0s autopkgtest [21:53:34]: starting date and time: 2024-03-13 21:53:34+0000 0s autopkgtest [21:53:34]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [21:53:34]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yvwjbry5/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-2@bos03-arm64-8.secgroup --name adt-noble-arm64-tombo-20240313-215334-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 70s autopkgtest [21:54:44]: testbed dpkg architecture: arm64 71s autopkgtest [21:54:45]: testbed apt version: 2.7.12 71s autopkgtest [21:54:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 71s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 71s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2818 kB] 72s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [450 kB] 72s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 72s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [42.3 kB] 72s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [603 kB] 72s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 72s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 72s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 72s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3218 kB] 72s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 72s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [42.3 kB] 72s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 73s Fetched 7327 kB in 1s (5248 kB/s) 73s Reading package lists... 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 77s Calculating upgrade... 77s The following packages will be REMOVED: 77s libssl3 77s The following NEW packages will be installed: 77s libssl3t64 77s The following packages will be upgraded: 77s console-setup console-setup-linux keyboard-configuration openssl 77s 4 upgraded, 1 newly installed, 1 to remove and 0 not upgraded. 77s Need to get 4955 kB of archives. 77s After this operation, 74.8 kB of additional disk space will be used. 77s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 78s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 78s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup-linux all 1.226ubuntu1 [1880 kB] 78s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup all 1.226ubuntu1 [110 kB] 78s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 keyboard-configuration all 1.226ubuntu1 [212 kB] 78s Preconfiguring packages ... 79s Fetched 4955 kB in 1s (6456 kB/s) 79s (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 ... 74759 files and directories currently installed.) 79s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 79s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 79s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 79s wget depends on libssl3 (>= 3.0.0). 79s u-boot-tools depends on libssl3 (>= 3.0.0). 79s tnftp depends on libssl3 (>= 3.0.0). 79s tcpdump depends on libssl3 (>= 3.0.0). 79s systemd-resolved depends on libssl3 (>= 3.0.0). 79s systemd depends on libssl3 (>= 3.0.0). 79s sudo depends on libssl3 (>= 3.0.0). 79s sbsigntool depends on libssl3 (>= 3.0.0). 79s rsync depends on libssl3 (>= 3.0.0). 79s python3-cryptography depends on libssl3 (>= 3.0.0). 79s openssh-server depends on libssl3 (>= 3.0.10). 79s openssh-client depends on libssl3 (>= 3.0.10). 79s mtd-utils depends on libssl3 (>= 3.0.0). 79s mokutil depends on libssl3 (>= 3.0.0). 79s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 79s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 79s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 79s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 79s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 79s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 79s libnvme1 depends on libssl3 (>= 3.0.0). 79s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 79s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 79s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 79s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 79s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 79s kmod depends on libssl3 (>= 3.0.0). 79s dhcpcd-base depends on libssl3 (>= 3.0.0). 79s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 79s 79s (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 ... 74759 files and directories currently installed.) 79s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 79s Selecting previously unselected package libssl3t64:arm64. 79s (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 ... 74748 files and directories currently installed.) 79s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 79s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 79s Preparing to unpack .../console-setup-linux_1.226ubuntu1_all.deb ... 79s Unpacking console-setup-linux (1.226ubuntu1) over (1.223ubuntu2) ... 80s Preparing to unpack .../console-setup_1.226ubuntu1_all.deb ... 80s Unpacking console-setup (1.226ubuntu1) over (1.223ubuntu2) ... 80s Preparing to unpack .../keyboard-configuration_1.226ubuntu1_all.deb ... 80s Unpacking keyboard-configuration (1.226ubuntu1) over (1.223ubuntu2) ... 80s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 80s Setting up keyboard-configuration (1.226ubuntu1) ... 85s Your console font configuration will be updated the next time your system 85s boots. If you want to update it now, run 'setupcon' from a virtual console. 86s update-initramfs: deferring update (trigger activated) 86s Setting up openssl (3.0.13-0ubuntu1) ... 86s Setting up console-setup-linux (1.226ubuntu1) ... 88s Setting up console-setup (1.226ubuntu1) ... 89s update-initramfs: deferring update (trigger activated) 90s Processing triggers for man-db (2.12.0-3) ... 90s Processing triggers for libc-bin (2.39-0ubuntu2) ... 90s Processing triggers for initramfs-tools (0.142ubuntu20) ... 91s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 91s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 108s System running in EFI mode, skipping. 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 111s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 111s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 111s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 112s Reading package lists... 112s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Calculating upgrade... 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s autopkgtest [21:55:29]: rebooting testbed after setup commands that affected boot 397s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 405s autopkgtest [22:00:19]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 409s autopkgtest [22:00:23]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 415s Get:1 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (dsc) [2292 B] 415s Get:2 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (tar) [22.3 MB] 415s Get:3 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (diff) [7024 B] 415s gpgv: Signature made Sun Dec 17 19:23:46 2023 UTC 415s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 415s gpgv: issuer "tille@debian.org" 415s gpgv: Can't check signature: No public key 415s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6.dsc: no acceptable signature found 415s autopkgtest [22:00:28]: testing package tombo version 1.5.1-6 415s autopkgtest [22:00:29]: build not needed 417s autopkgtest [22:00:31]: test run-unit-test: preparing testbed 423s Reading package lists... 423s Building dependency tree... 423s Reading state information... 424s Starting pkgProblemResolver with broken count: 0 424s Starting 2 pkgProblemResolver with broken count: 0 424s Done 425s The following additional packages will be installed: 425s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 425s libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax 425s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 425s libpython3.11-minimal libpython3.11-stdlib libsz2 python3-decorator 425s python3-h5py python3-h5py-serial python3-mappy python3-numpy python3-scipy 425s python3-tqdm python3.11 python3.11-minimal sphinx-rtd-theme-common tombo 425s tombo-doc 425s Suggested packages: 425s fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc 425s gfortran python3-dev python3-pytest python-scipy-doc python3.11-venv 425s python3.11-doc binfmt-support 425s Recommended packages: 425s javascript-common g++ | c++-compiler python3-pil python3-pyfaidx 425s python3-rpy2 425s The following NEW packages will be installed: 425s autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0 425s libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery 425s libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 425s libpython3.11-minimal libpython3.11-stdlib libsz2 python3-decorator 425s python3-h5py python3-h5py-serial python3-mappy python3-numpy python3-scipy 425s python3-tqdm python3.11 python3.11-minimal sphinx-rtd-theme-common tombo 425s tombo-doc 425s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 425s Need to get 68.9 MB/68.9 MB of archives. 425s After this operation, 253 MB of additional disk space will be used. 425s Get:1 /tmp/autopkgtest.gF1hyx/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 425s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 425s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 425s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-lato all 2.015-1 [2781 kB] 425s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 425s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 425s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 425s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 426s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 426s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 426s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 426s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 426s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-3.1ubuntu2 [1192 kB] 426s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-3.1ubuntu2 [55.8 kB] 426s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 426s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 426s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-sphinxdoc all 7.2.6-4 [149 kB] 426s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 426s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 426s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 426s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 426s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 426s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu2 [887 kB] 426s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-h5py all 3.10.0-1ubuntu2 [7980 B] 426s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mappy arm64 2.24+dfsg-3build2 [195 kB] 426s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-tqdm all 4.64.1-2 [95.2 kB] 426s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] 426s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 426s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 tombo arm64 1.5.1-6 [486 kB] 426s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 426s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 tombo-doc all 1.5.1-6 [21.7 MB] 428s Fetched 68.9 MB in 2s (32.5 MB/s) 428s Selecting previously unselected package libpython3.11-minimal:arm64. 428s (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 ... 74761 files and directories currently installed.) 428s Preparing to unpack .../00-libpython3.11-minimal_3.11.8-1_arm64.deb ... 428s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 429s Selecting previously unselected package python3.11-minimal. 429s Preparing to unpack .../01-python3.11-minimal_3.11.8-1_arm64.deb ... 429s Unpacking python3.11-minimal (3.11.8-1) ... 