{"action":"created","issue":{"url":"https://api.github.com/repos/fidelram/deepTools/issues/383","repository_url":"https://api.github.com/repos/fidelram/deepTools","labels_url":"https://api.github.com/repos/fidelram/deepTools/issues/383/labels{/name}","comments_url":"https://api.github.com/repos/fidelram/deepTools/issues/383/comments","events_url":"https://api.github.com/repos/fidelram/deepTools/issues/383/events","html_url":"https://github.com/fidelram/deepTools/issues/383","id":162327058,"number":383,"title":"computeGCBias is really slow in deepTools2 compared to deepTools 1.5","user":{"login":"asrichter","id":16194368,"avatar_url":"https://avatars.githubusercontent.com/u/16194368?v=3","gravatar_id":"","url":"https://api.github.com/users/asrichter","html_url":"https://github.com/asrichter","followers_url":"https://api.github.com/users/asrichter/followers","following_url":"https://api.github.com/users/asrichter/following{/other_user}","gists_url":"https://api.github.com/users/asrichter/gists{/gist_id}","starred_url":"https://api.github.com/users/asrichter/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/asrichter/subscriptions","organizations_url":"https://api.github.com/users/asrichter/orgs","repos_url":"https://api.github.com/users/asrichter/repos","events_url":"https://api.github.com/users/asrichter/events{/privacy}","received_events_url":"https://api.github.com/users/asrichter/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-06-26T13:08:36Z","updated_at":"2016-06-26T15:16:18Z","closed_at":null,"body":"computeGCBias is VERY SLOW in the current deepTools 2 develop version. Even on small input BAM files with only thousands of alignments, it runs hours. When using 16 or more CPUs for example, each thread is at about 5-10% CPU usage only, also at directly attached storage without NFS bottleneck. The problem occurs in both python 2 and 3.\r\nIn deepTools 1.5.9.1, it used to be much faster.\r\n\r\nAny ideas which change could have caused the performance loss?\r\n"},"comment":{"url":"https://api.github.com/repos/fidelram/deepTools/issues/comments/228606169","html_url":"https://github.com/fidelram/deepTools/issues/383#issuecomment-228606169","issue_url":"https://api.github.com/repos/fidelram/deepTools/issues/383","id":228606169,"user":{"login":"dpryan79","id":6399000,"avatar_url":"https://avatars.githubusercontent.com/u/6399000?v=3","gravatar_id":"","url":"https://api.github.com/users/dpryan79","html_url":"https://github.com/dpryan79","followers_url":"https://api.github.com/users/dpryan79/followers","following_url":"https://api.github.com/users/dpryan79/following{/other_user}","gists_url":"https://api.github.com/users/dpryan79/gists{/gist_id}","starred_url":"https://api.github.com/users/dpryan79/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpryan79/subscriptions","organizations_url":"https://api.github.com/users/dpryan79/orgs","repos_url":"https://api.github.com/users/dpryan79/repos","events_url":"https://api.github.com/users/dpryan79/events{/privacy}","received_events_url":"https://api.github.com/users/dpryan79/received_events","type":"User","site_admin":false},"created_at":"2016-06-26T15:16:18Z","updated_at":"2016-06-26T15:16:18Z","body":"Eeek"}}
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