{"action":"created","issue":{"url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/53","labels_url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/53/labels{/name}","comments_url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/53/comments","events_url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/53/events","html_url":"https://github.com/CGATOxford/CGATPipelines/issues/53","id":92077536,"number":53,"title":"Shared Memory Usage in STAR","user":{"login":"IanSudbery","id":5391758,"avatar_url":"https://avatars.githubusercontent.com/u/5391758?v=3","gravatar_id":"","url":"https://api.github.com/users/IanSudbery","html_url":"https://github.com/IanSudbery","followers_url":"https://api.github.com/users/IanSudbery/followers","following_url":"https://api.github.com/users/IanSudbery/following{/other_user}","gists_url":"https://api.github.com/users/IanSudbery/gists{/gist_id}","starred_url":"https://api.github.com/users/IanSudbery/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/IanSudbery/subscriptions","organizations_url":"https://api.github.com/users/IanSudbery/orgs","repos_url":"https://api.github.com/users/IanSudbery/repos","events_url":"https://api.github.com/users/IanSudbery/events{/privacy}","received_events_url":"https://api.github.com/users/IanSudbery/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-06-30T12:17:16Z","updated_at":"2015-06-30T13:34:50Z","closed_at":null,"body":"My STAR runs are failing with the error:\r\n\r\n```\r\nShared memory error: 4, errno: Cannot allocate memory(12)\r\nEXITING because of FATAL ERROR: problems with shared memory: error from shmget() or shm_open().\r\nSOLUTION: check shared memory settings as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory\r\n\r\nJun 30 12:38:47 ...... FATAL ERROR, exiting\r\n```\r\n\r\nHowever, the --genomeLoad setting is hard coded in pipeline_mapping. \r\n\r\nPerhaps this is due to the memeory issues we are having? I've also been having fastqc jobs failing with errors suggestive of a lack of memory.\r\n"},"comment":{"url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/comments/117186731","html_url":"https://github.com/CGATOxford/CGATPipelines/issues/53#issuecomment-117186731","issue_url":"https://api.github.com/repos/CGATOxford/CGATPipelines/issues/53","id":117186731,"user":{"login":"AndreasHeger","id":4426336,"avatar_url":"https://avatars.githubusercontent.com/u/4426336?v=3","gravatar_id":"","url":"https://api.github.com/users/AndreasHeger","html_url":"https://github.com/AndreasHeger","followers_url":"https://api.github.com/users/AndreasHeger/followers","following_url":"https://api.github.com/users/AndreasHeger/following{/other_user}","gists_url":"https://api.github.com/users/AndreasHeger/gists{/gist_id}","starred_url":"https://api.github.com/users/AndreasHeger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AndreasHeger/subscriptions","organizations_url":"https://api.github.com/users/AndreasHeger/orgs","repos_url":"https://api.github.com/users/AndreasHeger/repos","events_url":"https://api.github.com/users/AndreasHeger/events{/privacy}","received_events_url":"https://api.github.com/users/AndreasHeger/received_events","type":"User","site_admin":false},"created_at":"2015-06-30T13:34:50Z","updated_at":"2015-06-30T13:34:50Z","body":"Thanks. Can you keep monitoring this? Next time it fails we will look at the log-file to see which machine it was executed on and what the load status of the machine was."}}