429s Selecting previously unselected package fonts-lato. 429s Preparing to unpack .../02-fonts-lato_2.015-1_all.deb ... 429s Unpacking fonts-lato (2.015-1) ... 429s Selecting previously unselected package libpython3.11-stdlib:arm64. 430s Preparing to unpack .../03-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 430s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 430s Selecting previously unselected package python3.11. 431s Preparing to unpack .../04-python3.11_3.11.8-1_arm64.deb ... 431s Unpacking python3.11 (3.11.8-1) ... 431s Selecting previously unselected package fonts-font-awesome. 431s Preparing to unpack .../05-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 431s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 432s Selecting previously unselected package fonts-mathjax. 432s Preparing to unpack .../06-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 432s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 432s Selecting previously unselected package libaec0:arm64. 432s Preparing to unpack .../07-libaec0_1.1.2-1_arm64.deb ... 432s Unpacking libaec0:arm64 (1.1.2-1) ... 432s Selecting previously unselected package libblas3:arm64. 432s Preparing to unpack .../08-libblas3_3.12.0-3_arm64.deb ... 432s Unpacking libblas3:arm64 (3.12.0-3) ... 432s Selecting previously unselected package libgfortran5:arm64. 432s Preparing to unpack .../09-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 432s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 432s Selecting previously unselected package libsz2:arm64. 432s Preparing to unpack .../10-libsz2_1.1.2-1_arm64.deb ... 432s Unpacking libsz2:arm64 (1.1.2-1) ... 432s Selecting previously unselected package libhdf5-103-1t64:arm64. 432s Preparing to unpack .../11-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu2_arm64.deb ... 432s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 432s Selecting previously unselected package libhdf5-hl-100t64:arm64. 432s Preparing to unpack .../12-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu2_arm64.deb ... 432s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 432s Selecting previously unselected package libjs-jquery. 432s Preparing to unpack .../13-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 432s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 432s Selecting previously unselected package libjs-underscore. 432s Preparing to unpack .../14-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 432s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 433s Selecting previously unselected package libjs-sphinxdoc. 433s Preparing to unpack .../15-libjs-sphinxdoc_7.2.6-4_all.deb ... 433s Unpacking libjs-sphinxdoc (7.2.6-4) ... 433s Selecting previously unselected package liblapack3:arm64. 433s Preparing to unpack .../16-liblapack3_3.12.0-3_arm64.deb ... 433s Unpacking liblapack3:arm64 (3.12.0-3) ... 433s Selecting previously unselected package liblbfgsb0:arm64. 433s Preparing to unpack .../17-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 433s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 433s Selecting previously unselected package liblzf1:arm64. 433s Preparing to unpack .../18-liblzf1_3.6-4_arm64.deb ... 433s Unpacking liblzf1:arm64 (3.6-4) ... 433s Selecting previously unselected package python3-decorator. 433s Preparing to unpack .../19-python3-decorator_5.1.1-5_all.deb ... 433s Unpacking python3-decorator (5.1.1-5) ... 433s Selecting previously unselected package python3-numpy. 433s Preparing to unpack .../20-python3-numpy_1%3a1.24.2-2_arm64.deb ... 433s Unpacking python3-numpy (1:1.24.2-2) ... 433s Selecting previously unselected package python3-h5py-serial. 433s Preparing to unpack .../21-python3-h5py-serial_3.10.0-1ubuntu2_arm64.deb ... 433s Unpacking python3-h5py-serial (3.10.0-1ubuntu2) ... 433s Selecting previously unselected package python3-h5py. 433s Preparing to unpack .../22-python3-h5py_3.10.0-1ubuntu2_all.deb ... 433s Unpacking python3-h5py (3.10.0-1ubuntu2) ... 433s Selecting previously unselected package python3-mappy. 433s Preparing to unpack .../23-python3-mappy_2.24+dfsg-3build2_arm64.deb ... 433s Unpacking python3-mappy (2.24+dfsg-3build2) ... 433s Selecting previously unselected package python3-tqdm. 433s Preparing to unpack .../24-python3-tqdm_4.64.1-2_all.deb ... 433s Unpacking python3-tqdm (4.64.1-2) ... 433s Selecting previously unselected package sphinx-rtd-theme-common. 433s Preparing to unpack .../25-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... 433s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 433s Selecting previously unselected package python3-scipy. 433s Preparing to unpack .../26-python3-scipy_1.11.4-6_arm64.deb ... 433s Unpacking python3-scipy (1.11.4-6) ... 434s Selecting previously unselected package tombo. 434s Preparing to unpack .../27-tombo_1.5.1-6_arm64.deb ... 434s Unpacking tombo (1.5.1-6) ... 434s Selecting previously unselected package libjs-mathjax. 434s Preparing to unpack .../28-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 434s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 435s Selecting 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Setting up python3-numpy (1:1.24.2-2) ... 441s Setting up python3-scipy (1.11.4-6) ... 442s Setting up python3-h5py-serial (3.10.0-1ubuntu2) ... 443s Setting up python3-h5py (3.10.0-1ubuntu2) ... 443s Setting up tombo (1.5.1-6) ... 443s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' 443s CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])') 443s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' 443s '`conda list | grep "r-base\|rpy2"` (last columns should match).') 443s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' 443s re.match('\+', fastq_rec[2]) is None): 443s Setting up autopkgtest-satdep (0) ... 443s Processing triggers for systemd (255.2-3ubuntu2) ... 444s Processing triggers for man-db (2.12.0-3) ... 446s Processing triggers for libc-bin (2.39-0ubuntu2) ... 451s (Reading database ... 82835 files and directories currently installed.) 451s Removing autopkgtest-satdep (0) ... 451s autopkgtest [22:01:05]: test run-unit-test: [----------------------- 452s ********* Testing help commands ********** 452s usage: tombo [-h] [-v] 452s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} 452s ... 452s 452s ********** Tombo ********* 452s 452s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 452s 452s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 452s 452s Tombo command groups (additional help available within each command group): 452s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 452s preprocess Pre-process nanopore reads for Tombo processing. 452s filter Apply filter to Tombo index file for specified criterion. 452s detect_modifications Perform statistical testing to detect non-standard nucleotides. 452s text_output Output Tombo results in text files. 452s build_model Create canonical and alternative base Tombo models. 452s plot Save plots to visualize raw nanopore signal or testing results. 452s 452s options: 452s -h, --help show this help message and exit 452s -v, --version show Tombo version and exit. 452s usage: tombo resquiggle [--dna] [--rna] 452s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 452s [--q-score Q_SCORE] 452s [--signal-matching-score SIGNAL_MATCHING_SCORE] 452s [--processes PROCESSES] 452s [--corrected-group CORRECTED_GROUP] 452s [--basecall-group BASECALL_GROUP] 452s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 452s [--overwrite] 452s [--failed-reads-filename FAILED_READS_FILENAME] 452s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 452s [--print-advanced-arguments] [--quiet] [--help] 452s fast5s_basedir reference 452s 452s Required Arguments: 452s fast5s_basedir Directory containing fast5 files. All files ending in 452s "fast5" found recursively within this base directory 452s will be processed. 452s reference Reference genome/transcriptome FASTA file or minimap2 452s index (with "map-ont" preset) for mapping. 452s 452s Model Parameters: 452s --dna Explicitly select canonical DNA model. Default: 452s Automatically determine from FAST5s 452s --rna Explicitly select canonical RNA model. Default: 452s Automatically determine from FAST5s 452s 452s Read Filtering Argument: 452s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 452s Filter reads based on observations per base percentile 452s thresholds. Format thresholds as "percentile:thresh 452s [pctl2:thresh2 ...]". For example to filter reads with 452s 99th pctl > 200 obs/base or max > 5k obs/base use 452s "99:200 100:5000". 452s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 452s Default: 0.000000 452s --signal-matching-score SIGNAL_MATCHING_SCORE 452s Observed to expected signal matching score (higher 452s score indicates poor matching). Sample type defaults: 452s RNA : 2 || DNA : 1.1 452s 452s Multiprocessing Arguments: 452s --processes PROCESSES 452s Number of processes. Default: 1 452s 452s FAST5 Data Arguments: 452s --corrected-group CORRECTED_GROUP 452s FAST5 group created by resquiggle command. Default: 452s RawGenomeCorrected_000 452s --basecall-group BASECALL_GROUP 452s FAST5 group obtain original basecalls (under Analyses 452s group). Default: Basecall_1D_000 452s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 452s FAST5 subgroup(s) (under /Analyses/[--basecall- 452s group]/) containing basecalls and created within 452s [--corrected-group] containing re-squiggle results. 452s Default: ['BaseCalled_template'] 452s --overwrite Overwrite previous corrected group in FAST5 files. 452s Note: only effects --corrected-group or --new- 452s corrected-group. 452s 452s Input/Output Arguments: 452s --failed-reads-filename FAILED_READS_FILENAME 452s Output failed read filenames with assoicated error. 452s Default: Do not store failed reads. 452s --num-most-common-errors NUM_MOST_COMMON_ERRORS 452s Dynamically show this many most common errors so far 452s through run. Default: 0; Just show progress 452s 452s Advanced Arguments: 452s --print-advanced-arguments 452s Print advanced re-squiggle arguments and exit. 452s 452s Miscellaneous Arguments: 452s --quiet, -q Don't print status information. 452s --help, -h Print this help message and exit 452s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 452s --fastq-filenames 452s FASTQ_FILENAMES 452s [FASTQ_FILENAMES ...] 452s [--basecall-group BASECALL_GROUP] 452s [--basecall-subgroup BASECALL_SUBGROUP] 452s [--overwrite] 452s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 452s [--processes PROCESSES] 452s [--quiet] [--help] 452s 452s Required Arguments: 452s --fast5-basedir FAST5_BASEDIR 452s Directory containing fast5 files. 452s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 452s FASTQ filenames containing basecalls to be added to 452s raw FAST5 files. 452s 452s FAST5 Data Arguments: 452s --basecall-group BASECALL_GROUP 452s FAST5 group obtain original basecalls (under Analyses 452s group). Default: Basecall_1D_000 452s --basecall-subgroup BASECALL_SUBGROUP 452s FAST5 subgroup (under /Analyses/[--basecall-group]/) 452s under which to store basecalls from FASTQs. Default: 452s BaseCalled_template 452s --overwrite Overwrite previous corrected group in FAST5 files. 452s Note: only effects --corrected-group or --new- 452s corrected-group. 452s 452s Sequencing Summary Argument: 452s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 452s Sequencing summary filenames produced by albacore. 452s These can make annotation of raw FAST5 files with 452s FASTQ sequence much faster. 