{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/1460","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1460/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1460/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1460/events","html_url":"https://github.com/broadinstitute/gatk/issues/1460","id":130401070,"number":1460,"title":"Get walker BQSR tools in GATK4 to use less than 3.5Gb of RAM (request from production)","user":{"login":"droazen","id":798637,"avatar_url":"https://avatars.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/broadinstitute/gatk/labels/performance","name":"performance","color":"bfd4f2"},{"url":"https://api.github.com/repos/broadinstitute/gatk/labels/tools","name":"tools","color":"0052cc"}],"state":"open","locked":false,"assignee":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/broadinstitute/gatk/milestones/9","html_url":"https://github.com/broadinstitute/gatk/milestones/alpha-2","labels_url":"https://api.github.com/repos/broadinstitute/gatk/milestones/9/labels","id":1634880,"number":9,"title":"alpha-2","description":"","creator":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"open_issues":18,"closed_issues":1,"state":"open","created_at":"2016-03-09T17:39:39Z","updated_at":"2016-03-17T02:52:23Z","due_on":null,"closed_at":null},"comments":35,"created_at":"2016-02-01T15:54:39Z","updated_at":"2016-03-17T15:05:54Z","closed_at":null,"body":"There's been a request from production (https://broadinstitute.atlassian.net/browse/DSDEEPB-2789) to try to ensure that the walker BQSR tools in hellbender can run with less than 3.5 GB of RAM to get costs down."},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/197924164","html_url":"https://github.com/broadinstitute/gatk/issues/1460#issuecomment-197924164","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1460","id":197924164,"user":{"login":"yfarjoun","id":2745554,"avatar_url":"https://avatars.githubusercontent.com/u/2745554?v=3","gravatar_id":"","url":"https://api.github.com/users/yfarjoun","html_url":"https://github.com/yfarjoun","followers_url":"https://api.github.com/users/yfarjoun/followers","following_url":"https://api.github.com/users/yfarjoun/following{/other_user}","gists_url":"https://api.github.com/users/yfarjoun/gists{/gist_id}","starred_url":"https://api.github.com/users/yfarjoun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yfarjoun/subscriptions","organizations_url":"https://api.github.com/users/yfarjoun/orgs","repos_url":"https://api.github.com/users/yfarjoun/repos","events_url":"https://api.github.com/users/yfarjoun/events{/privacy}","received_events_url":"https://api.github.com/users/yfarjoun/received_events","type":"User","site_admin":false},"created_at":"2016-03-17T15:05:54Z","updated_at":"2016-03-17T15:05:54Z","body":":+1:\n\nOn Thu, Mar 17, 2016 at 11:04 AM, Adam Kiezun <notifications@github.com>\nwrote:\n\n> last time i checked it was:\n> https://github.com/broadinstitute/gatk/issues/1413\n>\n> On Thu, Mar 17, 2016 at 11:02 AM, Yossi Farjoun <notifications@github.com>\n> wrote:\n>\n> > I have to ask, the resulting table is the same, right?\n> >\n> > On Thu, Mar 17, 2016 at 9:11 AM, Adam Kiezun <notifications@github.com>\n> > wrote:\n> >\n> > > ok, so after setting -Xms and -Xmx to 3G, gatk4 can run applyBQSR of a\n> > > 100GB file in peak head of 1.28GB\n> > >\n> > > See heap after GC (check out the units on the y axis)\n> > > [image: image]\n> > > <\n> >\n> https://cloud.githubusercontent.com/assets/1993519/13846713/7a3d4ace-ec1f-11e5-8ed0-5ef88f3f87a7.png\n> > >\n> > >\n> > > Also, we're using IntelDeflater now and so this is 2x faster too even\n> > > though we use less memory.\n> > >\n> > > GATK3 with 32GB heap, unknown deflater, 55146.42 user time seconds\n> (wall\n> > > clock 13:24:10)\n> > > GATK4 with 32GB heap, JdkDeflater, 37011.46 user time seconds (wall\n> clock\n> > > 9:50:48)\n> > > *GATK4 with 3GB heap, IntelDeflater, 27718.06 user time seconds* (wall\n> > > clock 8:02:37)\n> > >\n> > > I'm declaring victory on BaseRecalibrator front. Moving to\n> > BaseRecalibrator\n> > >\n> > > —\n> > > You are receiving this because you were mentioned.\n> > > Reply to this email directly or view it on GitHub\n> > > <\n> >\n> https://github.com/broadinstitute/gatk/issues/1460#issuecomment-197872643>\n> >\n> > >\n> >\n> > —\n> > You are receiving this because you were mentioned.\n> > Reply to this email directly or view it on GitHub\n> > <\n> https://github.com/broadinstitute/gatk/issues/1460#issuecomment-197922729>\n>\n> >\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly or view it on GitHub\n> <https://github.com/broadinstitute/gatk/issues/1460#issuecomment-197923684>\n>\n"}}