{"action":"created","issue":{"url":"https://api.github.com/repos/nanoporetech/tombo/issues/70","repository_url":"https://api.github.com/repos/nanoporetech/tombo","labels_url":"https://api.github.com/repos/nanoporetech/tombo/issues/70/labels{/name}","comments_url":"https://api.github.com/repos/nanoporetech/tombo/issues/70/comments","events_url":"https://api.github.com/repos/nanoporetech/tombo/issues/70/events","html_url":"https://github.com/nanoporetech/tombo/issues/70","id":332427550,"node_id":"MDU6SXNzdWUzMzI0Mjc1NTA=","number":70,"title":"resquiggle hangs","user":{"login":"phiweger","id":3918306,"node_id":"MDQ6VXNlcjM5MTgzMDY=","avatar_url":"https://avatars3.githubusercontent.com/u/3918306?v=4","gravatar_id":"","url":"https://api.github.com/users/phiweger","html_url":"https://github.com/phiweger","followers_url":"https://api.github.com/users/phiweger/followers","following_url":"https://api.github.com/users/phiweger/following{/other_user}","gists_url":"https://api.github.com/users/phiweger/gists{/gist_id}","starred_url":"https://api.github.com/users/phiweger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/phiweger/subscriptions","organizations_url":"https://api.github.com/users/phiweger/orgs","repos_url":"https://api.github.com/users/phiweger/repos","events_url":"https://api.github.com/users/phiweger/events{/privacy}","received_events_url":"https://api.github.com/users/phiweger/received_events","type":"User","site_admin":false},"labels":[{"id":754143538,"node_id":"MDU6TGFiZWw3NTQxNDM1Mzg=","url":"https://api.github.com/repos/nanoporetech/tombo/labels/bug","name":"bug","color":"ee0701","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":8,"created_at":"2018-06-14T14:27:36Z","updated_at":"2018-06-14T20:28:28Z","closed_at":null,"author_association":"NONE","body":"I run tombo preprocess like so (from a snakemake file):\r\n\r\n```\r\n        tombo preprocess annotate_raw_with_fastqs \\\r\n            --overwrite \\\r\n            --fast5-basedir {input.signal} \\\r\n            --fastq-filenames {input.reads} \\\r\n            --sequencing-summary-filenames {input.map_} \\\r\n            --processes {threads}\r\n\r\n        tombo resquiggle \\\r\n            {input.signal} \\\r\n            {input.consensus} \\\r\n            --processes {threads}\r\n```\r\n\r\n`input.signal` is the `/path/to/fast5` and `input.reads` is the path to the concatenated fastq files from one barcode of a flow cell run w/ native barcoding. `input.consensus` is the nanopolished assembly of the barcoded reads.\r\n\r\nTombo starts but only annotates a part of the FAST5s (i.e. stops at iteration 297949/2046309 -- this coincides w/ the number of reads assigned to the barcode). It then seems to continue w/ the resquiggle command, but the CPU is idle, i.e. nothing happens anymore. There is no error thrown.\r\n\r\n```\r\n[16:10:12] Getting read filenames.\r\n[16:10:47] Parsing sequencing summary files.\r\n[16:10:54] Annotating FAST5s with sequence from FASTQs.\r\n 15%|███████▊                                              | 297949/2046309 [06:36<38:47, 751.21it/s]\r\n[16:17:31] Added sequences to a total of 297949 reads.\r\n[16:17:32] Loading minimap2 reference.\r\n[16:17:33] Getting file list.\r\n[16:18:06] Using default canonical ***** DNA ***** model.\r\n```\r\n\r\nWhat could be the issue here?\r\n\r\nThank you,\r\nAdrian"},"comment":{"url":"https://api.github.com/repos/nanoporetech/tombo/issues/comments/397427868","html_url":"https://github.com/nanoporetech/tombo/issues/70#issuecomment-397427868","issue_url":"https://api.github.com/repos/nanoporetech/tombo/issues/70","id":397427868,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NzQyNzg2OA==","user":{"login":"phiweger","id":3918306,"node_id":"MDQ6VXNlcjM5MTgzMDY=","avatar_url":"https://avatars3.githubusercontent.com/u/3918306?v=4","gravatar_id":"","url":"https://api.github.com/users/phiweger","html_url":"https://github.com/phiweger","followers_url":"https://api.github.com/users/phiweger/followers","following_url":"https://api.github.com/users/phiweger/following{/other_user}","gists_url":"https://api.github.com/users/phiweger/gists{/gist_id}","starred_url":"https://api.github.com/users/phiweger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/phiweger/subscriptions","organizations_url":"https://api.github.com/users/phiweger/orgs","repos_url":"https://api.github.com/users/phiweger/repos","events_url":"https://api.github.com/users/phiweger/events{/privacy}","received_events_url":"https://api.github.com/users/phiweger/received_events","type":"User","site_admin":false},"created_at":"2018-06-14T20:28:28Z","updated_at":"2018-06-14T20:28:28Z","author_association":"NONE","body":"However, if I understand this correctly, it seems resquiggle finishes, despite the threading issue?"}}
{"actor":{"display_login":"phiweger"}}