [--r-data-filename R_DATA_FILENAME] 323s [--corrected-group CORRECTED_GROUP] 323s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 323s [--quiet] [--help] 323s 323s Required Arguments: 323s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 323s Directories containing fast5 files. 323s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 323s Set of directories containing fast5 files for control 323s reads, containing only canonical nucleotides. 323s --statistics-filename STATISTICS_FILENAME 323s File to save/load genomic base anchored statistics. 323s 323s FASTA Sequence Argument: 323s --genome-fasta GENOME_FASTA 323s FASTA file used to re-squiggle. For faster sequence 323s access. 323s 323s Multiprocessing Argument: 323s --processes PROCESSES 323s Number of processes. Default: 1 323s 323s Plotting Region Arguments: 323s --num-regions NUM_REGIONS 323s Number of regions to plot. Default: 10 323s --num-bases NUM_BASES 323s Number of bases to plot/output. Default: 21 323s --slide-span SLIDE_SPAN 323s Number of bases offset over which to search when 323s computing distances for signal cluster plotting. 323s Default: 0 (exact position) 323s 323s Output Arguments: 323s --pdf-filename PDF_FILENAME 323s PDF filename to store plot(s). Default: 323s tombo_results.signal_clusters.pdf 323s --r-data-filename R_DATA_FILENAME 323s Filename to save R data structure. Default: Don't save 323s 323s FAST5 Data Arguments: 323s --corrected-group CORRECTED_GROUP 323s FAST5 group created by resquiggle command. Default: 323s RawGenomeCorrected_000 323s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 323s FAST5 subgroup(s) (under /Analyses/[--basecall- 323s group]/) containing basecalls and created within 323s [--corrected-group] containing re-squiggle results. 323s Default: ['BaseCalled_template'] 323s 323s Miscellaneous Arguments: 323s --quiet, -q Don't print status information. 323s --help, -h Print this help message and exit 323s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 323s 323s Required Arguments: 323s fast5s_basedir Directory containing fast5 files. All files ending in 323s "fast5" found recursively within this base directory will be 323s processed. 323s 323s Miscellaneous Arguments: 323s --quiet, -q Don't print status information. 323s --help, -h Print this help message and exit 323s usage: tombo build_model event_resquiggle 323s [--minimap2-executable MINIMAP2_EXECUTABLE] 323s [--minimap2-index MINIMAP2_INDEX] 323s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 323s [--graphmap-executable GRAPHMAP_EXECUTABLE] 323s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 323s [--normalization-type {median,pA,pA_raw,none}] 323s [--pore-model-filename PORE_MODEL_FILENAME] 323s [--outlier-threshold OUTLIER_THRESHOLD] 323s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 323s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 323s [--timeout TIMEOUT] 323s [--cpts-limit CPTS_LIMIT] 323s [--skip-index] [--overwrite] 323s [--failed-reads-filename FAILED_READS_FILENAME] 323s [--include-event-stdev] 323s [--corrected-group CORRECTED_GROUP] 323s [--basecall-group BASECALL_GROUP] 323s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 323s [--processes PROCESSES] 323s [--align-processes ALIGN_PROCESSES] 323s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 323s [--resquiggle-processes RESQUIGGLE_PROCESSES] 323s [--quiet] [--help] 323s fast5s_basedir reference_fasta 323s 323s Required Arguments: 323s fast5s_basedir Directory containing fast5 files. All files ending in 323s "fast5" found recursively within this base directory 323s will be processed. 323s reference_fasta Reference genome/transcriptome FASTA file for mapping. 323s 323s Mapper Arguments (One mapper is required): 323s --minimap2-executable MINIMAP2_EXECUTABLE 323s Path to minimap2 executable. 323s --minimap2-index MINIMAP2_INDEX 323s Path to minimap2 index (with map-ont preset) file 323s corresponding to the [genome_fasta] provided. 323s --bwa-mem-executable BWA_MEM_EXECUTABLE 323s Path to bwa-mem executable. 323s --graphmap-executable GRAPHMAP_EXECUTABLE 323s Path to graphmap executable. 323s --alignment-batch-size ALIGNMENT_BATCH_SIZE 323s Number of reads included in each alignment call. Note: 323s A new system mapping call is made for each batch 323s (including loading of the genome), so it is advised to 323s use larger values for larger genomes. Default: 1000 323s 323s Signal Processing Arguments: 323s --normalization-type {median,pA,pA_raw,none} 323s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 323s as in the ONT events (using offset, range and 323s digitization), "pA": k-mer-based correction for pA 323s drift as in nanopolish (requires [--pore-model- 323s filename]), "median": median and MAD from raw signal. 323s Default: median 323s --pore-model-filename PORE_MODEL_FILENAME 323s File containing kmer model parameters (level_mean and 323s level_stdv) used in order to compute kmer-based 323s corrected pA values. E.g. https://github.com/jts/nanop 323s olish/blob/master/etc/r9- 323s models/template_median68pA.5mers.model 323s --outlier-threshold OUTLIER_THRESHOLD 323s Windosrize the signal at this number of scale values. 