0s autopkgtest [17:08:14]: starting date and time: 2025-03-15 17:08:14+0000 0s autopkgtest [17:08:14]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:08:14]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.op1m1cwv/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-15.secgroup --name adt-plucky-arm64-tombo-20250315-170814-juju-7f2275-prod-proposed-migration-environment-20-ba8dad15-1bc4-41d3-9a8c-bc02925a727b --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 185s autopkgtest [17:11:19]: testbed dpkg architecture: arm64 185s autopkgtest [17:11:19]: testbed apt version: 2.9.33 186s autopkgtest [17:11:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 186s autopkgtest [17:11:20]: testbed release detected to be: None 187s autopkgtest [17:11:21]: updating testbed package index (apt update) 188s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 188s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 188s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 188s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 188s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 188s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 188s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 189s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 189s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 189s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 189s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 189s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 189s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 189s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 190s Fetched 1078 kB in 2s (557 kB/s) 190s Reading package lists... 191s Reading package lists... 191s Building dependency tree... 191s Reading state information... 192s Calculating upgrade... 192s Calculating upgrade... 192s The following packages will be upgraded: 192s pinentry-curses python3-jinja2 strace 193s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 193s Need to get 647 kB of archives. 193s After this operation, 11.3 kB of additional disk space will be used. 193s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 193s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 193s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 195s Fetched 647 kB in 1s (583 kB/s) 195s (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 ... 117701 files and directories currently installed.) 195s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 195s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 195s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 195s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 195s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 195s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 195s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 195s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 195s Setting up strace (6.13+ds-1ubuntu1) ... 195s Processing triggers for man-db (2.13.0-1) ... 196s Reading package lists... 197s Building dependency tree... 197s Reading state information... 198s Solving dependencies... 199s The following packages will be REMOVED: 199s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 199s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 199s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 199s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 199s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 199s After this operation, 267 MB disk space will be freed. 199s (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 ... 117701 files and directories currently installed.) 199s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 199s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 199s Removing libpython3.12t64:arm64 (3.12.9-1) ... 199s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 200s Removing libnsl2:arm64 (1.3.0-3build3) ... 200s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 200s Removing libunwind8:arm64 (1.6.2-3.1) ... 200s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 200s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 202s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 202s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 202s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 202s /etc/kernel/postrm.d/initramfs-tools: 202s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 203s /etc/kernel/postrm.d/zz-flash-kernel: 203s flash-kernel: Kernel 6.11.0-8-generic has been removed. 203s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 203s /etc/kernel/postrm.d/zz-update-grub: 203s Sourcing file `/etc/default/grub' 203s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 203s Generating grub configuration file ... 203s Found linux image: /boot/vmlinuz-6.14.0-10-generic 203s Found initrd image: /boot/initrd.img-6.14.0-10-generic 203s Warning: os-prober will not be executed to detect other bootable partitions. 203s Systems on them will not be added to the GRUB boot configuration. 203s Check GRUB_DISABLE_OS_PROBER documentation entry. 203s Adding boot menu entry for UEFI Firmware Settings ... 204s done 204s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 204s Processing triggers for libc-bin (2.41-1ubuntu1) ... 204s (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 ... 81650 files and directories currently installed.) 204s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 204s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 204s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 204s autopkgtest [17:11:38]: upgrading testbed (apt dist-upgrade and autopurge) 204s Reading package lists... 205s Building dependency tree... 205s Reading state information... 205s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 206s Starting 2 pkgProblemResolver with broken count: 0 206s Done 207s Entering ResolveByKeep 207s 207s Calculating upgrade... 208s The following packages will be upgraded: 208s libc-bin libc-dev-bin libc6 libc6-dev locales 208s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 208s Need to get 9530 kB of archives. 208s After this operation, 0 B of additional disk space will be used. 208s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 210s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 210s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 214s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 214s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 220s Preconfiguring packages ... 220s Fetched 9530 kB in 12s (780 kB/s) 220s (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 ... 81647 files and directories currently installed.) 220s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 220s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 221s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 221s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 221s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 221s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 221s Setting up libc6:arm64 (2.41-1ubuntu2) ... 221s (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 ... 81647 files and directories currently installed.) 221s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 221s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 221s Setting up libc-bin (2.41-1ubuntu2) ... 221s (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 ... 81647 files and directories currently installed.) 221s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 221s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 222s Setting up locales (2.41-1ubuntu2) ... 222s Generating locales (this might take a while)... 225s en_US.UTF-8... done 225s Generation complete. 225s Setting up libc-dev-bin (2.41-1ubuntu2) ... 225s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 225s Processing triggers for man-db (2.13.0-1) ... 226s Processing triggers for systemd (257.3-1ubuntu3) ... 227s Reading package lists... 227s Building dependency tree... 227s Reading state information... 227s Starting pkgProblemResolver with broken count: 0 227s Starting 2 pkgProblemResolver with broken count: 0 227s Done 228s Solving dependencies... 228s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 228s autopkgtest [17:12:02]: rebooting testbed after setup commands that affected boot 251s autopkgtest [17:12:25]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 254s autopkgtest [17:12:28]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo 280s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build2 (dsc) [2291 B] 280s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build2 (tar) [22.3 MB] 280s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tombo 1.5.1-7build2 (diff) [9628 B] 280s gpgv: Signature made Tue Mar 4 15:27:30 2025 UTC 280s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 280s gpgv: Can't check signature: No public key 280s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7build2.dsc: no acceptable signature found 281s autopkgtest [17:12:55]: testing package tombo version 1.5.1-7build2 281s autopkgtest [17:12:55]: build not needed 283s autopkgtest [17:12:57]: test run-unit-test: preparing testbed 283s Reading package lists... 283s Building dependency tree... 283s Reading state information... 283s Starting pkgProblemResolver with broken count: 0 283s Starting 2 pkgProblemResolver with broken count: 0 283s Done 284s The following NEW packages will be installed: 284s fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5 284s libhdf5-310 libhdf5-hl-310 libjs-jquery libjs-mathjax libjs-sphinxdoc 284s libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 python3-decorator 284s python3-h5py python3-h5py-serial python3-mappy python3-numpy 284s python3-numpy-dev python3-packaging python3-scipy python3-tqdm 284s sphinx-rtd-theme-common tombo tombo-doc 284s 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded. 284s Need to get 61.5 MB of archives. 284s After this operation, 198 MB of additional disk space will be used. 284s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB] 288s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 288s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 288s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 288s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 291s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 295s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 296s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 298s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 298s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 298s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 300s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 300s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 300s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 300s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.9 kB] 300s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 301s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 301s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 301s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.13.0-1 [1126 kB] 302s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.13.0-1 [7978 B] 302s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mappy arm64 2.27+dfsg-1build2 [171 kB] 302s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 302s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.1-2 [92.5 kB] 302s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 303s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu2 [16.7 MB] 321s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 tombo arm64 1.5.1-7build2 [455 kB] 322s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 328s Get:28 http://ftpmaster.internal/ubuntu plucky/universe arm64 tombo-doc all 1.5.1-7build2 [21.7 MB] 351s Fetched 61.5 MB in 1min 6s (932 kB/s) 351s Selecting previously unselected package fonts-lato. 351s (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 ... 