452s 452s Multiprocessing Argument: 452s --processes PROCESSES 452s Number of processes. Default: 1 452s 452s Miscellaneous Arguments: 452s --quiet, -q Don't print status information. 452s --help, -h Print this help message and exit 452s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS 452s [FAST5_BASEDIRS ...] 452s [--corrected-group CORRECTED_GROUP] 452s [--quiet] [--help] 452s 452s Required Argument: 452s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 452s Directories containing fast5 files. 452s 452s FAST5 Data Argument: 452s --corrected-group CORRECTED_GROUP 452s FAST5 group created by resquiggle command. Default: 452s RawGenomeCorrected_000 452s 452s Miscellaneous Arguments: 452s --quiet, -q Don't print status information. 452s --help, -h Print this help message and exit 452s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 452s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 452s [--corrected-group CORRECTED_GROUP] [--quiet] 452s [--help] 452s 452s Required Argument: 452s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 452s Directories containing fast5 files. 452s 452s Read Filtering Argument: 452s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 452s Filter reads based on observations per base percentile 452s thresholds. Format thresholds as "percentile:thresh 452s [pctl2:thresh2 ...]". For example to filter reads with 452s 99th pctl > 200 obs/base or max > 5k obs/base use 452s "99:200 100:5000". 452s 452s FAST5 Data Argument: 452s --corrected-group CORRECTED_GROUP 452s FAST5 group created by resquiggle command. Default: 452s RawGenomeCorrected_000 452s 452s Miscellaneous Arguments: 452s --quiet, -q Don't print status information. 452s --help, -h Print this help message and exit 452s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS 452s [FAST5_BASEDIRS ...] 452s [--percent-to-filter PERCENT_TO_FILTER] 452s [--corrected-group CORRECTED_GROUP] 452s [--quiet] [--help] 452s 452s Required Arguments: 452s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 452s Directories containing fast5 files. 452s 452s Read Filtering Argument: 452s --percent-to-filter PERCENT_TO_FILTER 452s Percentage of all reads to filter. Reads are randomly 452s selected weighted according to the approximate 452s coverage at the mapped genomic location. This can be 452s useful in modeling and testing. Default: 10.000000 452s 452s FAST5 Data Arguments: 452s --corrected-group CORRECTED_GROUP 452s FAST5 group created by resquiggle command. Default: 452s RawGenomeCorrected_000 452s 452s Miscellaneous Arguments: 452s --quiet, -q Don't print status information. 452s --help, -h Print this help message and exit 452s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS 452s [FAST5_BASEDIRS ...] [--q-score Q_SCORE] 452s [--corrected-group CORRECTED_GROUP] 452s [--basecall-group BASECALL_GROUP] [--quiet] 452s [--help] 452s 452s Required Arguments: 452s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 452s Directories containing fast5 files. 452s 452s Read Filtering Argument: 452s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 452s Default: 7.000000 452s 452s FAST5 Data Arguments: 452s --corrected-group CORRECTED_GROUP 452s FAST5 group created by resquiggle command. Default: 452s RawGenomeCorrected_000 452s --basecall-group BASECALL_GROUP 452s FAST5 group obtain original basecalls (under Analyses 452s group). Default: Basecall_1D_000 452s 452s Miscellaneous Arguments: 452s --quiet, -q Don't print status information. 452s --help, -h Print this help message and exit 452s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS 452s [FAST5_BASEDIRS ...] 452s --signal-matching-score 452s SIGNAL_MATCHING_SCORE 452s [--corrected-group CORRECTED_GROUP] 452s [--quiet] [--help] 452s 452s Required Arguments: 452s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 452s Directories containing fast5 files. 452s --signal-matching-score SIGNAL_MATCHING_SCORE 452s Observed to expected signal matching score (higher 452s score indicates poor matching). Sample type defaults: 452s RNA : 2 || DNA : 1.1 452s 452s FAST5 Data Arguments: 452s --corrected-group CORRECTED_GROUP 452s FAST5 group created by resquiggle command. Default: 452s RawGenomeCorrected_000 452s 452s Miscellaneous Arguments: 452s --quiet, -q Don't print status information. 452s --help, -h Print this help message and exit 453s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS 453s [FAST5_BASEDIRS ...] 453s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 453s [--include-partial-overlap] 453s [--corrected-group CORRECTED_GROUP] 453s [--quiet] [--help] 453s 453s Required Arguments: 453s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 453s Directories containing fast5 files. 453s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 453s Filter out reads not falling completely within include 453s regions. Omit start and end coordinates to include an 453s entire chromosome/sequence record. Format regions as 453s "chrm[:start-end] [chrm2[:start2-end2] ...]". 453s 453s Filter Argument: 453s --include-partial-overlap 453s Include reads that partially overlap the specified 453s region. Default: Only include reads completely 453s contained in a specified region 453s 453s FAST5 Data Argument: 453s --corrected-group CORRECTED_GROUP 453s FAST5 group created by resquiggle command. Default: 453s RawGenomeCorrected_000 453s 453s Miscellaneous Arguments: 453s --quiet, -q Don't print status information. 453s --help, -h Print this help message and exit 453s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS 453s [FAST5_BASEDIRS ...] 453s --statistics-file-basename 453s STATISTICS_FILE_BASENAME [--dna] 453s [--rna] 453s [--fishers-method-context FISHERS_METHOD_CONTEXT] 453s [--minimum-test-reads MINIMUM_TEST_READS] 453s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 453s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 453s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 453s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 453s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 453s [--processes PROCESSES] 453s [--corrected-group CORRECTED_GROUP] 453s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 453s [--quiet] [--help] 453s 453s Required Argument: 453s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 453s Directories containing fast5 files. 453s --statistics-file-basename STATISTICS_FILE_BASENAME 453s File base name to save base by base statistics from 453s testing. Filenames will be [--statistics-file- 453s basename].[--alternate-bases]?.tombo.stats 453s 453s Comparison Model Arguments: 453s --dna Explicitly select canonical DNA model. Default: 453s Automatically determine from FAST5s 453s --rna Explicitly select canonical RNA model. Default: 453s Automatically determine from FAST5s 453s 453s Significance Test Arguments: 453s --fishers-method-context FISHERS_METHOD_CONTEXT 453s Number of context bases up and downstream over which 453s to compute Fisher's method combined p-values. Note: 453s Not applicable for alternative model likelihood ratio 453s tests. Default: 1. 453s --minimum-test-reads MINIMUM_TEST_READS 453s Number of reads required at a position to perform 453s significance testing or contribute to model 453s estimation. Default: 1 453s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 453s P-value threshold when computing fraction of 453s significant reads at each genomic position. If two 453s values are provided, statistics between these values 453s are not considered. Default thresholds: DNA:0.15-0.5 , 453s RNA:0.05-0.4 453s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 453s Dampen fraction modified estimates for low coverage 453s sites. Two parameters are unmodified and modified 453s pseudo read counts. This is equivalent to a beta prior 453s on the fraction estimate. Set to "0 0" to disable 453s dampened fraction estimation. Default: [2, 0] 453s 453s Output Argument: 453s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 453s Base for binary files containing per-read statistics 453s from statistical testing. Filenames will be [--per- 453s read-statistics-basename].[--alternate- 453s bases]?.tombo.per_read_stats 453s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 453s Number of the most significant sites to store for 453s faster access. If a longer list of most significant 453s sites is required the list must be re-computed from 453s all batches. Very large values can increase RAM usage. 453s Default: 100000 453s 453s Multiprocessing Arguments: 453s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 453s Size of regions over which to multiprocesses statistic 453s computation. For very deep samples a smaller value is 453s recommmended in order to control memory consumption. 453s Default: 10000 453s --processes PROCESSES 453s Number of processes. Default: 1 453s 453s FAST5 Data Arguments: 453s --corrected-group CORRECTED_GROUP 453s FAST5 group created by resquiggle command. Default: 453s RawGenomeCorrected_000 453s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 453s FAST5 subgroup(s) (under /Analyses/[--basecall- 453s group]/) containing basecalls and created within 453s [--corrected-group] containing re-squiggle results. 453s Default: ['BaseCalled_template'] 453s 453s Miscellaneous Arguments: 453s --quiet, -q Don't print status information. 453s --help, -h Print this help message and exit 453s usage: tombo detect_modifications alternative_model 453s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 453s [--statistics-file-basename STATISTICS_FILE_BASENAME] 453s [--alternate-bases {5mC,6mA,dcm,CpG,dam} [{5mC,6mA,dcm,CpG,dam} ...]] 453s [--print-available-models] 453s [--dna] [--rna] 453s [--minimum-test-reads MINIMUM_TEST_READS] 453s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 453s [--standard-log-likelihood-ratio] 453s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 453s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 453s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 453s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 453s [--processes PROCESSES] 453s [--corrected-group CORRECTED_GROUP] 453s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 453s [--quiet] [--help] 453s 453s Required Argument: 453s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 453s Directories containing fast5 files. 453s --statistics-file-basename STATISTICS_FILE_BASENAME 453s File base name to save base by base statistics from 453s testing. Filenames will be [--statistics-file- 453s basename].[--alternate-bases]?.tombo.stats 453s --alternate-bases {5mC,6mA,dcm,CpG,dam} [{5mC,6mA,dcm,CpG,dam} ...] 453s Default non-standard base model for testing (not 453s required if user created --alternate-model-filenames 453s is provided). 453s 453s Comparison Arguments: 453s --print-available-models 453s Print available alternative models and exit. 453s --dna Explicitly select canonical DNA model. Default: 453s Automatically determine from FAST5s 453s --rna Explicitly select canonical RNA model. Default: 453s Automatically determine from FAST5s 453s 453s Significance Test Arguments: 453s --minimum-test-reads MINIMUM_TEST_READS 453s Number of reads required at a position to perform 453s significance testing or contribute to model 453s estimation. Default: 1 453s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 453s Log likelihood ratio threshold when computing fraction 453s of significant reads at each genomic position. If two 453s values are provided, statistics between these values 453s are not considered. Default thresholds: DNA:-1.5-2.5 , 453s RNA:-2.5-2.5 453s --standard-log-likelihood-ratio 453s Use a standard log likelihood ratio (LLR) statistic. 