323s Negative value disables outlier clipping. Default: 323s 5.000000 323s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 323s Specify the 2 parameters for segmentation 1) running 323s neighboring windows width 2) minimum raw observations 323s per genomic base. Sample type defaults: RNA : 12 6 || 323s DNA : 5 3 323s 323s Read Filtering Arguments: 323s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 323s Filter reads based on observations per base percentile 323s thresholds. Format thresholds as "percentile:thresh 323s [pctl2:thresh2 ...]". For example to filter reads with 323s 99th pctl > 200 obs/base or max > 5k obs/base use 323s "99:200 100:5000". 323s --timeout TIMEOUT Timeout in seconds for processing a single read. 323s Default: No timeout. 323s --cpts-limit CPTS_LIMIT 323s Maximum number of changepoints to find within a single 323s indel group. Default: No limit. 323s 323s Input/Output Arguments: 323s --skip-index Skip creation of tombo index. This drastically slows 323s downstream tombo commands. Default stores tombo index 323s named ".[--fast5-basedir].[--corrected- 323s group].tombo.index" to be loaded automatically for 323s downstream commands. 323s --overwrite Overwrite previous corrected group in FAST5 files. 323s Note: only effects --corrected-group or --new- 323s corrected-group. 323s --failed-reads-filename FAILED_READS_FILENAME 323s Output failed read filenames with assoicated error. 323s Default: Do not store failed reads. 323s --include-event-stdev 323s Include corrected event standard deviation in output 323s FAST5 data. 323s 323s FAST5 Data Arguments: 323s --corrected-group CORRECTED_GROUP 323s FAST5 group created by resquiggle command. Default: 323s RawGenomeCorrected_000 323s --basecall-group BASECALL_GROUP 323s FAST5 group obtain original basecalls (under Analyses 323s group). Default: Basecall_1D_000 323s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 323s FAST5 subgroup(s) (under /Analyses/[--basecall- 323s group]/) containing basecalls and created within 323s [--corrected-group] containing re-squiggle results. 323s Default: ['BaseCalled_template'] 323s 323s Multiprocessing Arguments: 323s --processes PROCESSES 323s Number of processes. Default: 2 323s --align-processes ALIGN_PROCESSES 323s Number of processes to use for parsing and aligning 323s original basecalls. Each process will independently 323s load the genome into memory, so use caution with 323s larger genomes (e.g. human). Default: 1 323s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 323s Number of threads to use for aligner system call. 323s Default: [--processes] / (2 * [--align-processes)] 323s --resquiggle-processes RESQUIGGLE_PROCESSES 323s Number of processes to use for resquiggle algorithm. 323s Default: [--processes] / 2 323s 323s Miscellaneous Arguments: 323s --quiet, -q Don't print status information. 323s --help, -h Print this help message and exit 323s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 323s [FAST5_BASEDIRS ...] 323s --tombo-model-filename 323s TOMBO_MODEL_FILENAME 323s [--estimate-mean] 323s [--kmer-specific-sd] 323s [--upstream-bases {0,1,2,3,4}] 323s [--downstream-bases {0,1,2,3,4}] 323s [--minimum-test-reads MINIMUM_TEST_READS] 323s [--coverage-threshold COVERAGE_THRESHOLD] 323s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 323s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 323s [--processes PROCESSES] 323s [--corrected-group CORRECTED_GROUP] 323s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 323s [--quiet] [--help] 323s 323s Required Arguments: 323s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 323s Directories containing fast5 files. 323s --tombo-model-filename TOMBO_MODEL_FILENAME 323s Filename to save Tombo model. 323s 323s Modeling Arguments: 323s --estimate-mean Use the mean instead of median for model level 323s estimation. Note: This can cause poor fits due to 323s outliers 323s --kmer-specific-sd Estimate standard deviation for each k-mers 323s individually. 323s --upstream-bases {0,1,2,3,4} 323s Upstream bases in k-mer. Default: 1 323s --downstream-bases {0,1,2,3,4} 323s Downstream bases in k-mer. Default: 2 323s 323s Filtering Arguments: 323s --minimum-test-reads MINIMUM_TEST_READS 323s Number of reads required at a position to perform 323s significance testing or contribute to model 323s estimation. Default: 10 323s --coverage-threshold COVERAGE_THRESHOLD 323s Maximum mean coverage per region when estimating k-mer 323s model (limits compute time for deep samples). Default: 323s 100 323s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 323s Number of each k-mer observations required in order to 323s produce a reference (genomic locations for standard 323s reference and per-read for alternative reference). 323s Default: 5 323s 323s Multiprocessing Arguments: 323s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 323s Size of regions over which to multiprocesses statistic 323s computation. For very deep samples a smaller value is 323s recommmended in order to control memory consumption. 323s Default: 10000 323s --processes PROCESSES 323s Number of processes. Default: 1 323s 323s FAST5 Data Arguments: 323s --corrected-group CORRECTED_GROUP 323s FAST5 group created by resquiggle command. Default: 323s RawGenomeCorrected_000 323s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 323s FAST5 subgroup(s) (under /Analyses/[--basecall- 323s group]/) containing basecalls and created within 323s [--corrected-group] containing re-squiggle results. 