81647 files and directories currently installed.) 351s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 351s Unpacking fonts-lato (2.015-1) ... 351s Selecting previously unselected package python3-numpy-dev:arm64. 351s Preparing to unpack .../01-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 351s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 351s Selecting previously unselected package libblas3:arm64. 351s Preparing to unpack .../02-libblas3_3.12.1-2_arm64.deb ... 351s Unpacking libblas3:arm64 (3.12.1-2) ... 351s Selecting previously unselected package libgfortran5:arm64. 351s Preparing to unpack .../03-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 351s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 351s Selecting previously unselected package liblapack3:arm64. 351s Preparing to unpack .../04-liblapack3_3.12.1-2_arm64.deb ... 351s Unpacking liblapack3:arm64 (3.12.1-2) ... 351s Selecting previously unselected package python3-numpy. 351s Preparing to unpack .../05-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 351s Unpacking python3-numpy (1:2.2.3+ds-5) ... 352s Selecting previously unselected package fonts-font-awesome. 352s Preparing to unpack .../06-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 352s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 352s Selecting previously unselected package fonts-mathjax. 352s Preparing to unpack .../07-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 352s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 352s Selecting previously unselected package libaec0:arm64. 352s Preparing to unpack .../08-libaec0_1.1.3-1_arm64.deb ... 352s Unpacking libaec0:arm64 (1.1.3-1) ... 352s Selecting previously unselected package libsz2:arm64. 352s Preparing to unpack .../09-libsz2_1.1.3-1_arm64.deb ... 352s Unpacking libsz2:arm64 (1.1.3-1) ... 352s Selecting previously unselected package libhdf5-310:arm64. 352s Preparing to unpack .../10-libhdf5-310_1.14.5+repack-3_arm64.deb ... 352s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 352s Selecting previously unselected package libhdf5-hl-310:arm64. 352s Preparing to unpack .../11-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... 352s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 352s Selecting previously unselected package libjs-jquery. 352s Preparing to unpack .../12-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 352s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 352s Selecting previously unselected package libjs-underscore. 352s Preparing to unpack .../13-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 352s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 352s Selecting previously unselected package libjs-sphinxdoc. 352s Preparing to unpack .../14-libjs-sphinxdoc_8.1.3-4_all.deb ... 352s Unpacking libjs-sphinxdoc (8.1.3-4) ... 352s Selecting previously unselected package liblbfgsb0:arm64. 352s Preparing to unpack .../15-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 352s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 352s Selecting previously unselected package liblzf1:arm64. 352s Preparing to unpack .../16-liblzf1_3.6-4_arm64.deb ... 352s Unpacking liblzf1:arm64 (3.6-4) ... 352s Selecting previously unselected package python3-decorator. 352s Preparing to unpack .../17-python3-decorator_5.1.1-5_all.deb ... 352s Unpacking python3-decorator (5.1.1-5) ... 352s Selecting previously unselected package python3-h5py-serial. 352s Preparing to unpack .../18-python3-h5py-serial_3.13.0-1_arm64.deb ... 352s Unpacking python3-h5py-serial (3.13.0-1) ... 352s Selecting previously unselected package python3-h5py. 352s Preparing to unpack .../19-python3-h5py_3.13.0-1_all.deb ... 352s Unpacking python3-h5py (3.13.0-1) ... 352s Selecting previously unselected package python3-mappy. 352s Preparing to unpack .../20-python3-mappy_2.27+dfsg-1build2_arm64.deb ... 353s Unpacking python3-mappy (2.27+dfsg-1build2) ... 353s Selecting previously unselected package python3-packaging. 353s Preparing to unpack .../21-python3-packaging_24.2-1_all.deb ... 353s Unpacking python3-packaging (24.2-1) ... 353s Selecting previously unselected package python3-tqdm. 353s Preparing to unpack .../22-python3-tqdm_4.67.1-2_all.deb ... 353s Unpacking python3-tqdm (4.67.1-2) ... 353s Selecting previously unselected package sphinx-rtd-theme-common. 353s Preparing to unpack .../23-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 353s Unpacking sphinx-rtd-theme-common 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Setting up python3-numpy (1:2.2.3+ds-5) ... 356s Setting up libjs-sphinxdoc (8.1.3-4) ... 356s Setting up tombo-doc (1.5.1-7build2) ... 356s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... 356s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 356s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 356s Setting up python3-scipy (1.14.1-4ubuntu2) ... 360s Setting up python3-h5py-serial (3.13.0-1) ... 360s Setting up python3-h5py (3.13.0-1) ... 360s Setting up tombo (1.5.1-7build2) ... 360s Processing triggers for man-db (2.13.0-1) ... 361s Processing triggers for libc-bin (2.41-1ubuntu2) ... 362s autopkgtest [17:14:16]: test run-unit-test: [----------------------- 362s ********* Testing help commands ********** 362s usage: tombo [-h] [-v] 362s {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot} ... 362s 362s ********** Tombo ********* 362s 362s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. 362s 362s Tombo also provides tools for the analysis and visualization of raw nanopore signal. 362s 362s Tombo command groups (additional help available within each command group): 362s resquiggle Re-annotate raw signal with genomic alignment from existing basecalls. 362s preprocess Pre-process nanopore reads for Tombo processing. 362s filter Apply filter to Tombo index file for specified criterion. 362s detect_modifications Perform statistical testing to detect non-standard nucleotides. 362s text_output Output Tombo results in text files. 362s build_model Create canonical and alternative base Tombo models. 362s plot Save plots to visualize raw nanopore signal or testing results. 362s 362s options: 362s -h, --help show this help message and exit 362s -v, --version show Tombo version and exit. 363s usage: tombo resquiggle [--dna] [--rna] 363s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 363s [--q-score Q_SCORE] 363s [--signal-matching-score SIGNAL_MATCHING_SCORE] 363s [--processes PROCESSES] 363s [--corrected-group CORRECTED_GROUP] 363s [--basecall-group BASECALL_GROUP] 363s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 363s [--overwrite] 363s [--failed-reads-filename FAILED_READS_FILENAME] 363s [--num-most-common-errors NUM_MOST_COMMON_ERRORS] 363s [--print-advanced-arguments] [--quiet] [--help] 363s fast5s_basedir reference 363s 363s Required Arguments: 363s fast5s_basedir Directory containing fast5 files. All files ending in 363s "fast5" found recursively within this base directory 363s will be processed. 363s reference Reference genome/transcriptome FASTA file or minimap2 363s index (with "map-ont" preset) for mapping. 363s 363s Model Parameters: 363s --dna Explicitly select canonical DNA model. Default: 363s Automatically determine from FAST5s 363s --rna Explicitly select canonical RNA model. Default: 363s Automatically determine from FAST5s 363s 363s Read Filtering Argument: 363s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 363s Filter reads based on observations per base percentile 363s thresholds. Format thresholds as "percentile:thresh 363s [pctl2:thresh2 ...]". For example to filter reads with 363s 99th pctl > 200 obs/base or max > 5k obs/base use 363s "99:200 100:5000". 363s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 363s Default: 0.000000 363s --signal-matching-score SIGNAL_MATCHING_SCORE 363s Observed to expected signal matching score (higher 363s score indicates poor matching). Sample type defaults: 363s RNA : 2 || DNA : 1.1 363s 363s Multiprocessing Arguments: 363s --processes PROCESSES 363s Number of processes. Default: 1 363s 363s FAST5 Data Arguments: 363s --corrected-group CORRECTED_GROUP 363s FAST5 group created by resquiggle command. Default: 363s RawGenomeCorrected_000 363s --basecall-group BASECALL_GROUP 363s FAST5 group obtain original basecalls (under Analyses 363s group). Default: Basecall_1D_000 363s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 363s FAST5 subgroup(s) (under /Analyses/[--basecall- 363s group]/) containing basecalls and created within 363s [--corrected-group] containing re-squiggle results. 363s Default: ['BaseCalled_template'] 363s --overwrite Overwrite previous corrected group in FAST5 files. 363s Note: only effects --corrected-group or --new- 363s corrected-group. 363s 363s Input/Output Arguments: 363s --failed-reads-filename FAILED_READS_FILENAME 363s Output failed read filenames with assoicated error. 363s Default: Do not store failed reads. 363s --num-most-common-errors NUM_MOST_COMMON_ERRORS 363s Dynamically show this many most common errors so far 363s through run. Default: 0; Just show progress 363s 363s Advanced Arguments: 363s --print-advanced-arguments 363s Print advanced re-squiggle arguments and exit. 363s 363s Miscellaneous Arguments: 363s --quiet, -q Don't print status information. 363s --help, -h Print this help message and exit 363s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR 363s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 363s [--basecall-group BASECALL_GROUP] 363s [--basecall-subgroup BASECALL_SUBGROUP] 363s [--overwrite] 363s [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]] 363s [--processes PROCESSES] 363s [--quiet] [--help] 363s 363s Required Arguments: 363s --fast5-basedir FAST5_BASEDIR 363s Directory containing fast5 files. 363s --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...] 363s FASTQ filenames containing basecalls to be added to 363s raw FAST5 files. 363s 363s FAST5 Data Arguments: 363s --basecall-group BASECALL_GROUP 363s FAST5 group obtain original basecalls (under Analyses 363s group). Default: Basecall_1D_000 363s --basecall-subgroup BASECALL_SUBGROUP 363s FAST5 subgroup (under /Analyses/[--basecall-group]/) 363s under which to store basecalls from FASTQs. Default: 363s BaseCalled_template 363s --overwrite Overwrite previous corrected group in FAST5 files. 363s Note: only effects --corrected-group or --new- 363s corrected-group. 363s 363s Sequencing Summary Argument: 363s --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...] 363s Sequencing summary filenames produced by albacore. 363s These can make annotation of raw FAST5 files with 363s FASTQ sequence much faster. 363s 363s Multiprocessing Argument: 363s --processes PROCESSES 363s Number of processes. Default: 1 363s 363s Miscellaneous Arguments: 363s --quiet, -q Don't print status information. 363s --help, -h Print this help message and exit 363s usage: tombo filter clear_filters 363s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s [--corrected-group CORRECTED_GROUP] 363s [--quiet] [--help] 363s 363s Required Argument: 363s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s Directories containing fast5 files. 