453s Default is to use an outlier-robust LLR-like 453s statistic. Detail in full online documentation. 453s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 453s Dampen fraction modified estimates for low coverage 453s sites. Two parameters are unmodified and modified 453s pseudo read counts. This is equivalent to a beta prior 453s on the fraction estimate. Set to "0 0" to disable 453s dampened fraction estimation. Default: [2, 0] 453s 453s Output Argument: 453s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 453s Base for binary files containing per-read statistics 453s from statistical testing. Filenames will be [--per- 453s read-statistics-basename].[--alternate- 453s bases]?.tombo.per_read_stats 453s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 453s Number of the most significant sites to store for 453s faster access. If a longer list of most significant 453s sites is required the list must be re-computed from 453s all batches. Very large values can increase RAM usage. 453s Default: 100000 453s 453s Multiprocessing Arguments: 453s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 453s Size of regions over which to multiprocesses statistic 453s computation. For very deep samples a smaller value is 453s recommmended in order to control memory consumption. 453s Default: 10000 453s --processes PROCESSES 453s Number of processes. Default: 1 453s 453s FAST5 Data Arguments: 453s --corrected-group CORRECTED_GROUP 453s FAST5 group created by resquiggle command. Default: 453s RawGenomeCorrected_000 453s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 453s FAST5 subgroup(s) (under /Analyses/[--basecall- 453s group]/) containing basecalls and created within 453s [--corrected-group] containing re-squiggle results. 453s Default: ['BaseCalled_template'] 453s 453s Miscellaneous Arguments: 453s --quiet, -q Don't print status information. 453s --help, -h Print this help message and exit 453s usage: tombo detect_modifications model_sample_compare --fast5-basedirs 453s FAST5_BASEDIRS 453s [FAST5_BASEDIRS ...] 453s --statistics-file-basename 453s STATISTICS_FILE_BASENAME 453s --control-fast5-basedirs 453s CONTROL_FAST5_BASEDIRS 453s [CONTROL_FAST5_BASEDIRS ...] 453s [--sample-only-estimates] 453s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 453s [--dna] [--rna] 453s [--fishers-method-context FISHERS_METHOD_CONTEXT] 453s [--minimum-test-reads MINIMUM_TEST_READS] 453s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 453s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 453s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 453s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 453s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 453s [--processes PROCESSES] 453s [--corrected-group CORRECTED_GROUP] 453s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 453s [--quiet] [--help] 453s 453s Required Argument: 453s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 453s Directories containing fast5 files. 453s --statistics-file-basename STATISTICS_FILE_BASENAME 453s File base name to save base by base statistics from 453s testing. Filenames will be [--statistics-file- 453s basename].[--alternate-bases]?.tombo.stats 453s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 453s Set of directories containing fast5 files for control 453s reads, containing only canonical nucleotides. 453s 453s Model Prior Arguments: 453s --sample-only-estimates 453s Only use canonical sample to estimate expected signal 453s level and spread. Default: Use canonical model to 453s improve estimtates (esp. for low coverage regions) 453s using baysian posterior estimates. 453s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 453s Prior weights (one each for mean and spread) applied 453s to canonical base model for estimating posterior model 453s parameters for sample comparison. Default: [5, 40] 453s --dna Explicitly select canonical DNA model. Default: 453s Automatically determine from FAST5s 453s --rna Explicitly select canonical RNA model. Default: 453s Automatically determine from FAST5s 453s 453s Significance Test Arguments: 453s --fishers-method-context FISHERS_METHOD_CONTEXT 453s Number of context bases up and downstream over which 453s to compute Fisher's method combined p-values. Note: 453s Not applicable for alternative model likelihood ratio 453s tests. Default: 1. 453s --minimum-test-reads MINIMUM_TEST_READS 453s Number of reads required at a position to perform 453s significance testing or contribute to model 453s estimation. Default: 1 453s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 453s P-value threshold when computing fraction of 453s significant reads at each genomic position. If two 453s values are provided, statistics between these values 453s are not considered. Default thresholds: DNA:0.15-0.5 , 453s RNA:0.05-0.4 453s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 453s Dampen fraction modified estimates for low coverage 453s sites. Two parameters are unmodified and modified 453s pseudo read counts. This is equivalent to a beta prior 453s on the fraction estimate. Set to "0 0" to disable 453s dampened fraction estimation. Default: [2, 0] 453s 453s Output Argument: 453s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 453s Base for binary files containing per-read statistics 453s from statistical testing. Filenames will be [--per- 453s read-statistics-basename].[--alternate- 453s bases]?.tombo.per_read_stats 453s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 453s Number of the most significant sites to store for 453s faster access. If a longer list of most significant 453s sites is required the list must be re-computed from 453s all batches. Very large values can increase RAM usage. 453s Default: 100000 453s 453s Multiprocessing Arguments: 453s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 453s Size of regions over which to multiprocesses statistic 453s computation. For very deep samples a smaller value is 453s recommmended in order to control memory consumption. 453s Default: 10000 453s --processes PROCESSES 453s Number of processes. Default: 1 453s 453s FAST5 Data Arguments: 453s --corrected-group CORRECTED_GROUP 453s FAST5 group created by resquiggle command. Default: 453s RawGenomeCorrected_000 453s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 453s FAST5 subgroup(s) (under /Analyses/[--basecall- 453s group]/) containing basecalls and created within 453s [--corrected-group] containing re-squiggle results. 453s Default: ['BaseCalled_template'] 453s 453s Miscellaneous Arguments: 453s --quiet, -q Don't print status information. 453s --help, -h Print this help message and exit 453s usage: tombo detect_modifications level_sample_compare --fast5-basedirs 453s FAST5_BASEDIRS 453s [FAST5_BASEDIRS ...] 453s --statistics-file-basename 453s STATISTICS_FILE_BASENAME 453s --alternate-fast5-basedirs 453s ALTERNATE_FAST5_BASEDIRS 453s [ALTERNATE_FAST5_BASEDIRS ...] 453s [--fishers-method-context FISHERS_METHOD_CONTEXT] 453s [--minimum-test-reads MINIMUM_TEST_READS] 453s [--statistic-type {ks,u,t}] 453s [--store-p-value] 453s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 453s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 453s [--processes PROCESSES] 453s [--corrected-group CORRECTED_GROUP] 453s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 453s [--quiet] [--help] 453s 453s Required Argument: 453s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 453s Directories containing fast5 files. 453s --statistics-file-basename STATISTICS_FILE_BASENAME 453s File base name to save base by base statistics from 453s testing. Filenames will be [--statistics-file- 453s basename].[--alternate-bases]?.tombo.stats 453s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 453s Set of directories containing fast5 files for 453s alternate set of reads. 453s 453s Significance Test Arguments: 453s --fishers-method-context FISHERS_METHOD_CONTEXT 453s Number of context bases up and downstream over which 453s to compute Fisher's method combined p-values. Note: 453s Not applicable for alternative model likelihood ratio 453s tests. Default: 1. 453s --minimum-test-reads MINIMUM_TEST_READS 453s Number of reads required at a position to perform 453s significance testing or contribute to model 453s estimation. Default: 50 453s --statistic-type {ks,u,t} 453s Type of statistical test to apply. Default: "ks" 453s --store-p-value Store p-value instead of effect-size statistic. 453s Statistics are D-statistic (KS-test), deviation from 453s even common language effect size (u-test), and Cohen's 453s D (t-test). 453s 453s Output Argument: 453s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 453s Number of the most significant sites to store for 453s faster access. If a longer list of most significant 453s sites is required the list must be re-computed from 453s all batches. Very large values can increase RAM usage. 453s Default: 100000 453s 453s Multiprocessing Arguments: 453s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 453s Size of regions over which to multiprocesses statistic 453s computation. For very deep samples a smaller value is 453s recommmended in order to control memory consumption. 453s Default: 10000 453s --processes PROCESSES 453s Number of processes. Default: 1 453s 453s FAST5 Data Arguments: 453s --corrected-group CORRECTED_GROUP 453s FAST5 group created by resquiggle command. Default: 453s RawGenomeCorrected_000 453s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 453s FAST5 subgroup(s) (under /Analyses/[--basecall- 453s group]/) containing basecalls and created within 453s [--corrected-group] containing re-squiggle results. 453s Default: ['BaseCalled_template'] 453s 453s Miscellaneous Arguments: 453s --quiet, -q Don't print status information. 453s --help, -h Print this help message and exit 454s usage: tombo detect_modifications aggregate_per_read_stats 454s --per-read-statistics-filename 454s PER_READ_STATISTICS_FILENAME 454s --statistics-filename 454s STATISTICS_FILENAME 454s --single-read-threshold 454s SINGLE_READ_THRESHOLD 454s [SINGLE_READ_THRESHOLD ...] 454s [--minimum-test-reads MINIMUM_TEST_READS] 454s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 454s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 454s [--processes PROCESSES] 454s [--corrected-group CORRECTED_GROUP] 454s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 454s [--quiet] [--help] 454s 454s Required Argument: 454s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 454s Binary file containing per-read statistics from 454s statistical testing. 454s --statistics-filename STATISTICS_FILENAME 454s File to save/load genomic base anchored statistics. 454s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 454s P-value or log likelihood ratio threshold when 454s computing fraction of significant reads at each 454s genomic position. If two values are provided, 454s statistics between these values are not considered. 454s 454s Significance Test Arguments: 454s --minimum-test-reads MINIMUM_TEST_READS 454s Number of reads required at a position to perform 454s significance testing or contribute to model 454s estimation. Default: 1 454s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 454s Dampen fraction modified estimates for low coverage 454s sites. Two parameters are unmodified and modified 454s pseudo read counts. This is equivalent to a beta prior 454s on the fraction estimate. Set to "0 0" to disable 454s dampened fraction estimation. Default: [2, 0] 454s 454s Output Argument: 454s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 454s Number of the most significant sites to store for 454s faster access. If a longer list of most significant 454s sites is required the list must be re-computed from 454s all batches. Very large values can increase RAM usage. 