{"action":"created","issue":{"url":"https://api.github.com/repos/FRED-2/OptiType/issues/25","repository_url":"https://api.github.com/repos/FRED-2/OptiType","labels_url":"https://api.github.com/repos/FRED-2/OptiType/issues/25/labels{/name}","comments_url":"https://api.github.com/repos/FRED-2/OptiType/issues/25/comments","events_url":"https://api.github.com/repos/FRED-2/OptiType/issues/25/events","html_url":"https://github.com/FRED-2/OptiType/issues/25","id":135983219,"number":25,"title":"Error message for too few reads","user":{"login":"alvinwt","id":3662163,"avatar_url":"https://avatars.githubusercontent.com/u/3662163?v=3","gravatar_id":"","url":"https://api.github.com/users/alvinwt","html_url":"https://github.com/alvinwt","followers_url":"https://api.github.com/users/alvinwt/followers","following_url":"https://api.github.com/users/alvinwt/following{/other_user}","gists_url":"https://api.github.com/users/alvinwt/gists{/gist_id}","starred_url":"https://api.github.com/users/alvinwt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alvinwt/subscriptions","organizations_url":"https://api.github.com/users/alvinwt/orgs","repos_url":"https://api.github.com/users/alvinwt/repos","events_url":"https://api.github.com/users/alvinwt/events{/privacy}","received_events_url":"https://api.github.com/users/alvinwt/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-02-24T07:34:04Z","updated_at":"2016-02-24T09:34:36Z","closed_at":null,"body":"Hi, I have been getting \r\n\r\n````\r\nTraceback (most recent call last):\r\n  File \"/data/rozencompute2/a0073895/optitest/OptiType/OptiTypePipeline.py\", line 304, in <module>\r\n    \"in your config file (currently %.3f), because you may need to resort to using unpaired reads.\") % unpaired_weight\r\nTypeError: not enough arguments for format string\r\n````\r\n\r\neven when I have changed the unpaired weights in the config.ini file to 1. I am wondering if this is a error message when there are few reads in the input fastq or if something else is happening."},"comment":{"url":"https://api.github.com/repos/FRED-2/OptiType/issues/comments/188161880","html_url":"https://github.com/FRED-2/OptiType/issues/25#issuecomment-188161880","issue_url":"https://api.github.com/repos/FRED-2/OptiType/issues/25","id":188161880,"user":{"login":"andras86","id":3963729,"avatar_url":"https://avatars.githubusercontent.com/u/3963729?v=3","gravatar_id":"","url":"https://api.github.com/users/andras86","html_url":"https://github.com/andras86","followers_url":"https://api.github.com/users/andras86/followers","following_url":"https://api.github.com/users/andras86/following{/other_user}","gists_url":"https://api.github.com/users/andras86/gists{/gist_id}","starred_url":"https://api.github.com/users/andras86/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andras86/subscriptions","organizations_url":"https://api.github.com/users/andras86/orgs","repos_url":"https://api.github.com/users/andras86/repos","events_url":"https://api.github.com/users/andras86/events{/privacy}","received_events_url":"https://api.github.com/users/andras86/received_events","type":"User","site_admin":false},"created_at":"2016-02-24T09:34:36Z","updated_at":"2016-02-24T09:34:36Z","body":"And forgot to answer your question: you get this warning if your HLA reads' individual ends can't be paired up consistently (i.e. both ends mapping to at least one common allele) for more than 10% of them. I could only see this happen for very long insert sizes where one end always falls in the exon2-exon3 reference window but the other is always left out."}}