363s 363s FAST5 Data Argument: 363s --corrected-group CORRECTED_GROUP 363s FAST5 group created by resquiggle command. Default: 363s RawGenomeCorrected_000 363s 363s Miscellaneous Arguments: 363s --quiet, -q Don't print status information. 363s --help, -h Print this help message and exit 363s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 363s [--corrected-group CORRECTED_GROUP] [--quiet] 363s [--help] 363s 363s Required Argument: 363s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s Directories containing fast5 files. 363s 363s Read Filtering Argument: 363s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 363s Filter reads based on observations per base percentile 363s thresholds. Format thresholds as "percentile:thresh 363s [pctl2:thresh2 ...]". For example to filter reads with 363s 99th pctl > 200 obs/base or max > 5k obs/base use 363s "99:200 100:5000". 363s 363s FAST5 Data Argument: 363s --corrected-group CORRECTED_GROUP 363s FAST5 group created by resquiggle command. Default: 363s RawGenomeCorrected_000 363s 363s Miscellaneous Arguments: 363s --quiet, -q Don't print status information. 363s --help, -h Print this help message and exit 363s usage: tombo filter level_coverage 363s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s [--percent-to-filter PERCENT_TO_FILTER] 363s [--corrected-group CORRECTED_GROUP] 363s [--quiet] [--help] 363s 363s Required Arguments: 363s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s Directories containing fast5 files. 363s 363s Read Filtering Argument: 363s --percent-to-filter PERCENT_TO_FILTER 363s Percentage of all reads to filter. Reads are randomly 363s selected weighted according to the approximate 363s coverage at the mapped genomic location. This can be 363s useful in modeling and testing. Default: 10.000000 363s 363s FAST5 Data Arguments: 363s --corrected-group CORRECTED_GROUP 363s FAST5 group created by resquiggle command. Default: 363s RawGenomeCorrected_000 363s 363s Miscellaneous Arguments: 363s --quiet, -q Don't print status information. 363s --help, -h Print this help message and exit 363s usage: tombo filter q_score 363s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s [--q-score Q_SCORE] 363s [--corrected-group CORRECTED_GROUP] 363s [--basecall-group BASECALL_GROUP] [--quiet] 363s [--help] 363s 363s Required Arguments: 363s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s Directories containing fast5 files. 363s 363s Read Filtering Argument: 363s --q-score Q_SCORE Q-score threshold for filtering low quality reads. 363s Default: 7.000000 363s 363s FAST5 Data Arguments: 363s --corrected-group CORRECTED_GROUP 363s FAST5 group created by resquiggle command. Default: 363s RawGenomeCorrected_000 363s --basecall-group BASECALL_GROUP 363s FAST5 group obtain original basecalls (under Analyses 363s group). Default: Basecall_1D_000 363s 363s Miscellaneous Arguments: 363s --quiet, -q Don't print status information. 363s --help, -h Print this help message and exit 363s usage: tombo filter raw_signal_matching 363s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s --signal-matching-score SIGNAL_MATCHING_SCORE 363s [--corrected-group CORRECTED_GROUP] 363s [--quiet] [--help] 363s 363s Required Arguments: 363s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s Directories containing fast5 files. 363s --signal-matching-score SIGNAL_MATCHING_SCORE 363s Observed to expected signal matching score (higher 363s score indicates poor matching). Sample type defaults: 363s RNA : 2 || DNA : 1.1 363s 363s FAST5 Data Arguments: 363s --corrected-group CORRECTED_GROUP 363s FAST5 group created by resquiggle command. Default: 363s RawGenomeCorrected_000 363s 363s Miscellaneous Arguments: 363s --quiet, -q Don't print status information. 363s --help, -h Print this help message and exit 363s usage: tombo filter genome_locations 363s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]] 363s [--include-partial-overlap] 363s [--corrected-group CORRECTED_GROUP] 363s [--quiet] [--help] 363s 363s Required Arguments: 363s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s Directories containing fast5 files. 363s --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...] 363s Filter out reads not falling completely within include 363s regions. Omit start and end coordinates to include an 363s entire chromosome/sequence record. Format regions as 363s "chrm[:start-end] [chrm2[:start2-end2] ...]". 363s 363s Filter Argument: 363s --include-partial-overlap 363s Include reads that partially overlap the specified 363s region. Default: Only include reads completely 363s contained in a specified region 363s 363s FAST5 Data Argument: 363s --corrected-group CORRECTED_GROUP 363s FAST5 group created by resquiggle command. Default: 363s RawGenomeCorrected_000 363s 363s Miscellaneous Arguments: 363s --quiet, -q Don't print status information. 363s --help, -h Print this help message and exit 363s usage: tombo detect_modifications de_novo 363s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s --statistics-file-basename STATISTICS_FILE_BASENAME 363s [--dna] [--rna] 363s [--fishers-method-context FISHERS_METHOD_CONTEXT] 363s [--minimum-test-reads MINIMUM_TEST_READS] 363s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 363s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 363s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 363s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 363s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 363s [--processes PROCESSES] 363s [--corrected-group CORRECTED_GROUP] 363s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 363s [--quiet] [--help] 363s 363s Required Argument: 363s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s Directories containing fast5 files. 363s --statistics-file-basename STATISTICS_FILE_BASENAME 363s File base name to save base by base statistics from 363s testing. Filenames will be [--statistics-file- 363s basename].[--alternate-bases]?.tombo.stats 363s 363s Comparison Model Arguments: 363s --dna Explicitly select canonical DNA model. Default: 363s Automatically determine from FAST5s 363s --rna Explicitly select canonical RNA model. Default: 363s Automatically determine from FAST5s 363s 363s Significance Test Arguments: 363s --fishers-method-context FISHERS_METHOD_CONTEXT 363s Number of context bases up and downstream over which 363s to compute Fisher's method combined p-values. Note: 363s Not applicable for alternative model likelihood ratio 363s tests. Default: 1. 363s --minimum-test-reads MINIMUM_TEST_READS 363s Number of reads required at a position to perform 363s significance testing or contribute to model 363s estimation. Default: 1 363s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 363s P-value threshold when computing fraction of 363s significant reads at each genomic position. If two 363s values are provided, statistics between these values 363s are not considered. Default thresholds: DNA:0.15-0.5 , 363s RNA:0.05-0.4 363s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 363s Dampen fraction modified estimates for low coverage 363s sites. Two parameters are unmodified and modified 363s pseudo read counts. This is equivalent to a beta prior 363s on the fraction estimate. Set to "0 0" to disable 363s dampened fraction estimation. Default: [2, 0] 363s 363s Output Argument: 363s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 363s Base for binary files containing per-read statistics 363s from statistical testing. Filenames will be [--per- 363s read-statistics-basename].[--alternate- 363s bases]?.tombo.per_read_stats 363s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 363s Number of the most significant sites to store for 363s faster access. If a longer list of most significant 363s sites is required the list must be re-computed from 363s all batches. Very large values can increase RAM usage. 363s Default: 100000 363s 363s Multiprocessing Arguments: 363s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 363s Size of regions over which to multiprocesses statistic 363s computation. For very deep samples a smaller value is 363s recommmended in order to control memory consumption. 363s Default: 10000 363s --processes PROCESSES 363s Number of processes. Default: 1 363s 363s FAST5 Data Arguments: 363s --corrected-group CORRECTED_GROUP 363s FAST5 group created by resquiggle command. Default: 363s RawGenomeCorrected_000 363s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 363s FAST5 subgroup(s) (under /Analyses/[--basecall- 363s group]/) containing basecalls and created within 363s [--corrected-group] containing re-squiggle results. 363s Default: ['BaseCalled_template'] 363s 363s Miscellaneous Arguments: 363s --quiet, -q Don't print status information. 363s --help, -h Print this help message and exit 363s usage: tombo detect_modifications alternative_model 363s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 363s [--statistics-file-basename STATISTICS_FILE_BASENAME] 363s [--alternate-bases {CpG,dam,6mA,5mC,dcm} [{CpG,dam,6mA,5mC,dcm} ...]] 363s [--print-available-models] 363s [--dna] [--rna] 363s [--minimum-test-reads MINIMUM_TEST_READS] 363s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 363s [--standard-log-likelihood-ratio] 363s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 363s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 363s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 363s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 363s [--processes PROCESSES] 363s [--corrected-group CORRECTED_GROUP] 363s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 363s [--quiet] [--help] 363s 363s Required Argument: 363s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 363s Directories containing fast5 files. 363s --statistics-file-basename STATISTICS_FILE_BASENAME 363s File base name to save base by base statistics from 363s testing. Filenames will be [--statistics-file- 363s basename].[--alternate-bases]?.tombo.stats 363s --alternate-bases {CpG,dam,6mA,5mC,dcm} [{CpG,dam,6mA,5mC,dcm} ...] 363s Default non-standard base model for testing (not 363s required if user created --alternate-model-filenames 363s is provided). 363s 363s Comparison Arguments: 363s --print-available-models 363s Print available alternative models and exit. 363s --dna Explicitly select canonical DNA model. Default: 363s Automatically determine from FAST5s 363s --rna Explicitly select canonical RNA model. Default: 363s Automatically determine from FAST5s 363s 363s Significance Test Arguments: 363s --minimum-test-reads MINIMUM_TEST_READS 363s Number of reads required at a position to perform 363s significance testing or contribute to model 363s estimation. Default: 1 363s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 363s Log likelihood ratio threshold when computing fraction 363s of significant reads at each genomic position. If two 363s values are provided, statistics between these values 363s are not considered. Default thresholds: DNA:-1.5-2.5 , 363s RNA:-2.5-2.5 363s --standard-log-likelihood-ratio 363s Use a standard log likelihood ratio (LLR) statistic. 363s Default is to use an outlier-robust LLR-like 363s statistic. Detail in full online documentation. 