{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/1034","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1034/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1034/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1034/events","html_url":"https://github.com/broadinstitute/gatk/issues/1034","id":112664706,"number":1034,"title":"Profile and optimize simple read walkers: PrintReads, CountReads","user":{"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},"labels":[{"url":"https://api.github.com/repos/broadinstitute/gatk/labels/profiling","name":"profiling","color":"bfd4f2"}],"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/5","html_url":"https://github.com/broadinstitute/gatk/milestones/alpha","labels_url":"https://api.github.com/repos/broadinstitute/gatk/milestones/5/labels","id":1220227,"number":5,"title":"alpha","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":61,"closed_issues":94,"state":"open","created_at":"2015-07-22T13:37:37Z","updated_at":"2015-10-24T06:00:14Z","due_on":"2015-11-20T05:00:00Z","closed_at":null},"comments":7,"created_at":"2015-10-21T19:43:41Z","updated_at":"2015-10-24T07:02:07Z","closed_at":null,"body":"the goal is to be at least same as gatk3.4 on single thread. This is for the walker version of the tools.\r\nThe ticket can be split into a) profile and b) optimize if needed\r\n\r\nThe reason to do this is to see if the engine itself adds any overhead.\r\n\r\nNeed to tests on NFS as well as on local drive"},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/150771701","html_url":"https://github.com/broadinstitute/gatk/issues/1034#issuecomment-150771701","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1034","id":150771701,"user":{"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},"created_at":"2015-10-24T07:02:07Z","updated_at":"2015-10-24T07:02:07Z","body":"case 4 CountReads on NFS (bigger region)\r\n\r\nReference: /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta\r\nBam: /humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37.NA12878.bam(~350GB)\r\ninterval 1:1-100000000\r\n\r\nLinux 2.6.32-573.3.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0-b132\r\n\r\n**7.5-7.6** (2 runs) minutes GATK 3.4-46-gbc02625\r\n**5-6.1** (2 runs) minutes  GATK4 .pre-alpha-45-g168cd60\r\nnote: runs were alternated between gatk3 and gatk4\r\n\r\ntime gatk3\r\n```\r\nreal\t7m44.406s\r\nuser\t13m20.540s\r\n```\r\n\r\ntime gatk4\r\n```\r\nreal\t6m6.971s\r\nuser\t6m21.120s\r\n```\r\n"}}