454s Default: 100000 454s 454s Multiprocessing Arguments: 454s --processes PROCESSES 454s Number of processes. Default: 1 454s 454s FAST5 Data Arguments: 454s --corrected-group CORRECTED_GROUP 454s FAST5 group created by resquiggle command. Default: 454s RawGenomeCorrected_000 454s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 454s FAST5 subgroup(s) (under /Analyses/[--basecall- 454s group]/) containing basecalls and created within 454s [--corrected-group] containing re-squiggle results. 454s Default: ['BaseCalled_template'] 454s 454s Miscellaneous Arguments: 454s --quiet, -q Don't print status information. 454s --help, -h Print this help message and exit 454s usage: tombo text_output browser_files 454s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 454s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 454s [--statistics-filename STATISTICS_FILENAME] 454s [--genome-fasta GENOME_FASTA] 454s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 454s [--browser-file-basename BROWSER_FILE_BASENAME] 454s [--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} ...]] 454s [--corrected-group CORRECTED_GROUP] 454s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 454s [--quiet] [--help] 454s 454s Data Arguments: 454s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 454s Directories containing fast5 files. 454s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 454s Set of directories containing fast5 files for control 454s reads, containing only canonical nucleotides. 454s --statistics-filename STATISTICS_FILENAME 454s File to save/load genomic base anchored statistics. 454s 454s Statistic Motif Filter Arguments: 454s --genome-fasta GENOME_FASTA 454s FASTA file used to re-squiggle. For faster sequence 454s access. 454s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 454s Ground truth, motif centered, modified base 454s descriptions for output filtering. Format descriptions 454s as: "motif:mod_pos:name". The mod_pos indicates the 454s modified base within the motif (1-based index). 454s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 454s output for identification of E. coli dam and dcm 454s methylation. 454s 454s Output Arguments: 454s --browser-file-basename BROWSER_FILE_BASENAME 454s Basename for output browser files. Two files (plus and 454s minus strand) will be produced for each --file-types 454s supplied. Filenames formatted as "[browser-file- 454s basename].[file- 454s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 454s Default: tombo_results 454s --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} ...] 454s Data types of genome browser files to produce. 454s Produced coverage files are in bedGraph format, while 454s all other file types will be in wiggle format 454s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 454s Default: "coverage" 454s 454s FAST5 Data Arguments: 454s --corrected-group CORRECTED_GROUP 454s FAST5 group created by resquiggle command. Default: 454s RawGenomeCorrected_000 454s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 454s FAST5 subgroup(s) (under /Analyses/[--basecall- 454s group]/) containing basecalls and created within 454s [--corrected-group] containing re-squiggle results. 454s Default: ['BaseCalled_template'] 454s 454s Miscellaneous Arguments: 454s --quiet, -q Don't print status information. 454s --help, -h Print this help message and exit 454s usage: tombo text_output signif_sequence_context --statistics-filename 454s STATISTICS_FILENAME 454s [--genome-fasta GENOME_FASTA] 454s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 454s [--num-regions NUM_REGIONS] 454s [--num-bases NUM_BASES] 454s [--sequences-filename SEQUENCES_FILENAME] 454s [--corrected-group CORRECTED_GROUP] 454s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 454s [--quiet] [--help] 454s 454s Required Argument: 454s --statistics-filename STATISTICS_FILENAME 454s File to save/load genomic base anchored statistics. 454s 454s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 454s --genome-fasta GENOME_FASTA 454s FASTA file used to re-squiggle. For faster sequence 454s access. 454s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 454s Directories containing fast5 files. 454s 454s Region Selection Arguments: 454s --num-regions NUM_REGIONS 454s Number of regions to plot. Default: 100 454s --num-bases NUM_BASES 454s Number of bases to plot/output. Default: 15 454s 454s Output Arguments: 454s --sequences-filename SEQUENCES_FILENAME 454s File for sequences from selected regions. Sequences 454s will be stored in FASTA format. Default: 454s tombo_results.significant_regions.fasta. 454s 454s FAST5 Data Arguments: 454s --corrected-group CORRECTED_GROUP 454s FAST5 group created by resquiggle command. Default: 454s RawGenomeCorrected_000 454s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 454s FAST5 subgroup(s) (under /Analyses/[--basecall- 454s group]/) containing basecalls and created within 454s [--corrected-group] containing re-squiggle results. 454s Default: ['BaseCalled_template'] 454s 454s Miscellaneous Arguments: 454s --quiet, -q Don't print status information. 454s --help, -h Print this help message and exit 454s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS 454s [FAST5_BASEDIRS ...] 454s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 454s [--plot-standard-model] 454s [--plot-alternate-model {5mC,6mA,dcm,CpG,dam}] 454s [--overplot-threshold OVERPLOT_THRESHOLD] 454s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 454s [--num-regions NUM_REGIONS] 454s [--num-bases NUM_BASES] 454s [--pdf-filename PDF_FILENAME] 454s [--corrected-group CORRECTED_GROUP] 454s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 454s [--quiet] [--help] 454s 454s Required Argument: 454s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 454s Directories containing fast5 files. 454s 454s Comparison Arguments: 454s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 454s Set of directories containing fast5 files for control 454s reads, containing only canonical nucleotides. 454s --plot-standard-model 454s Add default standard model distribution to the plot. 454s --plot-alternate-model {5mC,6mA,dcm,CpG,dam} 454s Add alternative model distribution to the plot. 454s 454s Overplotting Arguments: 454s --overplot-threshold OVERPLOT_THRESHOLD 454s Coverage level to trigger alternative plot type 454s instead of raw signal. Default: 50 454s --overplot-type {Downsample,Boxplot,Quantile,Density} 454s Plot type for regions with higher coverage. Default: 454s Downsample 454s 454s Plotting Region Arguments: 454s --num-regions NUM_REGIONS 454s Number of regions to plot. Default: 10 454s --num-bases NUM_BASES 454s Number of bases to plot/output. Default: 21 454s 454s Output Argument: 454s --pdf-filename PDF_FILENAME 454s PDF filename to store plot(s). Default: 454s tombo_results.max_coverage.pdf 454s 454s FAST5 Data Arguments: 454s --corrected-group CORRECTED_GROUP 454s FAST5 group created by resquiggle command. Default: 454s RawGenomeCorrected_000 454s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 454s FAST5 subgroup(s) (under /Analyses/[--basecall- 454s group]/) containing basecalls and created within 454s [--corrected-group] containing re-squiggle results. 454s Default: ['BaseCalled_template'] 454s 454s Miscellaneous Arguments: 454s --quiet, -q Don't print status information. 454s --help, -h Print this help message and exit 454s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS 454s [FAST5_BASEDIRS ...] --genome-locations 454s GENOME_LOCATIONS [GENOME_LOCATIONS ...] 454s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 454s [--plot-standard-model] 454s [--plot-alternate-model {dam,6mA,5mC,dcm,CpG}] 454s [--overplot-threshold OVERPLOT_THRESHOLD] 454s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 454s [--num-bases NUM_BASES] 454s [--pdf-filename PDF_FILENAME] 454s [--corrected-group CORRECTED_GROUP] 454s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 454s [--quiet] [--help] 454s 454s Required Arguments: 454s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 454s Directories containing fast5 files. 454s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 454s Genomic locations at which to plot signal. Format 454s locations as "chrm:position[:strand] 454s [chrm2:position2[:strand2] ...]" (strand not 454s applicable for all applications) 454s 454s Comparison Arguments: 454s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 454s Set of directories containing fast5 files for control 454s reads, containing only canonical nucleotides. 454s --plot-standard-model 454s Add default standard model distribution to the plot. 454s --plot-alternate-model {dam,6mA,5mC,dcm,CpG} 454s Add alternative model distribution to the plot. 454s 454s Overplotting Arguments: 454s --overplot-threshold OVERPLOT_THRESHOLD 454s Coverage level to trigger alternative plot type 454s instead of raw signal. Default: 50 454s --overplot-type {Downsample,Boxplot,Quantile,Density} 454s Plot type for regions with higher coverage. Default: 454s Downsample 454s 454s Plotting Region Argument: 454s --num-bases NUM_BASES 454s Number of bases to plot/output. Default: 21 454s 454s Output Argument: 454s --pdf-filename PDF_FILENAME 454s PDF filename to store plot(s). Default: 454s tombo_results.genome_locations.pdf 454s 454s FAST5 Data Arguments: 454s --corrected-group CORRECTED_GROUP 454s FAST5 group created by resquiggle command. Default: 454s RawGenomeCorrected_000 454s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 454s FAST5 subgroup(s) (under /Analyses/[--basecall- 454s group]/) containing basecalls and created within 454s [--corrected-group] containing re-squiggle results. 454s Default: ['BaseCalled_template'] 454s 454s Miscellaneous Arguments: 454s --quiet, -q Don't print status information. 454s --help, -h Print this help message and exit 454s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS 454s [FAST5_BASEDIRS ...] --motif MOTIF 454s --genome-fasta GENOME_FASTA 454s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 454s [--plot-standard-model] 454s [--plot-alternate-model {dcm,5mC,dam,CpG,6mA}] 454s [--overplot-threshold OVERPLOT_THRESHOLD] 454s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 454s [--num-regions NUM_REGIONS] 454s [--num-bases NUM_BASES] [--deepest-coverage] 454s [--pdf-filename PDF_FILENAME] 454s [--corrected-group CORRECTED_GROUP] 454s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 454s [--quiet] [--help] 454s 454s Required Arguments: 454s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 454s Directories containing fast5 files. 454s --motif MOTIF Motif of interest at which to plot signal and 454s statsitics. Supports IUPAC single letter codes (use T 454s for RNA). 454s --genome-fasta GENOME_FASTA 454s FASTA file used to re-squiggle. For faster sequence 454s access. 454s 454s Comparison Arguments: 454s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 454s Set of directories containing fast5 files for control 454s reads, containing only canonical nucleotides. 