363s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 363s Dampen fraction modified estimates for low coverage 363s sites. Two parameters are unmodified and modified 363s pseudo read counts. This is equivalent to a beta prior 363s on the fraction estimate. Set to "0 0" to disable 363s dampened fraction estimation. Default: [2, 0] 363s 363s Output Argument: 363s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 363s Base for binary files containing per-read statistics 363s from statistical testing. Filenames will be [--per- 363s read-statistics-basename].[--alternate- 363s bases]?.tombo.per_read_stats 363s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 363s Number of the most significant sites to store for 363s faster access. If a longer list of most significant 363s sites is required the list must be re-computed from 363s all batches. Very large values can increase RAM usage. 363s Default: 100000 363s 363s Multiprocessing Arguments: 363s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 363s Size of regions over which to multiprocesses statistic 363s computation. For very deep samples a smaller value is 363s recommmended in order to control memory consumption. 363s Default: 10000 363s --processes PROCESSES 363s Number of processes. Default: 1 363s 363s FAST5 Data Arguments: 363s --corrected-group CORRECTED_GROUP 363s FAST5 group created by resquiggle command. Default: 363s RawGenomeCorrected_000 363s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 363s FAST5 subgroup(s) (under /Analyses/[--basecall- 363s group]/) containing basecalls and created within 363s [--corrected-group] containing re-squiggle results. 363s Default: ['BaseCalled_template'] 363s 363s Miscellaneous Arguments: 363s --quiet, -q Don't print status information. 363s --help, -h Print this help message and exit 364s usage: tombo detect_modifications model_sample_compare 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s --statistics-file-basename STATISTICS_FILE_BASENAME 364s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 364s [--sample-only-estimates] 364s [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS] 364s [--dna] [--rna] 364s [--fishers-method-context FISHERS_METHOD_CONTEXT] 364s [--minimum-test-reads MINIMUM_TEST_READS] 364s [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]] 364s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 364s [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME] 364s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 364s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 364s [--processes PROCESSES] 364s [--corrected-group CORRECTED_GROUP] 364s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 364s [--quiet] [--help] 364s 364s Required Argument: 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s Directories containing fast5 files. 364s --statistics-file-basename STATISTICS_FILE_BASENAME 364s File base name to save base by base statistics from 364s testing. Filenames will be [--statistics-file- 364s basename].[--alternate-bases]?.tombo.stats 364s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 364s Set of directories containing fast5 files for control 364s reads, containing only canonical nucleotides. 364s 364s Model Prior Arguments: 364s --sample-only-estimates 364s Only use canonical sample to estimate expected signal 364s level and spread. Default: Use canonical model to 364s improve estimtates (esp. for low coverage regions) 364s using baysian posterior estimates. 364s --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS 364s Prior weights (one each for mean and spread) applied 364s to canonical base model for estimating posterior model 364s parameters for sample comparison. Default: [5, 40] 364s --dna Explicitly select canonical DNA model. Default: 364s Automatically determine from FAST5s 364s --rna Explicitly select canonical RNA model. Default: 364s Automatically determine from FAST5s 364s 364s Significance Test Arguments: 364s --fishers-method-context FISHERS_METHOD_CONTEXT 364s Number of context bases up and downstream over which 364s to compute Fisher's method combined p-values. Note: 364s Not applicable for alternative model likelihood ratio 364s tests. Default: 1. 364s --minimum-test-reads MINIMUM_TEST_READS 364s Number of reads required at a position to perform 364s significance testing or contribute to model 364s estimation. Default: 1 364s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 364s P-value threshold when computing fraction of 364s significant reads at each genomic position. If two 364s values are provided, statistics between these values 364s are not considered. Default thresholds: DNA:0.15-0.5 , 364s RNA:0.05-0.4 364s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 364s Dampen fraction modified estimates for low coverage 364s sites. Two parameters are unmodified and modified 364s pseudo read counts. This is equivalent to a beta prior 364s on the fraction estimate. Set to "0 0" to disable 364s dampened fraction estimation. Default: [2, 0] 364s 364s Output Argument: 364s --per-read-statistics-basename PER_READ_STATISTICS_BASENAME 364s Base for binary files containing per-read statistics 364s from statistical testing. Filenames will be [--per- 364s read-statistics-basename].[--alternate- 364s bases]?.tombo.per_read_stats 364s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 364s Number of the most significant sites to store for 364s faster access. If a longer list of most significant 364s sites is required the list must be re-computed from 364s all batches. Very large values can increase RAM usage. 364s Default: 100000 364s 364s Multiprocessing Arguments: 364s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 364s Size of regions over which to multiprocesses statistic 364s computation. For very deep samples a smaller value is 364s recommmended in order to control memory consumption. 364s Default: 10000 364s --processes PROCESSES 364s Number of processes. Default: 1 364s 364s FAST5 Data Arguments: 364s --corrected-group CORRECTED_GROUP 364s FAST5 group created by resquiggle command. Default: 364s RawGenomeCorrected_000 364s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 364s FAST5 subgroup(s) (under /Analyses/[--basecall- 364s group]/) containing basecalls and created within 364s [--corrected-group] containing re-squiggle results. 364s Default: ['BaseCalled_template'] 364s 364s Miscellaneous Arguments: 364s --quiet, -q Don't print status information. 364s --help, -h Print this help message and exit 364s usage: tombo detect_modifications level_sample_compare 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s --statistics-file-basename STATISTICS_FILE_BASENAME 364s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 364s [--fishers-method-context FISHERS_METHOD_CONTEXT] 364s [--minimum-test-reads MINIMUM_TEST_READS] 364s [--statistic-type {ks,u,t}] 364s [--store-p-value] 364s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 364s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 364s [--processes PROCESSES] 364s [--corrected-group CORRECTED_GROUP] 364s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 364s [--quiet] [--help] 364s 364s Required Argument: 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s Directories containing fast5 files. 364s --statistics-file-basename STATISTICS_FILE_BASENAME 364s File base name to save base by base statistics from 364s testing. Filenames will be [--statistics-file- 364s basename].[--alternate-bases]?.tombo.stats 364s --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...] 364s Set of directories containing fast5 files for 364s alternate set of reads. 364s 364s Significance Test Arguments: 364s --fishers-method-context FISHERS_METHOD_CONTEXT 364s Number of context bases up and downstream over which 364s to compute Fisher's method combined p-values. Note: 364s Not applicable for alternative model likelihood ratio 364s tests. Default: 1. 364s --minimum-test-reads MINIMUM_TEST_READS 364s Number of reads required at a position to perform 364s significance testing or contribute to model 364s estimation. Default: 50 364s --statistic-type {ks,u,t} 364s Type of statistical test to apply. Default: "ks" 364s --store-p-value Store p-value instead of effect-size statistic. 364s Statistics are D-statistic (KS-test), deviation from 364s even common language effect size (u-test), and Cohen's 364s D (t-test). 364s 364s Output Argument: 364s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 364s Number of the most significant sites to store for 364s faster access. If a longer list of most significant 364s sites is required the list must be re-computed from 364s all batches. Very large values can increase RAM usage. 364s Default: 100000 364s 364s Multiprocessing Arguments: 364s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 364s Size of regions over which to multiprocesses statistic 364s computation. For very deep samples a smaller value is 364s recommmended in order to control memory consumption. 364s Default: 10000 364s --processes PROCESSES 364s Number of processes. Default: 1 364s 364s FAST5 Data Arguments: 364s --corrected-group CORRECTED_GROUP 364s FAST5 group created by resquiggle command. Default: 364s RawGenomeCorrected_000 364s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 364s FAST5 subgroup(s) (under /Analyses/[--basecall- 364s group]/) containing basecalls and created within 364s [--corrected-group] containing re-squiggle results. 364s Default: ['BaseCalled_template'] 364s 364s Miscellaneous Arguments: 364s --quiet, -q Don't print status information. 364s --help, -h Print this help message and exit 364s usage: tombo detect_modifications aggregate_per_read_stats 364s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 364s --statistics-filename STATISTICS_FILENAME 364s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 364s [--minimum-test-reads MINIMUM_TEST_READS] 364s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 364s [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED] 364s [--processes PROCESSES] 364s [--corrected-group CORRECTED_GROUP] 364s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 364s [--quiet] [--help] 364s 364s Required Argument: 364s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 364s Binary file containing per-read statistics from 364s statistical testing. 364s --statistics-filename STATISTICS_FILENAME 364s File to save/load genomic base anchored statistics. 364s --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...] 364s P-value or log likelihood ratio threshold when 364s computing fraction of significant reads at each 364s genomic position. If two values are provided, 364s statistics between these values are not considered. 364s 364s Significance Test Arguments: 364s --minimum-test-reads MINIMUM_TEST_READS 364s Number of reads required at a position to perform 364s significance testing or contribute to model 364s estimation. Default: 1 364s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 364s Dampen fraction modified estimates for low coverage 364s sites. Two parameters are unmodified and modified 364s pseudo read counts. This is equivalent to a beta prior 364s on the fraction estimate. Set to "0 0" to disable 364s dampened fraction estimation. Default: [2, 0] 364s 364s Output Argument: 364s --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED 364s Number of the most significant sites to store for 364s faster access. If a longer list of most significant 364s sites is required the list must be re-computed from 364s all batches. Very large values can increase RAM usage. 