{"action":"created","issue":{"url":"https://api.github.com/repos/TheSEED/RASTtk-Distribution/issues/6","repository_url":"https://api.github.com/repos/TheSEED/RASTtk-Distribution","labels_url":"https://api.github.com/repos/TheSEED/RASTtk-Distribution/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/TheSEED/RASTtk-Distribution/issues/6/comments","events_url":"https://api.github.com/repos/TheSEED/RASTtk-Distribution/issues/6/events","html_url":"https://github.com/TheSEED/RASTtk-Distribution/issues/6","id":298039518,"number":6,"title":"JSONRPC error on rast-process-genome","user":{"login":"mberacochea","id":1123897,"avatar_url":"https://avatars3.githubusercontent.com/u/1123897?v=4","gravatar_id":"","url":"https://api.github.com/users/mberacochea","html_url":"https://github.com/mberacochea","followers_url":"https://api.github.com/users/mberacochea/followers","following_url":"https://api.github.com/users/mberacochea/following{/other_user}","gists_url":"https://api.github.com/users/mberacochea/gists{/gist_id}","starred_url":"https://api.github.com/users/mberacochea/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mberacochea/subscriptions","organizations_url":"https://api.github.com/users/mberacochea/orgs","repos_url":"https://api.github.com/users/mberacochea/repos","events_url":"https://api.github.com/users/mberacochea/events{/privacy}","received_events_url":"https://api.github.com/users/mberacochea/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-02-17T21:51:26Z","updated_at":"2018-04-10T22:48:20Z","closed_at":null,"author_association":"NONE","body":"I'm having some issues with `rast-process-genome`. Any help is appreciated.\r\n\r\n```\r\n~> rast-process-genome < uyso24_contigs_ordered.gto > uyso24_contigs_ordered.gto2\r\nJSONRPC error:\r\nError invoking method call_features_CDS_prodigal: error calling CDSs: 65280\r\non command rast_call_CDSs_using_prodigal --input /disks/tmp/i1fhSIPFq8 --output /disks/tmp/d1zqr_Thr0 --id-prefix fig|992418.8 --id-type peg\r\nUse of uninitialized value in pattern match (m//) at /disks/kb/deployment/plbin/rast_call_CDSs_using_prodigal.pl line 52, <$in_fh> line 1.\r\nUse of uninitialized value in concatenation (.) or string at /disks/kb/deployment/plbin/rast_call_CDSs_using_prodigal.pl line 53, <$in_fh> line 1.\r\nInvalid domain: \"\" at /disks/kb/deployment/plbin/rast_call_CDSs_using_prodigal.pl line 53, <$in_fh> line 1.\r\n\r\n\r\nJSONRPC error code: -32603\r\nJSONRPC error data:Error invoking method call_features_CDS_prodigal: error calling CDSs: 65280\r\non command rast_call_CDSs_using_prodigal --input /disks/tmp/i1fhSIPFq8 --output /disks/tmp/d1zqr_Thr0 --id-prefix fig|992418.8 --id-type peg\r\nUse of uninitialized value in pattern match (m//) at /disks/kb/deployment/plbin/rast_call_CDSs_using_prodigal.pl line 52, <$in_fh> line 1.\r\nUse of uninitialized value in concatenation (.) or string at /disks/kb/deployment/plbin/rast_call_CDSs_using_prodigal.pl line 53, <$in_fh> line 1.\r\nInvalid domain: \"\" at /disks/kb/deployment/plbin/rast_call_CDSs_using_prodigal.pl line 53, <$in_fh> line 1.\r\n\r\n\r\n\r\n\r\nTrace begun at /Applications/RASTtk.app/deployment/lib/Bio/KBase/GenomeAnnotation/Client.pm line 20857\r\nBio::KBase::GenomeAnnotation::Client::run_pipeline('Bio::KBase::GenomeAnnotation::Client=HASH(0x7bc23780)', 'HASH(0x7bc30cd0)', 'HASH(0x7bc30de0)') called at /Applications/RASTtk.app/deployment/plbin/rast-process-genome.pl line 142\r\n```"},"comment":{"url":"https://api.github.com/repos/TheSEED/RASTtk-Distribution/issues/comments/380271795","html_url":"https://github.com/TheSEED/RASTtk-Distribution/issues/6#issuecomment-380271795","issue_url":"https://api.github.com/repos/TheSEED/RASTtk-Distribution/issues/6","id":380271795,"user":{"login":"olsonanl","id":2152226,"avatar_url":"https://avatars0.githubusercontent.com/u/2152226?v=4","gravatar_id":"","url":"https://api.github.com/users/olsonanl","html_url":"https://github.com/olsonanl","followers_url":"https://api.github.com/users/olsonanl/followers","following_url":"https://api.github.com/users/olsonanl/following{/other_user}","gists_url":"https://api.github.com/users/olsonanl/gists{/gist_id}","starred_url":"https://api.github.com/users/olsonanl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/olsonanl/subscriptions","organizations_url":"https://api.github.com/users/olsonanl/orgs","repos_url":"https://api.github.com/users/olsonanl/repos","events_url":"https://api.github.com/users/olsonanl/events{/privacy}","received_events_url":"https://api.github.com/users/olsonanl/received_events","type":"User","site_admin":false},"created_at":"2018-04-10T22:48:20Z","updated_at":"2018-04-10T22:48:20Z","author_association":"CONTRIBUTOR","body":"Is it plasmid or phage or something? It's possible prodigal didn't find anything."}}
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