{"action":"created","issue":{"url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/147","repository_url":"https://api.github.com/repos/nextgenusfs/funannotate","labels_url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/147/labels{/name}","comments_url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/147/comments","events_url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/147/events","html_url":"https://github.com/nextgenusfs/funannotate/issues/147","id":301575685,"number":147,"title":"Funannotate clean error","user":{"login":"ignadb","id":36970114,"avatar_url":"https://avatars1.githubusercontent.com/u/36970114?v=4","gravatar_id":"","url":"https://api.github.com/users/ignadb","html_url":"https://github.com/ignadb","followers_url":"https://api.github.com/users/ignadb/followers","following_url":"https://api.github.com/users/ignadb/following{/other_user}","gists_url":"https://api.github.com/users/ignadb/gists{/gist_id}","starred_url":"https://api.github.com/users/ignadb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ignadb/subscriptions","organizations_url":"https://api.github.com/users/ignadb/orgs","repos_url":"https://api.github.com/users/ignadb/repos","events_url":"https://api.github.com/users/ignadb/events{/privacy}","received_events_url":"https://api.github.com/users/ignadb/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-03-01T22:00:46Z","updated_at":"2018-03-02T16:51:44Z","closed_at":null,"author_association":"NONE","body":"When running funannotate clean, it exits after a few seconds with the following error messages:\r\n\r\n-----------------------------------------------\r\n1,714 input contigs, 1,714 larger than 500 bp, N50 is 156,341 bp\r\nChecking duplication of 1,583 contigs shorter than N50\r\n-----------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"xxx/funannotate/bin/funannotate-contig_cleaner.py\", line 174, in <module>\r\n    runNucmer('query.fa', 'reference.fa', scaffolds[i])\r\n  File \"xxx/funannotate/bin/funannotate-contig_cleaner.py\", line 120, in runNucmer\r\n    os.remove(input)\r\nOSError: [Errno 2] No such file or directory: 'LLCB01001711.1.delta'\r\n\r\nThere is also a file called nucmer.error which contains the following info:\r\n20180301|225801| 18737| ERROR: mummer and/or mgaps returned non-zero\r\n\r\nUnfortunately I cannot seem to find any further log files to see what could be the issue, any ideas?\r\n\r\nThanks in advance!\r\n"},"comment":{"url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/comments/369980382","html_url":"https://github.com/nextgenusfs/funannotate/issues/147#issuecomment-369980382","issue_url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/147","id":369980382,"user":{"login":"nextgenusfs","id":6164308,"avatar_url":"https://avatars2.githubusercontent.com/u/6164308?v=4","gravatar_id":"","url":"https://api.github.com/users/nextgenusfs","html_url":"https://github.com/nextgenusfs","followers_url":"https://api.github.com/users/nextgenusfs/followers","following_url":"https://api.github.com/users/nextgenusfs/following{/other_user}","gists_url":"https://api.github.com/users/nextgenusfs/gists{/gist_id}","starred_url":"https://api.github.com/users/nextgenusfs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nextgenusfs/subscriptions","organizations_url":"https://api.github.com/users/nextgenusfs/orgs","repos_url":"https://api.github.com/users/nextgenusfs/repos","events_url":"https://api.github.com/users/nextgenusfs/events{/privacy}","received_events_url":"https://api.github.com/users/nextgenusfs/received_events","type":"User","site_admin":false},"created_at":"2018-03-02T16:51:44Z","updated_at":"2018-03-02T16:51:44Z","author_association":"OWNER","body":"Okay, and then there was an output file called `test.delta` that was created?  If so, then that isn't the error.  But there is obviously an error...\r\n```\r\nThere is also a file called nucmer.error which contains the following info:\r\n20180301|225801| 18737| ERROR: mummer and/or mgaps returned non-zero\r\n```\r\nHave you checked for any empty contigs in your fasta file?  Not sure what else the problem could be. "}}
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