{"action":"created","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/65","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/65/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/65/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/65/events","html_url":"https://github.com/marbl/canu/issues/65","id":138580249,"number":65,"title":"falcon_sense taking too long time","user":{"login":"kk86bioinfo","id":2483401,"avatar_url":"https://avatars.githubusercontent.com/u/2483401?v=3","gravatar_id":"","url":"https://api.github.com/users/kk86bioinfo","html_url":"https://github.com/kk86bioinfo","followers_url":"https://api.github.com/users/kk86bioinfo/followers","following_url":"https://api.github.com/users/kk86bioinfo/following{/other_user}","gists_url":"https://api.github.com/users/kk86bioinfo/gists{/gist_id}","starred_url":"https://api.github.com/users/kk86bioinfo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kk86bioinfo/subscriptions","organizations_url":"https://api.github.com/users/kk86bioinfo/orgs","repos_url":"https://api.github.com/users/kk86bioinfo/repos","events_url":"https://api.github.com/users/kk86bioinfo/events{/privacy}","received_events_url":"https://api.github.com/users/kk86bioinfo/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2016-03-04T20:35:31Z","updated_at":"2016-03-07T13:21:42Z","closed_at":null,"body":"Hi, would like to ask is falcon_sense (2-correction step) load time directly proportional with input reads amount? We have noticed that when we increase our input reads to canu, the time taken by falcon_sense seems taking much longer time (far more time needed compare to lesser input reads). In SGE, all process are still in 'r' stage but the file modified timestamp is no longer updated. Is there any way to check if there is any error occur? or it is just need longer time? Please advise."},"comment":{"url":"https://api.github.com/repos/marbl/canu/issues/comments/193245672","html_url":"https://github.com/marbl/canu/issues/65#issuecomment-193245672","issue_url":"https://api.github.com/repos/marbl/canu/issues/65","id":193245672,"user":{"login":"rafalwoycicki","id":17161885,"avatar_url":"https://avatars.githubusercontent.com/u/17161885?v=3","gravatar_id":"","url":"https://api.github.com/users/rafalwoycicki","html_url":"https://github.com/rafalwoycicki","followers_url":"https://api.github.com/users/rafalwoycicki/followers","following_url":"https://api.github.com/users/rafalwoycicki/following{/other_user}","gists_url":"https://api.github.com/users/rafalwoycicki/gists{/gist_id}","starred_url":"https://api.github.com/users/rafalwoycicki/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rafalwoycicki/subscriptions","organizations_url":"https://api.github.com/users/rafalwoycicki/orgs","repos_url":"https://api.github.com/users/rafalwoycicki/repos","events_url":"https://api.github.com/users/rafalwoycicki/events{/privacy}","received_events_url":"https://api.github.com/users/rafalwoycicki/received_events","type":"User","site_admin":false},"created_at":"2016-03-07T13:21:42Z","updated_at":"2016-03-07T13:21:42Z","body":"Hi, I am not sure if it will help, but I also had issues with falcon_sense running very slow and not using all threads when using defaults. For example in 6 jobs/4 threads setting each job was using just 1.5 thread. In 3/6 setting it was 2 threads per job (I have 24 thread single machine). The most optimal setting for me is with having 24 jobs each with 1 thread, then it uses 1 thread per job."}}