454s --plot-standard-model 454s Add default standard model distribution to the plot. 454s --plot-alternate-model {dcm,5mC,dam,CpG,6mA} 454s Add alternative model distribution to the plot. 454s 454s Overplotting Arguments: 454s --overplot-threshold OVERPLOT_THRESHOLD 454s Coverage level to trigger alternative plot type 454s instead of raw signal. Default: 50 454s --overplot-type {Downsample,Boxplot,Quantile,Density} 454s Plot type for regions with higher coverage. Default: 454s Downsample 454s 454s Plotting Region Arguments: 454s --num-regions NUM_REGIONS 454s Number of regions to plot. Default: 10 454s --num-bases NUM_BASES 454s Number of bases to plot/output. Default: 21 454s --deepest-coverage Plot the deepest coverage regions. 454s 454s Output Argument: 454s --pdf-filename PDF_FILENAME 454s PDF filename to store plot(s). Default: 454s tombo_results.motif_centered.pdf 454s 454s FAST5 Data Arguments: 454s --corrected-group CORRECTED_GROUP 454s FAST5 group created by resquiggle command. Default: 454s RawGenomeCorrected_000 454s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 454s FAST5 subgroup(s) (under /Analyses/[--basecall- 454s group]/) containing basecalls and created within 454s [--corrected-group] containing re-squiggle results. 454s Default: ['BaseCalled_template'] 454s 454s Miscellaneous Arguments: 454s --quiet, -q Don't print status information. 454s --help, -h Print this help message and exit 454s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS 454s [FAST5_BASEDIRS ...] --control-fast5-basedirs 454s CONTROL_FAST5_BASEDIRS 454s [CONTROL_FAST5_BASEDIRS ...] 454s [--overplot-threshold OVERPLOT_THRESHOLD] 454s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 454s [--num-regions NUM_REGIONS] 454s [--num-bases NUM_BASES] 454s [--pdf-filename PDF_FILENAME] 454s [--sequences-filename SEQUENCES_FILENAME] 454s [--corrected-group CORRECTED_GROUP] 454s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 454s [--quiet] [--help] 454s 454s Required Arguments: 454s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 454s Directories containing fast5 files. 454s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 454s Set of directories containing fast5 files for control 454s reads, containing only canonical nucleotides. 454s 454s Overplotting Arguments: 454s --overplot-threshold OVERPLOT_THRESHOLD 454s Coverage level to trigger alternative plot type 454s instead of raw signal. Default: 50 454s --overplot-type {Downsample,Boxplot,Quantile,Density} 454s Plot type for regions with higher coverage. Default: 454s Downsample 454s 454s Plotting Region Arguments: 454s --num-regions NUM_REGIONS 454s Number of regions to plot. Default: 10 454s --num-bases NUM_BASES 454s Number of bases to plot/output. Default: 21 454s 454s Output Arguments: 454s --pdf-filename PDF_FILENAME 454s PDF filename to store plot(s). Default: 454s tombo_results.max_difference.pdf 454s --sequences-filename SEQUENCES_FILENAME 454s File for sequences from selected regions. Sequences 454s will be stored in FASTA format. Default: None. 454s 454s FAST5 Data Arguments: 454s --corrected-group CORRECTED_GROUP 454s FAST5 group created by resquiggle command. Default: 454s RawGenomeCorrected_000 454s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 454s FAST5 subgroup(s) (under /Analyses/[--basecall- 454s group]/) containing basecalls and created within 454s [--corrected-group] containing re-squiggle results. 454s Default: ['BaseCalled_template'] 454s 454s Miscellaneous Arguments: 454s --quiet, -q Don't print status information. 454s --help, -h Print this help message and exit 454s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS 454s [FAST5_BASEDIRS ...] --statistics-filename 454s STATISTICS_FILENAME 454s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 454s [--plot-standard-model] 454s [--plot-alternate-model {CpG,6mA,5mC,dam,dcm}] 454s [--overplot-threshold OVERPLOT_THRESHOLD] 454s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 454s [--num-regions NUM_REGIONS] 454s [--num-bases NUM_BASES] 454s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 454s [--pdf-filename PDF_FILENAME] 454s [--sequences-filename SEQUENCES_FILENAME] 454s [--corrected-group CORRECTED_GROUP] 454s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 454s [--quiet] [--help] 454s 454s Required Arguments: 454s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 454s Directories containing fast5 files. 454s --statistics-filename STATISTICS_FILENAME 454s File to save/load genomic base anchored statistics. 454s 454s Comparison Arguments: 454s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 454s Set of directories containing fast5 files for control 454s reads, containing only canonical nucleotides. 454s --plot-standard-model 454s Add default standard model distribution to the plot. 454s --plot-alternate-model {CpG,6mA,5mC,dam,dcm} 454s Add alternative model distribution to the plot. 454s 454s Overplotting Arguments: 454s --overplot-threshold OVERPLOT_THRESHOLD 454s Coverage level to trigger alternative plot type 454s instead of raw signal. Default: 50 454s --overplot-type {Downsample,Boxplot,Quantile,Density} 454s Plot type for regions with higher coverage. Default: 454s Downsample 454s 454s Plotting Region Arguments: 454s --num-regions NUM_REGIONS 454s Number of regions to plot. Default: 10 454s --num-bases NUM_BASES 454s Number of bases to plot/output. Default: 21 454s 454s Statistical Argument: 454s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 454s Dampen fraction modified estimates for low coverage 454s sites. Two parameters are unmodified and modified 454s pseudo read counts. This is equivalent to a beta prior 454s on the fraction estimate. Set to "0 0" to disable 454s dampened fraction estimation. Default: [2, 0] 454s 454s Output Arguments: 454s --pdf-filename PDF_FILENAME 454s PDF filename to store plot(s). Default: 454s tombo_results.significant_difference.pdf 454s --sequences-filename SEQUENCES_FILENAME 454s File for sequences from selected regions. Sequences 454s will be stored in FASTA format. Default: None. 454s 454s FAST5 Data Arguments: 454s --corrected-group CORRECTED_GROUP 454s FAST5 group created by resquiggle command. Default: 454s RawGenomeCorrected_000 454s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 454s FAST5 subgroup(s) (under /Analyses/[--basecall- 454s group]/) containing basecalls and created within 454s [--corrected-group] containing re-squiggle results. 454s Default: ['BaseCalled_template'] 454s 454s Miscellaneous Arguments: 454s --quiet, -q Don't print status information. 454s --help, -h Print this help message and exit 454s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS 454s [FAST5_BASEDIRS ...] --motif MOTIF 454s --statistics-filename STATISTICS_FILENAME 454s --genome-fasta GENOME_FASTA 454s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 454s [--plot-standard-model] 454s [--plot-alternate-model {6mA,5mC,CpG,dam,dcm}] 454s [--overplot-threshold OVERPLOT_THRESHOLD] 454s [--num-regions NUM_REGIONS] 454s [--num-context NUM_CONTEXT] 454s [--num-statistics NUM_STATISTICS] 454s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 454s [--pdf-filename PDF_FILENAME] 454s [--corrected-group CORRECTED_GROUP] 454s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 454s [--quiet] [--help] 454s 454s Required Arguments: 454s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 454s Directories containing fast5 files. 454s --motif MOTIF Motif of interest at which to plot signal and 454s statsitics. Supports IUPAC single letter codes (use T 454s for RNA). 454s --statistics-filename STATISTICS_FILENAME 454s File to save/load genomic base anchored statistics. 454s --genome-fasta GENOME_FASTA 454s FASTA file used to re-squiggle. For faster sequence 454s access. 454s 454s Comparison Arguments: 454s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 454s Set of directories containing fast5 files for control 454s reads, containing only canonical nucleotides. 454s --plot-standard-model 454s Add default standard model distribution to the plot. 454s --plot-alternate-model {6mA,5mC,CpG,dam,dcm} 454s Add alternative model distribution to the plot. 454s 454s Overplotting Argument: 454s --overplot-threshold OVERPLOT_THRESHOLD 454s Coverage level to trigger alternative plot type 454s instead of raw signal. Default: 50 454s 454s Plotting Region Arguments: 454s --num-regions NUM_REGIONS 454s Number of regions to plot. Default: 3 454s --num-context NUM_CONTEXT 454s Number of context bases around motif. Default: 5 454s --num-statistics NUM_STATISTICS 454s Number of motif centered regions to include in 454s statistic distributions. Default: 200 454s 454s Statistical Argument: 454s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 454s Dampen fraction modified estimates for low coverage 454s sites. Two parameters are unmodified and modified 454s pseudo read counts. This is equivalent to a beta prior 454s on the fraction estimate. Set to "0 0" to disable 454s dampened fraction estimation. Default: [2, 0] 454s 454s Output Argument: 454s --pdf-filename PDF_FILENAME 454s PDF filename to store plot(s). Default: 454s tombo_results.motif_statistics.pdf 454s 454s FAST5 Data Arguments: 454s --corrected-group CORRECTED_GROUP 454s FAST5 group created by resquiggle command. Default: 454s RawGenomeCorrected_000 454s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 454s FAST5 subgroup(s) (under /Analyses/[--basecall- 454s group]/) containing basecalls and created within 454s [--corrected-group] containing re-squiggle results. 454s Default: ['BaseCalled_template'] 454s 454s Miscellaneous Arguments: 454s --quiet, -q Don't print status information. 454s --help, -h Print this help message and exit 455s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS 455s [GENOME_LOCATIONS ...] 455s --per-read-statistics-filename 455s PER_READ_STATISTICS_FILENAME 455s [--genome-fasta GENOME_FASTA] 455s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 455s [--num-reads NUM_READS] [--num-bases NUM_BASES] 455s [--box-center] [--pdf-filename PDF_FILENAME] 455s [--corrected-group CORRECTED_GROUP] 455s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 455s [--quiet] [--help] 455s 455s Required Arguments: 455s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 455s Genomic locations at which to plot signal. Format 455s locations as "chrm:position[:strand] 455s [chrm2:position2[:strand2] ...]" (strand not 455s applicable for all applications) 455s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 455s Binary file containing per-read statistics from 455s statistical testing. 455s 455s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 455s --genome-fasta GENOME_FASTA 455s FASTA file used to re-squiggle. For faster sequence 455s access. 455s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 455s Directories containing fast5 files. 455s 455s Plotting Region Arguments: 455s --num-reads NUM_READS 455s Number of reads to plot. Default: 100 455s --num-bases NUM_BASES 455s Number of bases to plot/output. Default: 51 455s --box-center Plot a box around the central base. 455s 455s Output Argument: 455s --pdf-filename PDF_FILENAME 455s PDF filename to store plot(s). Default: 455s tombo_results.per_read_stats.pdf 455s 455s FAST5 Data Arguments: 455s --corrected-group CORRECTED_GROUP 455s FAST5 group created by resquiggle command. Default: 455s RawGenomeCorrected_000 455s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 455s FAST5 subgroup(s) (under /Analyses/[--basecall- 455s group]/) containing basecalls and created within 455s [--corrected-group] containing re-squiggle results. 455s Default: ['BaseCalled_template'] 455s 455s Miscellaneous Arguments: 455s --quiet, -q Don't print status information. 455s --help, -h Print this help message and exit 455s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES 455s [STATISTICS_FILENAMES ...] 