{"action":"created","issue":{"url":"https://api.github.com/repos/tseemann/prokka/issues/138","labels_url":"https://api.github.com/repos/tseemann/prokka/issues/138/labels{/name}","comments_url":"https://api.github.com/repos/tseemann/prokka/issues/138/comments","events_url":"https://api.github.com/repos/tseemann/prokka/issues/138/events","html_url":"https://github.com/tseemann/prokka/issues/138","id":114865624,"number":138,"title":"A problem running prokka with rnammer","user":{"login":"JohnYu-yuzhongyi","id":15346928,"avatar_url":"https://avatars.githubusercontent.com/u/15346928?v=3","gravatar_id":"","url":"https://api.github.com/users/JohnYu-yuzhongyi","html_url":"https://github.com/JohnYu-yuzhongyi","followers_url":"https://api.github.com/users/JohnYu-yuzhongyi/followers","following_url":"https://api.github.com/users/JohnYu-yuzhongyi/following{/other_user}","gists_url":"https://api.github.com/users/JohnYu-yuzhongyi/gists{/gist_id}","starred_url":"https://api.github.com/users/JohnYu-yuzhongyi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JohnYu-yuzhongyi/subscriptions","organizations_url":"https://api.github.com/users/JohnYu-yuzhongyi/orgs","repos_url":"https://api.github.com/users/JohnYu-yuzhongyi/repos","events_url":"https://api.github.com/users/JohnYu-yuzhongyi/events{/privacy}","received_events_url":"https://api.github.com/users/JohnYu-yuzhongyi/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/tseemann/prokka/labels/question","name":"question","color":"cc317c"}],"state":"closed","locked":false,"assignee":{"login":"tseemann","id":453972,"avatar_url":"https://avatars.githubusercontent.com/u/453972?v=3","gravatar_id":"","url":"https://api.github.com/users/tseemann","html_url":"https://github.com/tseemann","followers_url":"https://api.github.com/users/tseemann/followers","following_url":"https://api.github.com/users/tseemann/following{/other_user}","gists_url":"https://api.github.com/users/tseemann/gists{/gist_id}","starred_url":"https://api.github.com/users/tseemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tseemann/subscriptions","organizations_url":"https://api.github.com/users/tseemann/orgs","repos_url":"https://api.github.com/users/tseemann/repos","events_url":"https://api.github.com/users/tseemann/events{/privacy}","received_events_url":"https://api.github.com/users/tseemann/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2015-11-03T17:20:17Z","updated_at":"2015-11-05T03:10:45Z","closed_at":"2015-11-05T03:10:45Z","body":"Hi I'm trying to run Prokka 1.11 with the rnammer option. But an error comes out when prokka is running rnammer:\r\n\r\n[17:02:38] Running: rnammer -S bac -multi -xml test1\\/rnammer\\.xml test1\\/PROKKA_11032015\\.fna\r\n\r\n\r\n\r\nCould not open file './85633.tsu.xml' for reading:No such file or directory\r\n[17:02:42] Could not run command: rnammer -S bac -multi -xml test1\\/rnammer\\.xml test1\\/PROKKA_11032015\\.fna\r\n\r\nI can't find anything online of someone having the same problem.\r\n\r\nI think it might be because my rnammer or hmmer is not properly installed because in the manual of rnammer it says I can run a test \r\nperl rnammer -S bac -m lsu,ssu,tsu -gff - < example/ecoli.fsa\r\nBut when I run it, it doesn't give any result, although it doesn't give any error either.\r\n\r\nI'm not sure what should I do to fix this issue?\r\n\r\nThanks!\r\n"},"comment":{"url":"https://api.github.com/repos/tseemann/prokka/issues/comments/153942050","html_url":"https://github.com/tseemann/prokka/issues/138#issuecomment-153942050","issue_url":"https://api.github.com/repos/tseemann/prokka/issues/138","id":153942050,"user":{"login":"tseemann","id":453972,"avatar_url":"https://avatars.githubusercontent.com/u/453972?v=3","gravatar_id":"","url":"https://api.github.com/users/tseemann","html_url":"https://github.com/tseemann","followers_url":"https://api.github.com/users/tseemann/followers","following_url":"https://api.github.com/users/tseemann/following{/other_user}","gists_url":"https://api.github.com/users/tseemann/gists{/gist_id}","starred_url":"https://api.github.com/users/tseemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tseemann/subscriptions","organizations_url":"https://api.github.com/users/tseemann/orgs","repos_url":"https://api.github.com/users/tseemann/repos","events_url":"https://api.github.com/users/tseemann/events{/privacy}","received_events_url":"https://api.github.com/users/tseemann/received_events","type":"User","site_admin":false},"created_at":"2015-11-05T03:10:45Z","updated_at":"2015-11-05T03:10:45Z","body":"This is not really a problem with Prokka. Your `rnammer` is not working. \r\n\r\nHave you read this?\r\n https://github.com/tseemann/prokka#option-3---rnammer "}}