{"action":"created","issue":{"url":"https://api.github.com/repos/merenlab/illumina-utils/issues/17","repository_url":"https://api.github.com/repos/merenlab/illumina-utils","labels_url":"https://api.github.com/repos/merenlab/illumina-utils/issues/17/labels{/name}","comments_url":"https://api.github.com/repos/merenlab/illumina-utils/issues/17/comments","events_url":"https://api.github.com/repos/merenlab/illumina-utils/issues/17/events","html_url":"https://github.com/merenlab/illumina-utils/issues/17","id":314098590,"number":17,"title":"Help interpreting iu-filter-quality-minoche crash","user":{"login":"jarrodscott","id":16192182,"avatar_url":"https://avatars1.githubusercontent.com/u/16192182?v=4","gravatar_id":"","url":"https://api.github.com/users/jarrodscott","html_url":"https://github.com/jarrodscott","followers_url":"https://api.github.com/users/jarrodscott/followers","following_url":"https://api.github.com/users/jarrodscott/following{/other_user}","gists_url":"https://api.github.com/users/jarrodscott/gists{/gist_id}","starred_url":"https://api.github.com/users/jarrodscott/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jarrodscott/subscriptions","organizations_url":"https://api.github.com/users/jarrodscott/orgs","repos_url":"https://api.github.com/users/jarrodscott/repos","events_url":"https://api.github.com/users/jarrodscott/events{/privacy}","received_events_url":"https://api.github.com/users/jarrodscott/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-04-13T13:02:07Z","updated_at":"2018-04-13T13:04:57Z","closed_at":null,"author_association":"NONE","body":"I am hoping someone can help me interpret this error message. I am using  `iu-filter-quality-minoche ` for some NextSeq metagenomes (4xR1, 4XR2 per sample) that i ran through `trimmomatic.` For most of the metagenomes I can run `iu-filter-quality-minoche ` just fine but a few always fail at the same point  in the processing. For this sample it is around 24,000 reads in. If I run  `iu-filter-quality-minoche ` on the raw data before `trimmomatic` I have no issues. So it seems `trimmomatic` is doing something to a read that is causing  `iu-filter-quality-minoche ` to crash. But I don't know how to interpret the error and thus troubleshoot the problem. \r\n\r\n`(num pairs processed: 23,000) `\r\n`(num pairs processed: 24,000)` \r\n`Traceback (most recent call last):`\r\n  `File \"/miniconda3/bin/iu-filter-quality-minoche\", line 313, in <module>`\r\n    `sys.exit(main(config, args))`\r\n  `File \"/miniconda3/bin/iu-filter-quality-minoche\", line 178, in main`\r\n    `p1_passed_qual, p1_trim_to, p1_fate = IsHighQuality(s1, q1, p)`\r\n  `File \"/miniconda3/bin/iu-filter-quality-minoche\", line 68, in IsHighQuality`\r\n    `trim_to = None if len(sequence) == trim_to else trim_to`\r\n`UnboundLocalError: local variable 'trim_to' referenced before assignment`"},"comment":{"url":"https://api.github.com/repos/merenlab/illumina-utils/issues/comments/381128768","html_url":"https://github.com/merenlab/illumina-utils/issues/17#issuecomment-381128768","issue_url":"https://api.github.com/repos/merenlab/illumina-utils/issues/17","id":381128768,"user":{"login":"meren","id":197307,"avatar_url":"https://avatars2.githubusercontent.com/u/197307?v=4","gravatar_id":"","url":"https://api.github.com/users/meren","html_url":"https://github.com/meren","followers_url":"https://api.github.com/users/meren/followers","following_url":"https://api.github.com/users/meren/following{/other_user}","gists_url":"https://api.github.com/users/meren/gists{/gist_id}","starred_url":"https://api.github.com/users/meren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/meren/subscriptions","organizations_url":"https://api.github.com/users/meren/orgs","repos_url":"https://api.github.com/users/meren/repos","events_url":"https://api.github.com/users/meren/events{/privacy}","received_events_url":"https://api.github.com/users/meren/received_events","type":"User","site_admin":false},"created_at":"2018-04-13T13:04:57Z","updated_at":"2018-04-13T13:04:57Z","author_association":"OWNER","body":"Hey Jarrod, which version is this? I thought I fixed that bug awhile ago."}}
{"actor":{"display_login":"meren"}}