{"action":"opened","issue":{"url":"https://api.github.com/repos/dib-lab/khmer/issues/1338","labels_url":"https://api.github.com/repos/dib-lab/khmer/issues/1338/labels{/name}","comments_url":"https://api.github.com/repos/dib-lab/khmer/issues/1338/comments","events_url":"https://api.github.com/repos/dib-lab/khmer/issues/1338/events","html_url":"https://github.com/dib-lab/khmer/issues/1338","id":127462120,"number":1338,"title":"How to debug 'Unpaired reads when require_paired is set!'?","user":{"login":"bede","id":1007616,"avatar_url":"https://avatars.githubusercontent.com/u/1007616?v=3","gravatar_id":"","url":"https://api.github.com/users/bede","html_url":"https://github.com/bede","followers_url":"https://api.github.com/users/bede/followers","following_url":"https://api.github.com/users/bede/following{/other_user}","gists_url":"https://api.github.com/users/bede/gists{/gist_id}","starred_url":"https://api.github.com/users/bede/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bede/subscriptions","organizations_url":"https://api.github.com/users/bede/orgs","repos_url":"https://api.github.com/users/bede/repos","events_url":"https://api.github.com/users/bede/events{/privacy}","received_events_url":"https://api.github.com/users/bede/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-01-19T14:50:18Z","updated_at":"2016-01-19T14:50:18Z","closed_at":null,"body":"I have a some interleaved reads which `normalize-by-median.py` doesn't like in paired end mode. They have been interleaved using `interleave-reads.py`  \r\nCommand:\r\n```\r\nnormalize-by-median.py -C {c} -k {k} -N 4 -x 1e9 -p  {out}/trim/{name}.fr.fastq\r\n```\r\nError:\r\n```\r\nERROR: Unpaired reads when require_paired is set!\r\n```\r\nI've put these reads them through a paired read validation script and they pass. A small subset of the reads works fine. Is there a way to get Screed to report the culprit line(s)? How do I debug this issue? I've set the logging level to `INFO` but it still doesn't provide any helpful info.\r\n\r\nBelow are the first two reads from one such file, but running just these two reads *doesn't* cause the crash:\r\n```\r\n@M02383:22:000000000-A9G0P:1:1101:14743:1579 1:N:0:4\r\nCATCAATTCAACTCTTCAGGTTGCCCCGAGAGGATGGCCAGCTGCAGACCCCTCGCCGATTTCGATCAAGGCTGGGGCCCTATCAGCTACGCCAACGGAAGCGGCCCCGAACACCGGCCCTACTGCTGGCACTATCCTCCAAAGCCTTGTG\r\n+\r\n1>AAADFFFFFFGGGGG3BFGGCFHHFEGEAA0BGEAEGHHGHHHFFEHGHGGGGGGGGGGGHFFGHFHHHHHHGGGGGGHHHHHHHHHHGGGGGGEGGGEGCGGGGGGGCCCGEGCGGGHHHHGHHGHGHHHHHHHHHHHHEHHHHHHHH\r\n@M02383:22:000000000-A9G0P:1:1101:14743:1579 2:N:0:4\r\nCACCCCTCCGATGACACAAGGAGGCGCTCCGCACACTTTGGTACATCCAGATGAGTTCATCCAGGTGCAACCGAACCAATTGCCCAACGGTGGCCTGGTGTTGTTGAGGACGAAGACGTCCGTATCATTCTCACCCCAGTTGTAGGTAGG\r\n+\r\nBBBBBBABBABBEBBFGGGBABBEFGGGGGFGGGGHHHHBFBD55DFGEGHHHEGHHHHHHHGFBFHHG@GHGGCGGHFHHHGHHHHGGGGHGHHHGGHHHGGHHHHHHHHG?FGGHGGGGGGHFHHHHHHHHHHHGGGHHGHHGHHB1E\r\n```\r\n"}}