364s Default: 100000 364s 364s Multiprocessing Arguments: 364s --processes PROCESSES 364s Number of processes. Default: 1 364s 364s FAST5 Data Arguments: 364s --corrected-group CORRECTED_GROUP 364s FAST5 group created by resquiggle command. Default: 364s RawGenomeCorrected_000 364s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 364s FAST5 subgroup(s) (under /Analyses/[--basecall- 364s group]/) containing basecalls and created within 364s [--corrected-group] containing re-squiggle results. 364s Default: ['BaseCalled_template'] 364s 364s Miscellaneous Arguments: 364s --quiet, -q Don't print status information. 364s --help, -h Print this help message and exit 364s usage: tombo text_output browser_files 364s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 364s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 364s [--statistics-filename STATISTICS_FILENAME] 364s [--genome-fasta GENOME_FASTA] 364s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 364s [--browser-file-basename BROWSER_FILE_BASENAME] 364s [--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} ...]] 364s [--corrected-group CORRECTED_GROUP] 364s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 364s [--quiet] [--help] 364s 364s Data Arguments: 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s Directories containing fast5 files. 364s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 364s Set of directories containing fast5 files for control 364s reads, containing only canonical nucleotides. 364s --statistics-filename STATISTICS_FILENAME 364s File to save/load genomic base anchored statistics. 364s 364s Statistic Motif Filter Arguments: 364s --genome-fasta GENOME_FASTA 364s FASTA file used to re-squiggle. For faster sequence 364s access. 364s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 364s Ground truth, motif centered, modified base 364s descriptions for output filtering. Format descriptions 364s as: "motif:mod_pos:name". The mod_pos indicates the 364s modified base within the motif (1-based index). 364s Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter 364s output for identification of E. coli dam and dcm 364s methylation. 364s 364s Output Arguments: 364s --browser-file-basename BROWSER_FILE_BASENAME 364s Basename for output browser files. Two files (plus and 364s minus strand) will be produced for each --file-types 364s supplied. Filenames formatted as "[browser-file- 364s basename].[file- 364s type].[sample|control]?.[plus|minus].[wig|bedgraph]". 364s Default: tombo_results 364s --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} ...] 364s Data types of genome browser files to produce. 364s Produced coverage files are in bedGraph format, while 364s all other file types will be in wiggle format 364s (https://genome.ucsc.edu/goldenpath/help/wiggle.html). 364s Default: "coverage" 364s 364s FAST5 Data Arguments: 364s --corrected-group CORRECTED_GROUP 364s FAST5 group created by resquiggle command. Default: 364s RawGenomeCorrected_000 364s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 364s FAST5 subgroup(s) (under /Analyses/[--basecall- 364s group]/) containing basecalls and created within 364s [--corrected-group] containing re-squiggle results. 364s Default: ['BaseCalled_template'] 364s 364s Miscellaneous Arguments: 364s --quiet, -q Don't print status information. 364s --help, -h Print this help message and exit 364s usage: tombo text_output signif_sequence_context 364s --statistics-filename STATISTICS_FILENAME 364s [--genome-fasta GENOME_FASTA] 364s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 364s [--num-regions NUM_REGIONS] 364s [--num-bases NUM_BASES] 364s [--sequences-filename SEQUENCES_FILENAME] 364s [--corrected-group CORRECTED_GROUP] 364s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 364s [--quiet] [--help] 364s 364s Required Argument: 364s --statistics-filename STATISTICS_FILENAME 364s File to save/load genomic base anchored statistics. 364s 364s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 364s --genome-fasta GENOME_FASTA 364s FASTA file used to re-squiggle. For faster sequence 364s access. 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s Directories containing fast5 files. 364s 364s Region Selection Arguments: 364s --num-regions NUM_REGIONS 364s Number of regions to plot. Default: 100 364s --num-bases NUM_BASES 364s Number of bases to plot/output. Default: 15 364s 364s Output Arguments: 364s --sequences-filename SEQUENCES_FILENAME 364s File for sequences from selected regions. Sequences 364s will be stored in FASTA format. Default: 364s tombo_results.significant_regions.fasta. 364s 364s FAST5 Data Arguments: 364s --corrected-group CORRECTED_GROUP 364s FAST5 group created by resquiggle command. Default: 364s RawGenomeCorrected_000 364s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 364s FAST5 subgroup(s) (under /Analyses/[--basecall- 364s group]/) containing basecalls and created within 364s [--corrected-group] containing re-squiggle results. 364s Default: ['BaseCalled_template'] 364s 364s Miscellaneous Arguments: 364s --quiet, -q Don't print status information. 364s --help, -h Print this help message and exit 364s usage: tombo plot max_coverage 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 364s [--plot-standard-model] 364s [--plot-alternate-model {5mC,dcm,6mA,dam,CpG}] 364s [--overplot-threshold OVERPLOT_THRESHOLD] 364s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 364s [--num-regions NUM_REGIONS] 364s [--num-bases NUM_BASES] 364s [--pdf-filename PDF_FILENAME] 364s [--corrected-group CORRECTED_GROUP] 364s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 364s [--quiet] [--help] 364s 364s Required Argument: 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s Directories containing fast5 files. 364s 364s Comparison Arguments: 364s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 364s Set of directories containing fast5 files for control 364s reads, containing only canonical nucleotides. 364s --plot-standard-model 364s Add default standard model distribution to the plot. 364s --plot-alternate-model {5mC,dcm,6mA,dam,CpG} 364s Add alternative model distribution to the plot. 364s 364s Overplotting Arguments: 364s --overplot-threshold OVERPLOT_THRESHOLD 364s Coverage level to trigger alternative plot type 364s instead of raw signal. Default: 50 364s --overplot-type {Downsample,Boxplot,Quantile,Density} 364s Plot type for regions with higher coverage. Default: 364s Downsample 364s 364s Plotting Region Arguments: 364s --num-regions NUM_REGIONS 364s Number of regions to plot. Default: 10 364s --num-bases NUM_BASES 364s Number of bases to plot/output. Default: 21 364s 364s Output Argument: 364s --pdf-filename PDF_FILENAME 364s PDF filename to store plot(s). Default: 364s tombo_results.max_coverage.pdf 364s 364s FAST5 Data Arguments: 364s --corrected-group CORRECTED_GROUP 364s FAST5 group created by resquiggle command. Default: 364s RawGenomeCorrected_000 364s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 364s FAST5 subgroup(s) (under /Analyses/[--basecall- 364s group]/) containing basecalls and created within 364s [--corrected-group] containing re-squiggle results. 364s Default: ['BaseCalled_template'] 364s 364s Miscellaneous Arguments: 364s --quiet, -q Don't print status information. 364s --help, -h Print this help message and exit 364s usage: tombo plot genome_locations 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 364s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 364s [--plot-standard-model] 364s [--plot-alternate-model {dcm,6mA,5mC,CpG,dam}] 364s [--overplot-threshold OVERPLOT_THRESHOLD] 364s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 364s [--num-bases NUM_BASES] 364s [--pdf-filename PDF_FILENAME] 364s [--corrected-group CORRECTED_GROUP] 364s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 364s [--quiet] [--help] 364s 364s Required Arguments: 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s Directories containing fast5 files. 364s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 364s Genomic locations at which to plot signal. Format 364s locations as "chrm:position[:strand] 364s [chrm2:position2[:strand2] ...]" (strand not 364s applicable for all applications) 364s 364s Comparison Arguments: 364s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 364s Set of directories containing fast5 files for control 364s reads, containing only canonical nucleotides. 364s --plot-standard-model 364s Add default standard model distribution to the plot. 364s --plot-alternate-model {dcm,6mA,5mC,CpG,dam} 364s Add alternative model distribution to the plot. 364s 364s Overplotting Arguments: 364s --overplot-threshold OVERPLOT_THRESHOLD 364s Coverage level to trigger alternative plot type 364s instead of raw signal. Default: 50 364s --overplot-type {Downsample,Boxplot,Quantile,Density} 364s Plot type for regions with higher coverage. Default: 364s Downsample 364s 364s Plotting Region Argument: 364s --num-bases NUM_BASES 364s Number of bases to plot/output. Default: 21 364s 364s Output Argument: 364s --pdf-filename PDF_FILENAME 364s PDF filename to store plot(s). Default: 364s tombo_results.genome_locations.pdf 364s 364s FAST5 Data Arguments: 364s --corrected-group CORRECTED_GROUP 364s FAST5 group created by resquiggle command. Default: 364s RawGenomeCorrected_000 364s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 364s FAST5 subgroup(s) (under /Analyses/[--basecall- 364s group]/) containing basecalls and created within 364s [--corrected-group] containing re-squiggle results. 364s Default: ['BaseCalled_template'] 364s 364s Miscellaneous Arguments: 364s --quiet, -q Don't print status information. 364s --help, -h Print this help message and exit 364s usage: tombo plot motif_centered 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s --motif MOTIF --genome-fasta GENOME_FASTA 364s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 364s [--plot-standard-model] 364s [--plot-alternate-model {dam,CpG,5mC,dcm,6mA}] 364s [--overplot-threshold OVERPLOT_THRESHOLD] 364s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 364s [--num-regions NUM_REGIONS] 364s [--num-bases NUM_BASES] [--deepest-coverage] 364s [--pdf-filename PDF_FILENAME] 364s [--corrected-group CORRECTED_GROUP] 364s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 364s [--quiet] [--help] 364s 364s Required Arguments: 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s Directories containing fast5 files. 364s --motif MOTIF Motif of interest at which to plot signal and 364s statsitics. Supports IUPAC single letter codes (use T 364s for RNA). 364s --genome-fasta GENOME_FASTA 364s FASTA file used to re-squiggle. For faster sequence 364s access. 364s 364s Comparison Arguments: 364s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 364s Set of directories containing fast5 files for control 364s reads, containing only canonical nucleotides. 364s --plot-standard-model 364s Add default standard model distribution to the plot. 364s --plot-alternate-model {dam,CpG,5mC,dcm,6mA} 364s Add alternative model distribution to the plot. 364s 364s Overplotting Arguments: 364s --overplot-threshold OVERPLOT_THRESHOLD 364s Coverage level to trigger alternative plot type 364s instead of raw signal. Default: 50 364s --overplot-type {Downsample,Boxplot,Quantile,Density} 364s Plot type for regions with higher coverage. Default: 364s Downsample 364s 364s Plotting Region Arguments: 364s --num-regions NUM_REGIONS 364s Number of regions to plot. Default: 10 364s --num-bases NUM_BASES 364s Number of bases to plot/output. Default: 21 364s --deepest-coverage Plot the deepest coverage regions. 