{"action":"created","issue":{"url":"https://api.github.com/repos/jts/nanopolish/issues/73","repository_url":"https://api.github.com/repos/jts/nanopolish","labels_url":"https://api.github.com/repos/jts/nanopolish/issues/73/labels{/name}","comments_url":"https://api.github.com/repos/jts/nanopolish/issues/73/comments","events_url":"https://api.github.com/repos/jts/nanopolish/issues/73/events","html_url":"https://github.com/jts/nanopolish/issues/73","id":179455767,"number":73,"title":"Corrupt read, but which one?","user":{"login":"hjjansen","id":8056295,"avatar_url":"https://avatars.githubusercontent.com/u/8056295?v=3","gravatar_id":"","url":"https://api.github.com/users/hjjansen","html_url":"https://github.com/hjjansen","followers_url":"https://api.github.com/users/hjjansen/followers","following_url":"https://api.github.com/users/hjjansen/following{/other_user}","gists_url":"https://api.github.com/users/hjjansen/gists{/gist_id}","starred_url":"https://api.github.com/users/hjjansen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hjjansen/subscriptions","organizations_url":"https://api.github.com/users/hjjansen/orgs","repos_url":"https://api.github.com/users/hjjansen/repos","events_url":"https://api.github.com/users/hjjansen/events{/privacy}","received_events_url":"https://api.github.com/users/hjjansen/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2016-09-27T10:31:46Z","updated_at":"2016-09-30T14:00:33Z","closed_at":null,"body":"Hi Jared,\r\n\r\nI'm running nanopolish 0.5. When I align the sequences with bwa mem all reads align and no errors are reported. When I then use eventalign to align the events one error is reported:\r\n```\r\nHDF5-DIAG: Error detected in HDF5 (1.8.14) thread 140689784518592:\r\n  #000: H5Dio.c line 173 in H5Dread(): can't read data\r\n    major: Dataset\r\n    minor: Read failed\r\n  #001: H5Dio.c line 550 in H5D__read(): can't read data\r\n    major: Dataset\r\n    minor: Read failed\r\n  #002: H5Dchunk.c line 1872 in H5D__chunk_read(): unable to read raw data chunk\r\n    major: Low-level I/O\r\n    minor: Read failed\r\n  #003: H5Dchunk.c line 2902 in H5D__chunk_lock(): data pipeline read failed\r\n    major: Data filters\r\n    minor: Filter operation failed\r\n  #004: H5Z.c line 1382 in H5Z_pipeline(): filter returned failure during read\r\n    major: Data filters\r\n    minor: Read failed\r\n  #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed\r\n    major: Data filters\r\n    minor: Unable to initialize object\r\nterminate called after throwing an instance of 'hdf5_tools::Exception'\r\n  what():  /Analyses/Basecall_1D_000/BaseCalled_template/Events: error in H5Dread\r\nAborted (core dumped)\r\n```\r\neventalign will finish and produce an alignment file which is used to polish the contigs. Unfortunately four 10 Kbp chunks of one contig are missing and the merge command will fail when it tries to merge the corrected chunks.\r\nFrom the error message I suspect one of the reads has a problem in the event part of the hdf5 file.\r\nIs there a way to find out which read is corrupt so I can remove it from the dataset?\r\n\r\nThanks,\r\n\r\n Hans Jansen"},"comment":{"url":"https://api.github.com/repos/jts/nanopolish/issues/comments/250751649","html_url":"https://github.com/jts/nanopolish/issues/73#issuecomment-250751649","issue_url":"https://api.github.com/repos/jts/nanopolish/issues/73","id":250751649,"user":{"login":"jts","id":389535,"avatar_url":"https://avatars.githubusercontent.com/u/389535?v=3","gravatar_id":"","url":"https://api.github.com/users/jts","html_url":"https://github.com/jts","followers_url":"https://api.github.com/users/jts/followers","following_url":"https://api.github.com/users/jts/following{/other_user}","gists_url":"https://api.github.com/users/jts/gists{/gist_id}","starred_url":"https://api.github.com/users/jts/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jts/subscriptions","organizations_url":"https://api.github.com/users/jts/orgs","repos_url":"https://api.github.com/users/jts/repos","events_url":"https://api.github.com/users/jts/events{/privacy}","received_events_url":"https://api.github.com/users/jts/received_events","type":"User","site_admin":false},"created_at":"2016-09-30T14:00:32Z","updated_at":"2016-09-30T14:00:32Z","body":"If you can isolate the read(s) that cause the problem using the code @mateidavid provides above, we'd be happy to take a closer look."}}
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