{"action":"created","issue":{"url":"https://api.github.com/repos/Victorian-Bioinformatics-Consortium/prokka/issues/32","labels_url":"https://api.github.com/repos/Victorian-Bioinformatics-Consortium/prokka/issues/32/labels{/name}","comments_url":"https://api.github.com/repos/Victorian-Bioinformatics-Consortium/prokka/issues/32/comments","events_url":"https://api.github.com/repos/Victorian-Bioinformatics-Consortium/prokka/issues/32/events","html_url":"https://github.com/Victorian-Bioinformatics-Consortium/prokka/issues/32","id":40604609,"number":32,"title":"Overly long locustag/prefix results in bad GenBank LOCUS lines","user":{"login":"peterjc","id":63959,"avatar_url":"https://avatars.githubusercontent.com/u/63959?v=3","gravatar_id":"","url":"https://api.github.com/users/peterjc","html_url":"https://github.com/peterjc","followers_url":"https://api.github.com/users/peterjc/followers","following_url":"https://api.github.com/users/peterjc/following{/other_user}","gists_url":"https://api.github.com/users/peterjc/gists{/gist_id}","starred_url":"https://api.github.com/users/peterjc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/peterjc/subscriptions","organizations_url":"https://api.github.com/users/peterjc/orgs","repos_url":"https://api.github.com/users/peterjc/repos","events_url":"https://api.github.com/users/peterjc/events{/privacy}","received_events_url":"https://api.github.com/users/peterjc/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/Victorian-Bioinformatics-Consortium/prokka/labels/bug","name":"bug","color":"fc2929"}],"state":"open","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":5,"created_at":"2014-08-19T15:38:30Z","updated_at":"2015-02-14T05:22:18Z","closed_at":null,"body":"Prokka 1.10 can produce broken GenBank output with over-long identifiers in the LOCUS lines.\r\n\r\nSample input (anonymised since this is for a collaborator):\r\n\r\n```\r\n/opt/prokka-1.10/bin/prokka --outdir XYZ123draft2_prokka --prefix XYZ123draft2 --locustag XYZ123draft2 --compliant --kingdom Bacteria --gram neg --genus ... --species ... --strain XYZ123 --quiet XZY123_draft2.fasta\r\n```\r\n\r\nSample output:\r\n\r\n```\r\n$ grep LOCUS XYZ123draft2.gbk \r\nLOCUS       XYZ123draft2_contig000001119615 bp   DNA   linear       19-AUG-2014\r\nLOCUS       XYZ123draft2_contig000002170983 bp   DNA   linear       19-AUG-2014\r\n...\r\n```\r\n\r\nThe LOCUS identifier is too long for the strict GenBank format, and there is no white space between the (truncated) identifier and the sequence length, meaning for example Biopython complains.\r\n\r\nPossible output with truncation (not ideal) to ensure a white space would be something like this:\r\n\r\n```\r\n$ grep LOCUS XYZ123draft2.gbk \r\nLOCUS       XYZ123draft2_contig0000 1119615 bp   DNA   linear       19-AUG-2014\r\nLOCUS       XYZ123draft2_contig0000 2170983 bp   DNA   linear       19-AUG-2014\r\n...\r\n```\r\n\r\nPossible output abusing the LOCUS line (also not ideal, but some parsers will cope):\r\n\r\n```\r\n$ grep LOCUS XYZ123draft2.gbk \r\nLOCUS       XYZ123draft2_contig000001 1119615 bp   DNA   linear       19-AUG-2014\r\nLOCUS       XYZ123draft2_contig000002 2170983 bp   DNA   linear       19-AUG-2014\r\n...\r\n```\r\n\r\nExpected output: Fail early complaining about the overly long identifiers which will cause problems, specifying which option should be changed."},"comment":{"url":"https://api.github.com/repos/Victorian-Bioinformatics-Consortium/prokka/issues/comments/74362538","html_url":"https://github.com/Victorian-Bioinformatics-Consortium/prokka/issues/32#issuecomment-74362538","issue_url":"https://api.github.com/repos/Victorian-Bioinformatics-Consortium/prokka/issues/32","id":74362538,"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":"2015-02-14T05:22:18Z","updated_at":"2015-02-14T05:22:18Z","body":"Although the LOCUS is limited to 16 characters in the spec, the LENGTH  is right-justified and given 11 characters. Because contigs in Bacteria are rarely more than 10Mbp, it only uses 7 of those, leaving 4 extra for the LOCUS. tbl2asn seems to honour this. I'm going to set my MAXCONTIGIDLEN to 20."}}