323s Default: ['BaseCalled_template'] 323s 323s Miscellaneous Arguments: 323s --quiet, -q Don't print status information. 323s --help, -h Print this help message and exit 323s usage: tombo build_model estimate_alt_reference --alternate-model-filename 323s ALTERNATE_MODEL_FILENAME 323s --alternate-model-name 323s ALTERNATE_MODEL_NAME 323s --alternate-model-base 323s {A,C,G,T} 323s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 323s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 323s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 323s [--control-density-filename CONTROL_DENSITY_FILENAME] 323s [--dna] [--rna] 323s [--tombo-model-filename TOMBO_MODEL_FILENAME] 323s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 323s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 323s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 323s [--save-density-basename SAVE_DENSITY_BASENAME] 323s [--processes PROCESSES] 323s [--corrected-group CORRECTED_GROUP] 323s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 323s [--quiet] [--help] 323s 323s Required Arguments: 323s --alternate-model-filename ALTERNATE_MODEL_FILENAME 323s Tombo model for alternative likelihood ratio 323s significance testing. 323s --alternate-model-name ALTERNATE_MODEL_NAME 323s A short name to associate with this alternate model 323s (e.g. 5mC, 6mA, etc.). This text will be included in 323s output filenames when this model is used for testing. 323s --alternate-model-base {A,C,G,T} 323s Non-standard base is an alternative to this base. 323s 323s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 323s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 323s Directories containing fast5 files. 323s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 323s Set of directories containing fast5 files for control 323s reads, containing only canonical nucleotides. 323s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 323s File containing k-mer level kernel density estimates 323s for the alternative sample saved using --save-density- 323s basename. 323s --control-density-filename CONTROL_DENSITY_FILENAME 323s File containing k-mer level kernel density estimates 323s for the control sample saved using --save-density- 323s basename. 323s 323s Standard Model Arguments: 323s --dna Explicitly select canonical DNA model. Default: 323s Automatically determine from FAST5s 323s --rna Explicitly select canonical RNA model. Default: 323s Automatically determine from FAST5s 323s --tombo-model-filename TOMBO_MODEL_FILENAME 323s Tombo model filename. If no file is provided, the 323s default DNA or RNA Tombo model will be used. 323s 323s Model Fitting Arguments: 323s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 323s When esitmating the alternative base incorporation 323s rate, this percent of k-mers are assumed to have 323s significantly shifted signal so the alternative 323s distribution minimally overlaps the standard base 323s distribution. Default: 5.000000 323s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 323s Bandwidth applied when performing Gaussian kernal 323s density esitmation on standard and alternative base 323s signal distributions. Default: 0.050000 323s 323s Filtering Argument: 323s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 323s Number of each k-mer observations required in order to 323s produce a reference (genomic locations for standard 323s reference and per-read for alternative reference). 323s Default: 1000 323s 323s Output Argument: 323s --save-density-basename SAVE_DENSITY_BASENAME 323s Basename to save alternative model estimation density 323s estimation information. See scripts/debug_est_alt.R 323s for info use example. Default: Don't save. 323s 323s Multiprocessing Arguments: 323s --processes PROCESSES 323s Number of processes. Default: 1 323s 323s FAST5 Data Arguments: 323s --corrected-group CORRECTED_GROUP 323s FAST5 group created by resquiggle command. Default: 323s RawGenomeCorrected_000 323s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 323s FAST5 subgroup(s) (under /Analyses/[--basecall- 323s group]/) containing basecalls and created within 323s [--corrected-group] containing re-squiggle results. 323s Default: ['BaseCalled_template'] 323s 323s Miscellaneous Arguments: 323s --quiet, -q Don't print status information. 323s --help, -h Print this help message and exit 323s This test only tests the help system 323s There is an extensive test in 323s 323s tombo/tests/shell_tests.sh 323s 323s but this requires to download larger data 323s sets which is not done for the moment. 323s autopkgtest [20:07:07]: test run-unit-test: -----------------------] 324s run-unit-test PASS 324s autopkgtest [20:07:08]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 324s autopkgtest [20:07:08]: @@@@@@@@@@@@@@@@@@@@ summary 324s run-unit-test PASS 354s Creating nova instance adt-noble-ppc64el-tombo-20240314-200144-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240314.img (UUID a031584c-aec8-4412-bff6-4238354f4d17)...