364s 364s Output Argument: 364s --pdf-filename PDF_FILENAME 364s PDF filename to store plot(s). Default: 364s tombo_results.motif_centered.pdf 364s 364s FAST5 Data Arguments: 364s --corrected-group CORRECTED_GROUP 364s FAST5 group created by resquiggle command. Default: 364s RawGenomeCorrected_000 364s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 364s FAST5 subgroup(s) (under /Analyses/[--basecall- 364s group]/) containing basecalls and created within 364s [--corrected-group] containing re-squiggle results. 364s Default: ['BaseCalled_template'] 364s 364s Miscellaneous Arguments: 364s --quiet, -q Don't print status information. 364s --help, -h Print this help message and exit 364s usage: tombo plot max_difference 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 364s [--overplot-threshold OVERPLOT_THRESHOLD] 364s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 364s [--num-regions NUM_REGIONS] 364s [--num-bases NUM_BASES] 364s [--pdf-filename PDF_FILENAME] 364s [--sequences-filename SEQUENCES_FILENAME] 364s [--corrected-group CORRECTED_GROUP] 364s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 364s [--quiet] [--help] 364s 364s Required Arguments: 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s Directories containing fast5 files. 364s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 364s Set of directories containing fast5 files for control 364s reads, containing only canonical nucleotides. 364s 364s Overplotting Arguments: 364s --overplot-threshold OVERPLOT_THRESHOLD 364s Coverage level to trigger alternative plot type 364s instead of raw signal. Default: 50 364s --overplot-type {Downsample,Boxplot,Quantile,Density} 364s Plot type for regions with higher coverage. Default: 364s Downsample 364s 364s Plotting Region Arguments: 364s --num-regions NUM_REGIONS 364s Number of regions to plot. Default: 10 364s --num-bases NUM_BASES 364s Number of bases to plot/output. Default: 21 364s 364s Output Arguments: 364s --pdf-filename PDF_FILENAME 364s PDF filename to store plot(s). Default: 364s tombo_results.max_difference.pdf 364s --sequences-filename SEQUENCES_FILENAME 364s File for sequences from selected regions. Sequences 364s will be stored in FASTA format. Default: None. 364s 364s FAST5 Data Arguments: 364s --corrected-group CORRECTED_GROUP 364s FAST5 group created by resquiggle command. Default: 364s RawGenomeCorrected_000 364s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 364s FAST5 subgroup(s) (under /Analyses/[--basecall- 364s group]/) containing basecalls and created within 364s [--corrected-group] containing re-squiggle results. 364s Default: ['BaseCalled_template'] 364s 364s Miscellaneous Arguments: 364s --quiet, -q Don't print status information. 364s --help, -h Print this help message and exit 364s usage: tombo plot most_significant 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s --statistics-filename STATISTICS_FILENAME 364s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 364s [--plot-standard-model] 364s [--plot-alternate-model {5mC,dcm,6mA,dam,CpG}] 364s [--overplot-threshold OVERPLOT_THRESHOLD] 364s [--overplot-type {Downsample,Boxplot,Quantile,Density}] 364s [--num-regions NUM_REGIONS] 364s [--num-bases NUM_BASES] 364s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 364s [--pdf-filename PDF_FILENAME] 364s [--sequences-filename SEQUENCES_FILENAME] 364s [--corrected-group CORRECTED_GROUP] 364s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 364s [--quiet] [--help] 364s 364s Required Arguments: 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s Directories containing fast5 files. 364s --statistics-filename STATISTICS_FILENAME 364s File to save/load genomic base anchored statistics. 364s 364s Comparison Arguments: 364s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 364s Set of directories containing fast5 files for control 364s reads, containing only canonical nucleotides. 364s --plot-standard-model 364s Add default standard model distribution to the plot. 364s --plot-alternate-model {5mC,dcm,6mA,dam,CpG} 364s Add alternative model distribution to the plot. 364s 364s Overplotting Arguments: 364s --overplot-threshold OVERPLOT_THRESHOLD 364s Coverage level to trigger alternative plot type 364s instead of raw signal. Default: 50 364s --overplot-type {Downsample,Boxplot,Quantile,Density} 364s Plot type for regions with higher coverage. Default: 364s Downsample 364s 364s Plotting Region Arguments: 364s --num-regions NUM_REGIONS 364s Number of regions to plot. Default: 10 364s --num-bases NUM_BASES 364s Number of bases to plot/output. Default: 21 364s 364s Statistical Argument: 364s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 364s Dampen fraction modified estimates for low coverage 364s sites. Two parameters are unmodified and modified 364s pseudo read counts. This is equivalent to a beta prior 364s on the fraction estimate. Set to "0 0" to disable 364s dampened fraction estimation. Default: [2, 0] 364s 364s Output Arguments: 364s --pdf-filename PDF_FILENAME 364s PDF filename to store plot(s). Default: 364s tombo_results.significant_difference.pdf 364s --sequences-filename SEQUENCES_FILENAME 364s File for sequences from selected regions. Sequences 364s will be stored in FASTA format. Default: None. 364s 364s FAST5 Data Arguments: 364s --corrected-group CORRECTED_GROUP 364s FAST5 group created by resquiggle command. Default: 364s RawGenomeCorrected_000 364s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 364s FAST5 subgroup(s) (under /Analyses/[--basecall- 364s group]/) containing basecalls and created within 364s [--corrected-group] containing re-squiggle results. 364s Default: ['BaseCalled_template'] 364s 364s Miscellaneous Arguments: 364s --quiet, -q Don't print status information. 364s --help, -h Print this help message and exit 364s usage: tombo plot motif_with_stats 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s --motif MOTIF 364s --statistics-filename STATISTICS_FILENAME 364s --genome-fasta GENOME_FASTA 364s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 364s [--plot-standard-model] 364s [--plot-alternate-model {dam,5mC,CpG,6mA,dcm}] 364s [--overplot-threshold OVERPLOT_THRESHOLD] 364s [--num-regions NUM_REGIONS] 364s [--num-context NUM_CONTEXT] 364s [--num-statistics NUM_STATISTICS] 364s [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS] 364s [--pdf-filename PDF_FILENAME] 364s [--corrected-group CORRECTED_GROUP] 364s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 364s [--quiet] [--help] 364s 364s Required Arguments: 364s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 364s Directories containing fast5 files. 364s --motif MOTIF Motif of interest at which to plot signal and 364s statsitics. Supports IUPAC single letter codes (use T 364s for RNA). 364s --statistics-filename STATISTICS_FILENAME 364s File to save/load genomic base anchored statistics. 364s --genome-fasta GENOME_FASTA 364s FASTA file used to re-squiggle. For faster sequence 364s access. 364s 364s Comparison Arguments: 364s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 364s Set of directories containing fast5 files for control 364s reads, containing only canonical nucleotides. 364s --plot-standard-model 364s Add default standard model distribution to the plot. 364s --plot-alternate-model {dam,5mC,CpG,6mA,dcm} 364s Add alternative model distribution to the plot. 364s 364s Overplotting Argument: 364s --overplot-threshold OVERPLOT_THRESHOLD 364s Coverage level to trigger alternative plot type 364s instead of raw signal. Default: 50 364s 364s Plotting Region Arguments: 364s --num-regions NUM_REGIONS 364s Number of regions to plot. Default: 3 364s --num-context NUM_CONTEXT 364s Number of context bases around motif. Default: 5 364s --num-statistics NUM_STATISTICS 364s Number of motif centered regions to include in 364s statistic distributions. Default: 200 364s 364s Statistical Argument: 364s --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS 364s Dampen fraction modified estimates for low coverage 364s sites. Two parameters are unmodified and modified 364s pseudo read counts. This is equivalent to a beta prior 364s on the fraction estimate. Set to "0 0" to disable 364s dampened fraction estimation. Default: [2, 0] 364s 364s Output Argument: 364s --pdf-filename PDF_FILENAME 364s PDF filename to store plot(s). Default: 364s tombo_results.motif_statistics.pdf 364s 364s FAST5 Data Arguments: 364s --corrected-group CORRECTED_GROUP 364s FAST5 group created by resquiggle command. Default: 364s RawGenomeCorrected_000 364s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 364s FAST5 subgroup(s) (under /Analyses/[--basecall- 364s group]/) containing basecalls and created within 364s [--corrected-group] containing re-squiggle results. 364s Default: ['BaseCalled_template'] 364s 364s Miscellaneous Arguments: 364s --quiet, -q Don't print status information. 364s --help, -h Print this help message and exit 365s usage: tombo plot per_read 365s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 365s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 365s [--genome-fasta GENOME_FASTA] 365s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 365s [--num-reads NUM_READS] [--num-bases NUM_BASES] 365s [--box-center] [--pdf-filename PDF_FILENAME] 365s [--corrected-group CORRECTED_GROUP] 365s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 365s [--quiet] [--help] 365s 365s Required Arguments: 365s --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...] 365s Genomic locations at which to plot signal. Format 365s locations as "chrm:position[:strand] 365s [chrm2:position2[:strand2] ...]" (strand not 365s applicable for all applications) 365s --per-read-statistics-filename PER_READ_STATISTICS_FILENAME 365s Binary file containing per-read statistics from 365s statistical testing. 365s 365s Sequence Arguments (Provide either FAST5s dir or genome FASTA): 365s --genome-fasta GENOME_FASTA 365s FASTA file used to re-squiggle. For faster sequence 365s access. 365s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 365s Directories containing fast5 files. 365s 365s Plotting Region Arguments: 365s --num-reads NUM_READS 365s Number of reads to plot. Default: 100 365s --num-bases NUM_BASES 365s Number of bases to plot/output. Default: 51 365s --box-center Plot a box around the central base. 365s 365s Output Argument: 365s --pdf-filename PDF_FILENAME 365s PDF filename to store plot(s). Default: 365s tombo_results.per_read_stats.pdf 365s 365s FAST5 Data Arguments: 365s --corrected-group CORRECTED_GROUP 365s FAST5 group created by resquiggle command. Default: 365s RawGenomeCorrected_000 365s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 365s FAST5 subgroup(s) (under /Analyses/[--basecall- 365s group]/) containing basecalls and created within 365s [--corrected-group] containing re-squiggle results. 365s Default: ['BaseCalled_template'] 365s 365s Miscellaneous Arguments: 365s --quiet, -q Don't print status information. 365s --help, -h Print this help message and exit 365s usage: tombo plot roc 365s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 365s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 365s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 365s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 365s [--genome-fasta GENOME_FASTA] 365s [--pdf-filename PDF_FILENAME] 365s [--statistics-per-block STATISTICS_PER_BLOCK] 365s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 365s [--quiet] [--help] 365s 365s Required Argument: 365s --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...] 