{"action":"opened","issue":{"url":"https://api.github.com/repos/PASApipeline/PASApipeline/issues/94","repository_url":"https://api.github.com/repos/PASApipeline/PASApipeline","labels_url":"https://api.github.com/repos/PASApipeline/PASApipeline/issues/94/labels{/name}","comments_url":"https://api.github.com/repos/PASApipeline/PASApipeline/issues/94/comments","events_url":"https://api.github.com/repos/PASApipeline/PASApipeline/issues/94/events","html_url":"https://github.com/PASApipeline/PASApipeline/issues/94","id":390883938,"node_id":"MDU6SXNzdWUzOTA4ODM5Mzg=","number":94,"title":"Long runtime for annotation comparison: less than one core used","user":{"login":"EarlyEvol","id":25826275,"node_id":"MDQ6VXNlcjI1ODI2Mjc1","avatar_url":"https://avatars1.githubusercontent.com/u/25826275?v=4","gravatar_id":"","url":"https://api.github.com/users/EarlyEvol","html_url":"https://github.com/EarlyEvol","followers_url":"https://api.github.com/users/EarlyEvol/followers","following_url":"https://api.github.com/users/EarlyEvol/following{/other_user}","gists_url":"https://api.github.com/users/EarlyEvol/gists{/gist_id}","starred_url":"https://api.github.com/users/EarlyEvol/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/EarlyEvol/subscriptions","organizations_url":"https://api.github.com/users/EarlyEvol/orgs","repos_url":"https://api.github.com/users/EarlyEvol/repos","events_url":"https://api.github.com/users/EarlyEvol/events{/privacy}","received_events_url":"https://api.github.com/users/EarlyEvol/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-12-13T22:17:24Z","updated_at":"2018-12-13T22:17:24Z","closed_at":null,"author_association":"NONE","body":"Hi Brian,\r\n\r\nI'm comparing gene prediction derived from \"funannotate predict\" with a PASA assembly and it has been running on less than one core for about 24 hours.  The command used was:\r\n``` \r\n~/apps/PASApipeline/Launch_PASA_pipeline.pl -c update_misc/pasa/annotCompare.txt -g update_misc/genome.fa -t update_misc/trinity.fasta.clean -A -L --CPU 27 --annots update_misc/genome.gff3\r\n```\r\nThings look like they are still working. At least pasa_DB.annotation_compare.4647.out is continuously getting written to.\r\n\r\nIf the single core nature is pretty set, should I break up the assembly/annotations and run the comparison in parallel myself?  That should be pretty easy for the existing annotation gff, but I don't know how pasa would handle annotations/contigs in the database that are not found in the gff.\r\n\r\nAgain, thanks for all the continuing help.\r\nEarl "}}
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