{"action":"created","issue":{"url":"https://api.github.com/repos/alexdobin/STAR/issues/27","labels_url":"https://api.github.com/repos/alexdobin/STAR/issues/27/labels{/name}","comments_url":"https://api.github.com/repos/alexdobin/STAR/issues/27/comments","events_url":"https://api.github.com/repos/alexdobin/STAR/issues/27/events","html_url":"https://github.com/alexdobin/STAR/issues/27","id":60319420,"number":27,"title":"STAR speed slowing down during run","user":{"login":"cyrilcros","id":10993194,"avatar_url":"https://avatars.githubusercontent.com/u/10993194?v=3","gravatar_id":"","url":"https://api.github.com/users/cyrilcros","html_url":"https://github.com/cyrilcros","followers_url":"https://api.github.com/users/cyrilcros/followers","following_url":"https://api.github.com/users/cyrilcros/following{/other_user}","gists_url":"https://api.github.com/users/cyrilcros/gists{/gist_id}","starred_url":"https://api.github.com/users/cyrilcros/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cyrilcros/subscriptions","organizations_url":"https://api.github.com/users/cyrilcros/orgs","repos_url":"https://api.github.com/users/cyrilcros/repos","events_url":"https://api.github.com/users/cyrilcros/events{/privacy}","received_events_url":"https://api.github.com/users/cyrilcros/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-03-09T09:47:03Z","updated_at":"2015-04-22T07:41:52Z","closed_at":"2015-04-21T19:37:17Z","body":"Hi, I am trying to run a STAR job, but it is taking an unusually long time. I see the mapping speed declined drastically in time (50M reads paired end unstranded, mouse genome mm10, it has been running for 3 days...). I am using 7 threads on a desktop computer with 32Gb RAM running Xubuntu. Not really a dedicated server, really...\r\nI see in the closed issues that there was a similar case, but the error came from an external memory leak. Here, I launch STAR inside a bash shell script function so there are no 3rd party software causing a leak.\r\nI have been reading the manual for the previous version of STAR (2.3.0.1): there is a paragraph on the genomeLoad parameter usage which is not in the new manual. I was thinking of maybe trying to load the genome in the shared memory and see how it goes, after settting the kernel shmmax and shmall parameters.\r\nI have pasted the log files below. The genome index was built successfully,\r\nThanks a lot for your help!\r\nCyril Cros\r\n\r\nhttp://pastebin.com/dfDpt8wR   <-  Log file\r\nhttp://pastebin.com/2LzzPCid    <-  Log progress file\r\n\r\nEDIT1: I am running several jobs with genomeLoad=LoadAndKeep and an unsorted BAM output (to avoid reserving shared memory for the BAM sorting). A first job was finished sucessfully in 15min only, all went well. I suggest you add to the new version of the manual the paragraph on the option genomeLoad.\r\n"},"comment":{"url":"https://api.github.com/repos/alexdobin/STAR/issues/comments/95063239","html_url":"https://github.com/alexdobin/STAR/issues/27#issuecomment-95063239","issue_url":"https://api.github.com/repos/alexdobin/STAR/issues/27","id":95063239,"user":{"login":"cyrilcros","id":10993194,"avatar_url":"https://avatars.githubusercontent.com/u/10993194?v=3","gravatar_id":"","url":"https://api.github.com/users/cyrilcros","html_url":"https://github.com/cyrilcros","followers_url":"https://api.github.com/users/cyrilcros/followers","following_url":"https://api.github.com/users/cyrilcros/following{/other_user}","gists_url":"https://api.github.com/users/cyrilcros/gists{/gist_id}","starred_url":"https://api.github.com/users/cyrilcros/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cyrilcros/subscriptions","organizations_url":"https://api.github.com/users/cyrilcros/orgs","repos_url":"https://api.github.com/users/cyrilcros/repos","events_url":"https://api.github.com/users/cyrilcros/events{/privacy}","received_events_url":"https://api.github.com/users/cyrilcros/received_events","type":"User","site_admin":false},"created_at":"2015-04-22T07:41:52Z","updated_at":"2015-04-22T07:41:52Z","body":"Thanks a lot,\nI will be doing some new runs shortly.\nRegards,\nCyril Cros\n\nLe 4/21/2015 9:37 PM, alexdobin a écrit :\n>\n> Closed #27 <https://github.com/alexdobin/STAR/issues/27>.\n>\n> —\n> Reply to this email directly or view it on GitHub \n> <https://github.com/alexdobin/STAR/issues/27#event-286555985>.\n>\n\n"}}