{"action":"opened","issue":{"url":"https://api.github.com/repos/infphilo/hisat2/issues/33","repository_url":"https://api.github.com/repos/infphilo/hisat2","labels_url":"https://api.github.com/repos/infphilo/hisat2/issues/33/labels{/name}","comments_url":"https://api.github.com/repos/infphilo/hisat2/issues/33/comments","events_url":"https://api.github.com/repos/infphilo/hisat2/issues/33/events","html_url":"https://github.com/infphilo/hisat2/issues/33","id":147993801,"number":33,"title":"Corrupted index makes hisat2 run forever","user":{"login":"sklages","id":1837422,"avatar_url":"https://avatars.githubusercontent.com/u/1837422?v=3","gravatar_id":"","url":"https://api.github.com/users/sklages","html_url":"https://github.com/sklages","followers_url":"https://api.github.com/users/sklages/followers","following_url":"https://api.github.com/users/sklages/following{/other_user}","gists_url":"https://api.github.com/users/sklages/gists{/gist_id}","starred_url":"https://api.github.com/users/sklages/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sklages/subscriptions","organizations_url":"https://api.github.com/users/sklages/orgs","repos_url":"https://api.github.com/users/sklages/repos","events_url":"https://api.github.com/users/sklages/events{/privacy}","received_events_url":"https://api.github.com/users/sklages/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-04-13T09:03:22Z","updated_at":"2016-04-13T09:03:22Z","closed_at":null,"body":"Hi,\r\n\r\nwe created a GRCh37 index (with some extra MHC haplotype sequences included). There was no \"eye-catching\" error and we went on aligning or datasets with `hisat2` against this index.\r\nThese jobs were running on one single cpu core (-p 12 was used) \"forever\". \r\n`strace` was just dumping `read(6, \"\", 4096) = 0` ... and obviously nothing happened ...\r\nSo we took a closer look at the index. There were two files missing (5+6).\r\n\r\n* In case of an error you could make the error message more \"eye-catching\" during or after building the index. You could even remove the incomplete index to make people aware that there was sth. serious going wrong.\r\n\r\n* the alignment process (or the wrapper hisat2) should probably check if the index is complete and not corrupted.\r\n\r\nGreat tool though, .. just my 2p ;-)\r\nSven"}}