365s Files to load genomic base anchored statistics. 365s 365s Ground Truth Arguments (provide bed files or motifs): 365s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 365s Modification description and bed format files 365s containing single base locations of ground truth 365s modified sites. Bed files should contain 6 fields 365s including strand. Format descriptions as 365s "mod_name:locs.bed". Example: "CpG 365s bisulfite":bisulfite_locs.bed 365s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 365s Bed format files containing single base locations of 365s ground truth unmodified sites. Bed files should 365s contain 6 fields including strand. 365s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 365s Ground truth, motif centered, modified base 365s descriptions for computing ROC and PR curves. Each 365s statistics file is associated with a set of motif 365s descriptions. Format descriptions as: 365s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 365s mod_pos indicates the alternate-base within the motif 365s (1-based index). Example: CCWGG:2:"dcm 365s 5mC"::GATC:2:"dam 6mA" would assess the performance of 365s a single Tombo statistics file for identification of 365s E. coli dam and dcm methylation. 365s --genome-fasta GENOME_FASTA 365s FASTA file used to re-squiggle. For faster sequence 365s access. 365s 365s Output Arguments: 365s --pdf-filename PDF_FILENAME 365s PDF filename to store plot(s). Default: 365s tombo_results.roc.pdf 365s 365s Down-sampling Arguments: 365s --statistics-per-block STATISTICS_PER_BLOCK 365s Number of randomly selected per-read, per-base 365s statistics to extract from each genomic block for 365s plotting. Default: Include all stats 365s --total-statistics-limit TOTAL_STATISTICS_LIMIT 365s Total per-read statistics to be extracted for 365s plotting. Avoids memory overflow for large runs. 365s Default: 5000000 365s 365s Miscellaneous Arguments: 365s --quiet, -q Don't print status information. 365s --help, -h Print this help message and exit 365s usage: tombo plot per_read_roc 365s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 365s [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]] 365s [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]] 365s [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]] 365s [--genome-fasta GENOME_FASTA] 365s [--statistics-per-block STATISTICS_PER_BLOCK] 365s [--total-statistics-limit TOTAL_STATISTICS_LIMIT] 365s [--pdf-filename PDF_FILENAME] [--quiet] 365s [--help] 365s 365s Required Argument: 365s --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...] 365s Binary files containing per-read statistics from 365s statistical testing. 365s 365s Ground Truth Arguments (provide bed files or motifs): 365s --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...] 365s Modification description and bed format files 365s containing single base locations of ground truth 365s modified sites. Bed files should contain 6 fields 365s including strand. Format descriptions as 365s "mod_name:locs.bed". Example: "CpG 365s bisulfite":bisulfite_locs.bed 365s --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...] 365s Bed format files containing single base locations of 365s ground truth unmodified sites. Bed files should 365s contain 6 fields including strand. 365s --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...] 365s Ground truth, motif centered, modified base 365s descriptions for computing ROC and PR curves. Each 365s statistics file is associated with a set of motif 365s descriptions. Format descriptions as: 365s "motif:mod_pos:name[::motif2:mod_pos2:name2...]". 365s mod_pos indicates the alternate-base within the motif 365s (1-based index). Example: CCWGG:2:"dcm 365s 5mC"::GATC:2:"dam 6mA" would assess the performance of 365s a single Tombo statistics file for identification of 365s E. coli dam and dcm methylation. 365s --genome-fasta GENOME_FASTA 365s FASTA file used to re-squiggle. For faster sequence 365s access. 365s 365s Down-sampling Arguments: 365s --statistics-per-block STATISTICS_PER_BLOCK 365s Number of randomly selected per-read, per-base 365s statistics to extract from each genomic block for 365s plotting. Default: 100000 365s --total-statistics-limit TOTAL_STATISTICS_LIMIT 365s Total per-read statistics to be extracted for 365s plotting. Avoids memory overflow for large runs. 365s Default: 5000000 365s 365s Output Arguments: 365s --pdf-filename PDF_FILENAME 365s PDF filename to store plot(s). Default: 365s tombo_results.per_reads_roc.pdf 365s 365s Miscellaneous Arguments: 365s --quiet, -q Don't print status information. 365s --help, -h Print this help message and exit 365s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 365s [--upstream-bases {0,1,2,3,4}] 365s [--downstream-bases {0,1,2,3,4}] [--read-mean] 365s [--num-kmer-threshold NUM_KMER_THRESHOLD] 365s [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME] 365s [--r-data-filename R_DATA_FILENAME] [--dont-plot] 365s [--corrected-group CORRECTED_GROUP] 365s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 365s [--quiet] [--help] 365s 365s Required Argument: 365s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 365s Directories containing fast5 files. 365s 365s Data Processing Arguments: 365s --upstream-bases {0,1,2,3,4} 365s Upstream bases in k-mer. Default: 1 365s --downstream-bases {0,1,2,3,4} 365s Downstream bases in k-mer. Default: 2 365s --read-mean Plot k-mer means across whole reads as opposed to 365s individual k-mer event levels. 365s --num-kmer-threshold NUM_KMER_THRESHOLD 365s Observations of each k-mer required to include a read 365s in read level averages. Default: 1 365s 365s Plotting Region Arguments: 365s --num-reads NUM_READS 365s Number of reads to plot. Default: 100 365s 365s Output Arguments: 365s --pdf-filename PDF_FILENAME 365s PDF filename to store plot(s). Default: 365s tombo_results.kmer_distribution.pdf 365s --r-data-filename R_DATA_FILENAME 365s Filename to save R data structure. Default: Don't save 365s --dont-plot Don't plot result. Useful to produce only R data file. 365s 365s FAST5 Data Arguments: 365s --corrected-group CORRECTED_GROUP 365s FAST5 group created by resquiggle command. Default: 365s RawGenomeCorrected_000 365s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 365s FAST5 subgroup(s) (under /Analyses/[--basecall- 365s group]/) containing basecalls and created within 365s [--corrected-group] containing re-squiggle results. 365s Default: ['BaseCalled_template'] 365s 365s Miscellaneous Arguments: 365s --quiet, -q Don't print status information. 365s --help, -h Print this help message and exit 365s usage: tombo plot cluster_most_significant 365s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 365s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 365s --statistics-filename STATISTICS_FILENAME 365s [--genome-fasta GENOME_FASTA] 365s [--processes PROCESSES] 365s [--num-regions NUM_REGIONS] 365s [--num-bases NUM_BASES] 365s [--slide-span SLIDE_SPAN] 365s [--pdf-filename PDF_FILENAME] 365s [--r-data-filename R_DATA_FILENAME] 365s [--corrected-group CORRECTED_GROUP] 365s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 365s [--quiet] [--help] 365s 365s Required Arguments: 365s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 365s Directories containing fast5 files. 365s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 365s Set of directories containing fast5 files for control 365s reads, containing only canonical nucleotides. 365s --statistics-filename STATISTICS_FILENAME 365s File to save/load genomic base anchored statistics. 365s 365s FASTA Sequence Argument: 365s --genome-fasta GENOME_FASTA 365s FASTA file used to re-squiggle. For faster sequence 365s access. 365s 365s Multiprocessing Argument: 365s --processes PROCESSES 365s Number of processes. Default: 1 365s 365s Plotting Region Arguments: 365s --num-regions NUM_REGIONS 365s Number of regions to plot. Default: 10 365s --num-bases NUM_BASES 365s Number of bases to plot/output. Default: 21 365s --slide-span SLIDE_SPAN 365s Number of bases offset over which to search when 365s computing distances for signal cluster plotting. 365s Default: 0 (exact position) 365s 365s Output Arguments: 365s --pdf-filename PDF_FILENAME 365s PDF filename to store plot(s). Default: 365s tombo_results.signal_clusters.pdf 365s --r-data-filename R_DATA_FILENAME 365s Filename to save R data structure. Default: Don't save 365s 365s FAST5 Data Arguments: 365s --corrected-group CORRECTED_GROUP 365s FAST5 group created by resquiggle command. Default: 365s RawGenomeCorrected_000 365s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 365s FAST5 subgroup(s) (under /Analyses/[--basecall- 365s group]/) containing basecalls and created within 365s [--corrected-group] containing re-squiggle results. 365s Default: ['BaseCalled_template'] 365s 365s Miscellaneous Arguments: 365s --quiet, -q Don't print status information. 365s --help, -h Print this help message and exit 365s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir 365s 365s Required Arguments: 365s fast5s_basedir Directory containing fast5 files. All files ending in 365s "fast5" found recursively within this base directory will be 365s processed. 365s 365s Miscellaneous Arguments: 365s --quiet, -q Don't print status information. 365s --help, -h Print this help message and exit 365s usage: tombo build_model event_resquiggle 365s [--minimap2-executable MINIMAP2_EXECUTABLE] 365s [--minimap2-index MINIMAP2_INDEX] 365s [--bwa-mem-executable BWA_MEM_EXECUTABLE] 365s [--graphmap-executable GRAPHMAP_EXECUTABLE] 365s [--alignment-batch-size ALIGNMENT_BATCH_SIZE] 365s [--normalization-type {median,pA,pA_raw,none}] 365s [--pore-model-filename PORE_MODEL_FILENAME] 365s [--outlier-threshold OUTLIER_THRESHOLD] 365s [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS] 365s [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]] 365s [--timeout TIMEOUT] 365s [--cpts-limit CPTS_LIMIT] 365s [--skip-index] [--overwrite] 365s [--failed-reads-filename FAILED_READS_FILENAME] 365s [--include-event-stdev] 365s [--corrected-group CORRECTED_GROUP] 365s [--basecall-group BASECALL_GROUP] 365s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 365s [--processes PROCESSES] 365s [--align-processes ALIGN_PROCESSES] 365s [--align-threads-per-process ALIGN_THREADS_PER_PROCESS] 365s [--resquiggle-processes RESQUIGGLE_PROCESSES] 365s [--quiet] [--help] 365s fast5s_basedir reference_fasta 365s 365s Required Arguments: 365s fast5s_basedir Directory containing fast5 files. All files ending in 365s "fast5" found recursively within this base directory 365s will be processed. 365s reference_fasta Reference genome/transcriptome FASTA file for mapping. 365s 365s Mapper Arguments (One mapper is required): 365s --minimap2-executable MINIMAP2_EXECUTABLE 365s Path to minimap2 executable. 365s --minimap2-index MINIMAP2_INDEX 365s Path to minimap2 index (with map-ont preset) file 365s corresponding to the [genome_fasta] provided. 365s --bwa-mem-executable BWA_MEM_EXECUTABLE 365s Path to bwa-mem executable. 365s --graphmap-executable GRAPHMAP_EXECUTABLE 365s Path to graphmap executable. 365s --alignment-batch-size ALIGNMENT_BATCH_SIZE 365s Number of reads included in each alignment call. Note: 365s A new system mapping call is made for each batch 365s (including loading of the genome), so it is advised to 365s use larger values for larger genomes. Default: 1000 365s 365s Signal Processing Arguments: 365s --normalization-type {median,pA,pA_raw,none} 365s Choices: "none": raw 16-bit DAQ values, "pA_raw": pA 365s as in the ONT events (using offset, range and 365s digitization), "pA": k-mer-based correction for pA 365s drift as in nanopolish (requires [--pore-model- 365s filename]), "median": median and MAD from raw signal. 