455s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 455s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 455s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 455s [--genome-fasta GENOME_FASTA] 455s [--pdf-filename PDF_FILENAME] 455s [--statistics-per-block STATISTICS_PER_BLOCK] 455s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 455s [--quiet] [--help] 455s 455s Required Argument: 455s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 455s Files to load genomic base anchored statistics. 455s 455s Ground Truth Arguments (provide bed files or motifs): 455s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 455s Modification description and bed format files 455s containing single base locations of ground truth 455s modified sites. Bed files should contain 6 fields 455s including strand. Format descriptions as 455s "mod_name:locs.bed". Example: "CpG 455s bisulfite":bisulfite_locs.bed 455s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 455s Bed format files containing single base locations of 455s ground truth unmodified sites. Bed files should 455s contain 6 fields including strand. 455s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 455s Ground truth, motif centered, modified base 455s descriptions for computing ROC and PR curves. Each 455s statistics file is associated with a set of motif 455s descriptions. Format descriptions as: 455s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 455s mod_pos indicates the alternate-base within the motif 455s (1-based index). Example: CCWGG:2:"dcm 455s 5mC"::GATC:2:"dam 6mA" would assess the performance of 455s a single Tombo statistics file for identification of 455s E. coli dam and dcm methylation. 455s --genome-fasta GENOME_FASTA 455s FASTA file used to re-squiggle. For faster sequence 455s access. 455s 455s Output Arguments: 455s --pdf-filename PDF_FILENAME 455s PDF filename to store plot(s). Default: 455s tombo_results.roc.pdf 455s 455s Down-sampling Arguments: 455s --statistics-per-block STATISTICS_PER_BLOCK 455s Number of randomly selected per-read, per-base 455s statistics to extract from each genomic block for 455s plotting. Default: Include all stats 455s --total-statistics-limit TOTAL_STATISTICS_LIMIT 455s Total per-read statistics to be extracted for 455s plotting. Avoids memory overflow for large runs. 455s Default: 5000000 455s 455s Miscellaneous Arguments: 455s --quiet, -q Don't print status information. 455s --help, -h Print this help message and exit 455s usage: tombo plot per_read_roc --per-read-statistics-filenames 455s PER_READ_STATISTICS_FILENAMES 455s [PER_READ_STATISTICS_FILENAMES ...] 455s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 455s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 455s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 455s [--genome-fasta GENOME_FASTA] 455s [--statistics-per-block STATISTICS_PER_BLOCK] 455s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 455s [--pdf-filename PDF_FILENAME] [--quiet] 455s [--help] 455s 455s Required Argument: 455s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 455s Binary files containing per-read statistics from 455s statistical testing. 455s 455s Ground Truth Arguments (provide bed files or motifs): 455s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 455s Modification description and bed format files 455s containing single base locations of ground truth 455s modified sites. Bed files should contain 6 fields 455s including strand. Format descriptions as 455s "mod_name:locs.bed". Example: "CpG 455s bisulfite":bisulfite_locs.bed 455s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 455s Bed format files containing single base locations of 455s ground truth unmodified sites. Bed files should 455s contain 6 fields including strand. 455s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 455s Ground truth, motif centered, modified base 455s descriptions for computing ROC and PR curves. Each 455s statistics file is associated with a set of motif 455s descriptions. Format descriptions as: 455s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 455s mod_pos indicates the alternate-base within the motif 455s (1-based index). Example: CCWGG:2:"dcm 455s 5mC"::GATC:2:"dam 6mA" would assess the performance of 455s a single Tombo statistics file for identification of 455s E. coli dam and dcm methylation. 455s --genome-fasta GENOME_FASTA 455s FASTA file used to re-squiggle. For faster sequence 455s access. 455s 455s Down-sampling Arguments: 455s --statistics-per-block STATISTICS_PER_BLOCK 455s Number of randomly selected per-read, per-base 455s statistics to extract from each genomic block for 455s plotting. Default: 100000 455s --total-statistics-limit TOTAL_STATISTICS_LIMIT 455s Total per-read statistics to be extracted for 455s plotting. Avoids memory overflow for large runs. 455s Default: 5000000 455s 455s Output Arguments: 455s --pdf-filename PDF_FILENAME 455s PDF filename to store plot(s). Default: 455s tombo_results.per_reads_roc.pdf 455s 455s Miscellaneous Arguments: 455s --quiet, -q Don't print status information. 455s --help, -h Print this help message and exit 455s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 455s [--upstream-bases {0,1,2,3,4}] 455s [--downstream-bases {0,1,2,3,4}] [--read-mean] 455s [--num-kmer-threshold NUM_KMER_THRESHOLD] 455s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 455s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 455s [--corrected-group CORRECTED_GROUP] 455s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 455s [--quiet] [--help] 455s 455s Required Argument: 455s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 455s Directories containing fast5 files. 455s 455s Data Processing Arguments: 455s --upstream-bases {0,1,2,3,4} 455s Upstream bases in k-mer. Default: 1 455s --downstream-bases {0,1,2,3,4} 455s Downstream bases in k-mer. Default: 2 455s --read-mean Plot k-mer means across whole reads as opposed to 455s individual k-mer event levels. 455s --num-kmer-threshold NUM_KMER_THRESHOLD 455s Observations of each k-mer required to include a read 455s in read level averages. Default: 1 455s 455s Plotting Region Arguments: 455s --num-reads NUM_READS 455s Number of reads to plot. Default: 100 455s 455s Output Arguments: 455s --pdf-filename PDF_FILENAME 455s PDF filename to store plot(s). Default: 455s tombo_results.kmer_distribution.pdf 455s --r-data-filename R_DATA_FILENAME 455s Filename to save R data structure. Default: Don't save 455s --dont-plot Don't plot result. Useful to produce only R data file. 455s 455s FAST5 Data Arguments: 455s --corrected-group CORRECTED_GROUP 455s FAST5 group created by resquiggle command. Default: 455s RawGenomeCorrected_000 455s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 455s FAST5 subgroup(s) (under /Analyses/[--basecall- 455s group]/) containing basecalls and created within 455s [--corrected-group] containing re-squiggle results. 455s Default: ['BaseCalled_template'] 455s 455s Miscellaneous Arguments: 455s --quiet, -q Don't print status information. 455s --help, -h Print this help message and exit 455s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS 455s [FAST5_BASEDIRS ...] 455s --control-fast5-basedirs 455s CONTROL_FAST5_BASEDIRS 455s [CONTROL_FAST5_BASEDIRS ...] 455s --statistics-filename 455s STATISTICS_FILENAME 455s [--genome-fasta GENOME_FASTA] 455s [--processes PROCESSES] 455s [--num-regions NUM_REGIONS] 455s [--num-bases NUM_BASES] 455s [--slide-span SLIDE_SPAN] 455s [--pdf-filename PDF_FILENAME] 455s [--r-data-filename R_DATA_FILENAME] 455s [--corrected-group CORRECTED_GROUP] 455s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 455s [--quiet] [--help] 455s 455s Required Arguments: 455s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 455s Directories containing fast5 files. 455s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 455s Set of directories containing fast5 files for control 455s reads, containing only canonical nucleotides. 455s --statistics-filename STATISTICS_FILENAME 455s File to save/load genomic base anchored statistics. 455s 455s FASTA Sequence Argument: 455s --genome-fasta GENOME_FASTA 455s FASTA file used to re-squiggle. For faster sequence 455s access. 455s 455s Multiprocessing Argument: 455s --processes PROCESSES 455s Number of processes. Default: 1 455s 455s Plotting Region Arguments: 455s --num-regions NUM_REGIONS 455s Number of regions to plot. Default: 10 455s --num-bases NUM_BASES 455s Number of bases to plot/output. Default: 21 455s --slide-span SLIDE_SPAN 455s Number of bases offset over which to search when 455s computing distances for signal cluster plotting. 455s Default: 0 (exact position) 455s 455s Output Arguments: 455s --pdf-filename PDF_FILENAME 455s PDF filename to store plot(s). Default: 455s tombo_results.signal_clusters.pdf 455s --r-data-filename R_DATA_FILENAME 455s Filename to save R data structure. Default: Don't save 455s 455s FAST5 Data Arguments: 455s --corrected-group CORRECTED_GROUP 455s FAST5 group created by resquiggle command. Default: 455s RawGenomeCorrected_000 455s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 455s FAST5 subgroup(s) (under /Analyses/[--basecall- 455s group]/) containing basecalls and created within 455s [--corrected-group] containing re-squiggle results. 455s Default: ['BaseCalled_template'] 455s 455s Miscellaneous Arguments: 455s --quiet, -q Don't print status information. 455s --help, -h Print this help message and exit 455s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 455s 455s Required Arguments: 455s fast5s_basedir Directory containing fast5 files. All files ending in 455s "fast5" found recursively within this base directory will be 455s processed. 455s 455s Miscellaneous Arguments: 455s --quiet, -q Don't print status information. 455s --help, -h Print this help message and exit 455s usage: tombo build_model event_resquiggle 455s [--minimap2-executable MINIMAP2_EXECUTABLE] 455s [--minimap2-index MINIMAP2_INDEX] 455s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 455s [--graphmap-executable GRAPHMAP_EXECUTABLE] 455s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 455s [--normalization-type {median,pA,pA_raw,none}] 455s [--pore-model-filename PORE_MODEL_FILENAME] 455s [--outlier-threshold OUTLIER_THRESHOLD] 455s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 455s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 455s [--timeout TIMEOUT] 455s [--cpts-limit CPTS_LIMIT] 455s [--skip-index] [--overwrite] 455s [--failed-reads-filename FAILED_READS_FILENAME] 455s [--include-event-stdev] 455s [--corrected-group CORRECTED_GROUP] 455s [--basecall-group BASECALL_GROUP] 455s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 455s [--processes PROCESSES] 455s [--align-processes ALIGN_PROCESSES] 455s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 455s [--resquiggle-processes RESQUIGGLE_PROCESSES] 455s [--quiet] [--help] 455s fast5s_basedir reference_fasta 455s 455s Required Arguments: 455s fast5s_basedir Directory containing fast5 files. All files ending in 455s "fast5" found recursively within this base directory 455s will be processed. 455s reference_fasta Reference genome/transcriptome FASTA file for mapping. 455s 455s Mapper Arguments (One mapper is required): 455s --minimap2-executable MINIMAP2_EXECUTABLE 455s Path to minimap2 executable. 455s --minimap2-index MINIMAP2_INDEX 455s Path to minimap2 index (with map-ont preset) file 455s corresponding to the [genome_fasta] provided. 455s --bwa-mem-executable BWA_MEM_EXECUTABLE 455s Path to bwa-mem executable. 455s --graphmap-executable GRAPHMAP_EXECUTABLE 455s Path to graphmap executable. 