365s Default: median 365s --pore-model-filename PORE_MODEL_FILENAME 365s File containing kmer model parameters (level_mean and 365s level_stdv) used in order to compute kmer-based 365s corrected pA values. E.g. https://github.com/jts/nanop 365s olish/blob/master/etc/r9- 365s models/template_median68pA.5mers.model 365s --outlier-threshold OUTLIER_THRESHOLD 365s Windosrize the signal at this number of scale values. 365s Negative value disables outlier clipping. Default: 365s 5.000000 365s --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS 365s Specify the 2 parameters for segmentation 1) running 365s neighboring windows width 2) minimum raw observations 365s per genomic base. Sample type defaults: RNA : 12 6 || 365s DNA : 5 3 365s 365s Read Filtering Arguments: 365s --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...] 365s Filter reads based on observations per base percentile 365s thresholds. Format thresholds as "percentile:thresh 365s [pctl2:thresh2 ...]". For example to filter reads with 365s 99th pctl > 200 obs/base or max > 5k obs/base use 365s "99:200 100:5000". 365s --timeout TIMEOUT Timeout in seconds for processing a single read. 365s Default: No timeout. 365s --cpts-limit CPTS_LIMIT 365s Maximum number of changepoints to find within a single 365s indel group. Default: No limit. 365s 365s Input/Output Arguments: 365s --skip-index Skip creation of tombo index. This drastically slows 365s downstream tombo commands. Default stores tombo index 365s named ".[--fast5-basedir].[--corrected- 365s group].tombo.index" to be loaded automatically for 365s downstream commands. 365s --overwrite Overwrite previous corrected group in FAST5 files. 365s Note: only effects --corrected-group or --new- 365s corrected-group. 365s --failed-reads-filename FAILED_READS_FILENAME 365s Output failed read filenames with assoicated error. 365s Default: Do not store failed reads. 365s --include-event-stdev 365s Include corrected event standard deviation in output 365s FAST5 data. 365s 365s FAST5 Data Arguments: 365s --corrected-group CORRECTED_GROUP 365s FAST5 group created by resquiggle command. Default: 365s RawGenomeCorrected_000 365s --basecall-group BASECALL_GROUP 365s FAST5 group obtain original basecalls (under Analyses 365s group). Default: Basecall_1D_000 365s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 365s FAST5 subgroup(s) (under /Analyses/[--basecall- 365s group]/) containing basecalls and created within 365s [--corrected-group] containing re-squiggle results. 365s Default: ['BaseCalled_template'] 365s 365s Multiprocessing Arguments: 365s --processes PROCESSES 365s Number of processes. Default: 2 365s --align-processes ALIGN_PROCESSES 365s Number of processes to use for parsing and aligning 365s original basecalls. Each process will independently 365s load the genome into memory, so use caution with 365s larger genomes (e.g. human). Default: 1 365s --align-threads-per-process ALIGN_THREADS_PER_PROCESS 365s Number of threads to use for aligner system call. 365s Default: [--processes] / (2 * [--align-processes)] 365s --resquiggle-processes RESQUIGGLE_PROCESSES 365s Number of processes to use for resquiggle algorithm. 365s Default: [--processes] / 2 365s 365s Miscellaneous Arguments: 365s --quiet, -q Don't print status information. 365s --help, -h Print this help message and exit 365s usage: tombo build_model estimate_reference 365s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 365s --tombo-model-filename TOMBO_MODEL_FILENAME 365s [--estimate-mean] 365s [--kmer-specific-sd] 365s [--upstream-bases {0,1,2,3,4}] 365s [--downstream-bases {0,1,2,3,4}] 365s [--minimum-test-reads MINIMUM_TEST_READS] 365s [--coverage-threshold COVERAGE_THRESHOLD] 365s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 365s [--multiprocess-region-size MULTIPROCESS_REGION_SIZE] 365s [--processes PROCESSES] 365s [--corrected-group CORRECTED_GROUP] 365s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 365s [--quiet] [--help] 365s 365s Required Arguments: 365s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 365s Directories containing fast5 files. 365s --tombo-model-filename TOMBO_MODEL_FILENAME 365s Filename to save Tombo model. 365s 365s Modeling Arguments: 365s --estimate-mean Use the mean instead of median for model level 365s estimation. Note: This can cause poor fits due to 365s outliers 365s --kmer-specific-sd Estimate standard deviation for each k-mers 365s individually. 365s --upstream-bases {0,1,2,3,4} 365s Upstream bases in k-mer. Default: 1 365s --downstream-bases {0,1,2,3,4} 365s Downstream bases in k-mer. Default: 2 365s 365s Filtering Arguments: 365s --minimum-test-reads MINIMUM_TEST_READS 365s Number of reads required at a position to perform 365s significance testing or contribute to model 365s estimation. Default: 10 365s --coverage-threshold COVERAGE_THRESHOLD 365s Maximum mean coverage per region when estimating k-mer 365s model (limits compute time for deep samples). Default: 365s 100 365s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 365s Number of each k-mer observations required in order to 365s produce a reference (genomic locations for standard 365s reference and per-read for alternative reference). 365s Default: 5 365s 365s Multiprocessing Arguments: 365s --multiprocess-region-size MULTIPROCESS_REGION_SIZE 365s Size of regions over which to multiprocesses statistic 365s computation. For very deep samples a smaller value is 365s recommmended in order to control memory consumption. 365s Default: 10000 365s --processes PROCESSES 365s Number of processes. Default: 1 365s 365s FAST5 Data Arguments: 365s --corrected-group CORRECTED_GROUP 365s FAST5 group created by resquiggle command. Default: 365s RawGenomeCorrected_000 365s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 365s FAST5 subgroup(s) (under /Analyses/[--basecall- 365s group]/) containing basecalls and created within 365s [--corrected-group] containing re-squiggle results. 365s Default: ['BaseCalled_template'] 365s 365s Miscellaneous Arguments: 365s --quiet, -q Don't print status information. 365s --help, -h Print this help message and exit 365s usage: tombo build_model estimate_alt_reference 365s --alternate-model-filename ALTERNATE_MODEL_FILENAME 365s --alternate-model-name ALTERNATE_MODEL_NAME 365s --alternate-model-base {A,C,G,T} 365s [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]] 365s [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]] 365s [--alternate-density-filename ALTERNATE_DENSITY_FILENAME] 365s [--control-density-filename CONTROL_DENSITY_FILENAME] 365s [--dna] [--rna] 365s [--tombo-model-filename TOMBO_MODEL_FILENAME] 365s [--alt-fraction-percentile ALT_FRACTION_PERCENTILE] 365s [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH] 365s [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS] 365s [--save-density-basename SAVE_DENSITY_BASENAME] 365s [--processes PROCESSES] 365s [--corrected-group CORRECTED_GROUP] 365s [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]] 365s [--quiet] [--help] 365s 365s Required Arguments: 365s --alternate-model-filename ALTERNATE_MODEL_FILENAME 365s Tombo model for alternative likelihood ratio 365s significance testing. 365s --alternate-model-name ALTERNATE_MODEL_NAME 365s A short name to associate with this alternate model 365s (e.g. 5mC, 6mA, etc.). This text will be included in 365s output filenames when this model is used for testing. 365s --alternate-model-base {A,C,G,T} 365s Non-standard base is an alternative to this base. 365s 365s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates): 365s --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...] 365s Directories containing fast5 files. 365s --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...] 365s Set of directories containing fast5 files for control 365s reads, containing only canonical nucleotides. 365s --alternate-density-filename ALTERNATE_DENSITY_FILENAME 365s File containing k-mer level kernel density estimates 365s for the alternative sample saved using --save-density- 365s basename. 365s --control-density-filename CONTROL_DENSITY_FILENAME 365s File containing k-mer level kernel density estimates 365s for the control sample saved using --save-density- 365s basename. 365s 365s Standard Model Arguments: 365s --dna Explicitly select canonical DNA model. Default: 365s Automatically determine from FAST5s 365s --rna Explicitly select canonical RNA model. Default: 365s Automatically determine from FAST5s 365s --tombo-model-filename TOMBO_MODEL_FILENAME 365s Tombo model filename. If no file is provided, the 365s default DNA or RNA Tombo model will be used. 365s 365s Model Fitting Arguments: 365s --alt-fraction-percentile ALT_FRACTION_PERCENTILE 365s When esitmating the alternative base incorporation 365s rate, this percent of k-mers are assumed to have 365s significantly shifted signal so the alternative 365s distribution minimally overlaps the standard base 365s distribution. Default: 5.000000 365s --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH 365s Bandwidth applied when performing Gaussian kernal 365s density esitmation on standard and alternative base 365s signal distributions. Default: 0.050000 365s 365s Filtering Argument: 365s --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS 365s Number of each k-mer observations required in order to 365s produce a reference (genomic locations for standard 365s reference and per-read for alternative reference). 365s Default: 1000 365s 365s Output Argument: 365s --save-density-basename SAVE_DENSITY_BASENAME 365s Basename to save alternative model estimation density 365s estimation information. See scripts/debug_est_alt.R 365s for info use example. Default: Don't save. 365s 365s Multiprocessing Arguments: 365s --processes PROCESSES 365s Number of processes. Default: 1 365s 365s FAST5 Data Arguments: 365s --corrected-group CORRECTED_GROUP 365s FAST5 group created by resquiggle command. Default: 365s RawGenomeCorrected_000 365s --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...] 365s FAST5 subgroup(s) (under /Analyses/[--basecall- 365s group]/) containing basecalls and created within 365s [--corrected-group] containing re-squiggle results. 365s Default: ['BaseCalled_template'] 365s 365s Miscellaneous Arguments: 365s --quiet, -q Don't print status information. 365s --help, -h Print this help message and exit 365s This test only tests the help system 365s There is an extensive test in 365s 365s tombo/tests/shell_tests.sh 365s 365s but this requires to download larger data 365s sets which is not done for the moment. 366s autopkgtest [17:14:20]: test run-unit-test: -----------------------] 366s autopkgtest [17:14:20]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 366s run-unit-test PASS 367s autopkgtest [17:14:21]: @@@@@@@@@@@@@@@@@@@@ summary 367s run-unit-test PASS 372s nova [W] Using flock in prodstack6-arm64 372s flock: timeout while waiting to get lock 372s Creating nova instance adt-plucky-arm64-tombo-20250315-170814-juju-7f2275-prod-proposed-migration-environment-20-ba8dad15-1bc4-41d3-9a8c-bc02925a727b from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 372s nova [W] Timed out waiting for b5735906-a05d-4ec8-92ad-7c13dc959c4e to get deleted.