455s --alignment-batch-size ALIGNMENT_BATCH_SIZE 455s Number of reads included in each alignment call. Note: 455s A new system mapping call is made for each batch 455s (including loading of the genome), so it is advised to 455s use larger values for larger genomes. Default: 1000 455s 455s Signal Processing Arguments: 455s --normalization-type {median,pA,pA_raw,none} 455s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 455s as in the ONT events (using offset, range and 455s digitization), "pA": k-mer-based correction for pA 455s drift as in nanopolish (requires [--pore-model- 455s filename]), "median": median and MAD from raw signal. 455s Default: median 455s --pore-model-filename PORE_MODEL_FILENAME 455s File containing kmer model parameters (level_mean and 455s level_stdv) used in order to compute kmer-based 455s corrected pA values. E.g. https://github.com/jts/nanop 455s olish/blob/master/etc/r9- 455s models/template_median68pA.5mers.model 455s --outlier-threshold OUTLIER_THRESHOLD 455s Windosrize the signal at this number of scale values. 455s Negative value disables outlier clipping. Default: 455s 5.000000 455s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 455s Specify the 2 parameters for segmentation 1) running 455s neighboring windows width 2) minimum raw observations 455s per genomic base. Sample type defaults: RNA : 12 6 || 455s DNA : 5 3 455s 455s Read Filtering Arguments: 455s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 455s Filter reads based on observations per base percentile 455s thresholds. Format thresholds as "percentile:thresh 455s [pctl2:thresh2 ...]". For example to filter reads with 455s 99th pctl > 200 obs/base or max > 5k obs/base use 455s "99:200 100:5000". 455s --timeout TIMEOUT Timeout in seconds for processing a single read. 455s Default: No timeout. 455s --cpts-limit CPTS_LIMIT 455s Maximum number of changepoints to find within a single 455s indel group. Default: No limit. 455s 455s Input/Output Arguments: 455s --skip-index Skip creation of tombo index. This drastically slows 455s downstream tombo commands. Default stores tombo index 455s named ".[--fast5-basedir].[--corrected- 455s group].tombo.index" to be loaded automatically for 455s downstream commands. 455s --overwrite Overwrite previous corrected group in FAST5 files. 455s Note: only effects --corrected-group or --new- 455s corrected-group. 455s --failed-reads-filename FAILED_READS_FILENAME 455s Output failed read filenames with assoicated error. 455s Default: Do not store failed reads. 455s --include-event-stdev 455s Include corrected event standard deviation in output 455s FAST5 data. 455s 455s FAST5 Data Arguments: 455s --corrected-group CORRECTED_GROUP 455s FAST5 group created by resquiggle command. Default: 455s RawGenomeCorrected_000 455s --basecall-group BASECALL_GROUP 455s FAST5 group obtain original basecalls (under Analyses 455s group). Default: Basecall_1D_000 455s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 455s FAST5 subgroup(s) (under /Analyses/[--basecall- 455s group]/) containing basecalls and created within 455s [--corrected-group] containing re-squiggle results. 455s Default: ['BaseCalled_template'] 455s 455s Multiprocessing Arguments: 455s --processes PROCESSES 455s Number of processes. Default: 2 455s --align-processes ALIGN_PROCESSES 455s Number of processes to use for parsing and aligning 455s original basecalls. Each process will independently 455s load the genome into memory, so use caution with 455s larger genomes (e.g. human). Default: 1 455s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 455s Number of threads to use for aligner system call. 455s Default: [--processes] / (2 * [--align-processes)] 455s --resquiggle-processes RESQUIGGLE_PROCESSES 455s Number of processes to use for resquiggle algorithm. 455s Default: [--processes] / 2 455s 455s Miscellaneous Arguments: 455s --quiet, -q Don't print status information. 455s --help, -h Print this help message and exit 455s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS 455s [FAST5_BASEDIRS ...] 455s --tombo-model-filename 455s TOMBO_MODEL_FILENAME 455s [--estimate-mean] 455s [--kmer-specific-sd] 455s [--upstream-bases {0,1,2,3,4}] 455s [--downstream-bases {0,1,2,3,4}] 455s [--minimum-test-reads MINIMUM_TEST_READS] 455s [--coverage-threshold COVERAGE_THRESHOLD] 455s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 455s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 455s [--processes PROCESSES] 455s [--corrected-group CORRECTED_GROUP] 455s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 455s [--quiet] [--help] 455s 455s Required Arguments: 455s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 455s Directories containing fast5 files. 455s --tombo-model-filename TOMBO_MODEL_FILENAME 455s Filename to save Tombo model. 455s 455s Modeling Arguments: 455s --estimate-mean Use the mean instead of median for model level 455s estimation. Note: This can cause poor fits due to 455s outliers 455s --kmer-specific-sd Estimate standard deviation for each k-mers 455s individually. 455s --upstream-bases {0,1,2,3,4} 455s Upstream bases in k-mer. Default: 1 455s --downstream-bases {0,1,2,3,4} 455s Downstream bases in k-mer. Default: 2 455s 455s Filtering Arguments: 455s --minimum-test-reads MINIMUM_TEST_READS 455s Number of reads required at a position to perform 455s significance testing or contribute to model 455s estimation. Default: 10 455s --coverage-threshold COVERAGE_THRESHOLD 455s Maximum mean coverage per region when estimating k-mer 455s model (limits compute time for deep samples). Default: 455s 100 455s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 455s Number of each k-mer observations required in order to 455s produce a reference (genomic locations for standard 455s reference and per-read for alternative reference). 455s Default: 5 455s 455s Multiprocessing Arguments: 455s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 455s Size of regions over which to multiprocesses statistic 455s computation. For very deep samples a smaller value is 455s recommmended in order to control memory consumption. 455s Default: 10000 455s --processes PROCESSES 455s Number of processes. Default: 1 455s 455s FAST5 Data Arguments: 455s --corrected-group CORRECTED_GROUP 455s FAST5 group created by resquiggle command. Default: 455s RawGenomeCorrected_000 455s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 455s FAST5 subgroup(s) (under /Analyses/[--basecall- 455s group]/) containing basecalls and created within 455s [--corrected-group] containing re-squiggle results. 455s Default: ['BaseCalled_template'] 455s 455s Miscellaneous Arguments: 455s --quiet, -q Don't print status information. 455s --help, -h Print this help message and exit 455s usage: tombo build_model estimate_alt_reference --alternate-model-filename 455s ALTERNATE_MODEL_FILENAME 455s --alternate-model-name 455s ALTERNATE_MODEL_NAME 455s --alternate-model-base 455s {A,C,G,T} 455s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 455s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 455s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 455s [--control-density-filename CONTROL_DENSITY_FILENAME] 455s [--dna] [--rna] 455s [--tombo-model-filename TOMBO_MODEL_FILENAME] 455s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 455s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 455s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 455s [--save-density-basename SAVE_DENSITY_BASENAME] 455s [--processes PROCESSES] 455s [--corrected-group CORRECTED_GROUP] 455s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 455s [--quiet] [--help] 455s 455s Required Arguments: 455s --alternate-model-filename ALTERNATE_MODEL_FILENAME 455s Tombo model for alternative likelihood ratio 455s significance testing. 455s --alternate-model-name ALTERNATE_MODEL_NAME 455s A short name to associate with this alternate model 455s (e.g. 5mC, 6mA, etc.). This text will be included in 455s output filenames when this model is used for testing. 455s --alternate-model-base {A,C,G,T} 455s Non-standard base is an alternative to this base. 455s 455s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 455s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 455s Directories containing fast5 files. 455s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 455s Set of directories containing fast5 files for control 455s reads, containing only canonical nucleotides. 455s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 455s File containing k-mer level kernel density estimates 455s for the alternative sample saved using --save-density- 455s basename. 455s --control-density-filename CONTROL_DENSITY_FILENAME 455s File containing k-mer level kernel density estimates 455s for the control sample saved using --save-density- 455s basename. 455s 455s Standard Model Arguments: 455s --dna Explicitly select canonical DNA model. Default: 455s Automatically determine from FAST5s 455s --rna Explicitly select canonical RNA model. Default: 455s Automatically determine from FAST5s 455s --tombo-model-filename TOMBO_MODEL_FILENAME 455s Tombo model filename. If no file is provided, the 455s default DNA or RNA Tombo model will be used. 455s 455s Model Fitting Arguments: 455s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 455s When esitmating the alternative base incorporation 455s rate, this percent of k-mers are assumed to have 455s significantly shifted signal so the alternative 455s distribution minimally overlaps the standard base 455s distribution. Default: 5.000000 455s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 455s Bandwidth applied when performing Gaussian kernal 455s density esitmation on standard and alternative base 455s signal distributions. Default: 0.050000 455s 455s Filtering Argument: 455s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 455s Number of each k-mer observations required in order to 455s produce a reference (genomic locations for standard 455s reference and per-read for alternative reference). 455s Default: 1000 455s 455s Output Argument: 455s --save-density-basename SAVE_DENSITY_BASENAME 455s Basename to save alternative model estimation density 455s estimation information. See scripts/debug_est_alt.R 455s for info use example. Default: Don't save. 455s 455s Multiprocessing Arguments: 455s --processes PROCESSES 455s Number of processes. Default: 1 455s 455s FAST5 Data Arguments: 455s --corrected-group CORRECTED_GROUP 455s FAST5 group created by resquiggle command. Default: 455s RawGenomeCorrected_000 455s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 455s FAST5 subgroup(s) (under /Analyses/[--basecall- 455s group]/) containing basecalls and created within 455s [--corrected-group] containing re-squiggle results. 455s Default: ['BaseCalled_template'] 455s 455s Miscellaneous Arguments: 455s --quiet, -q Don't print status information. 455s --help, -h Print this help message and exit 455s This test only tests the help system 455s There is an extensive test in 455s 455s tombo/tests/shell_tests.sh 455s 455s but this requires to download larger data 455s sets which is not done for the moment. 456s autopkgtest [22:01:10]: test run-unit-test: -----------------------] 457s autopkgtest [22:01:11]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 457s run-unit-test PASS 457s autopkgtest [22:01:11]: @@@@@@@@@@@@@@@@@@@@ summary 457s run-unit-test PASS 477s Creating nova instance adt-noble-arm64-tombo-20240313-215334-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240313.img (UUID 363cdc04-8630-403e-ac93-f1c7b1a75157)...