{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/308","repository_url":"https://api.github.com/repos/PacificBiosciences/FALCON","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/308/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/308/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/308/events","html_url":"https://github.com/PacificBiosciences/FALCON/issues/308","id":141161313,"number":308,"title":"Falcon assembly","user":{"login":"yilunhuangyue","id":16872303,"avatar_url":"https://avatars.githubusercontent.com/u/16872303?v=3","gravatar_id":"","url":"https://api.github.com/users/yilunhuangyue","html_url":"https://github.com/yilunhuangyue","followers_url":"https://api.github.com/users/yilunhuangyue/followers","following_url":"https://api.github.com/users/yilunhuangyue/following{/other_user}","gists_url":"https://api.github.com/users/yilunhuangyue/gists{/gist_id}","starred_url":"https://api.github.com/users/yilunhuangyue/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yilunhuangyue/subscriptions","organizations_url":"https://api.github.com/users/yilunhuangyue/orgs","repos_url":"https://api.github.com/users/yilunhuangyue/repos","events_url":"https://api.github.com/users/yilunhuangyue/events{/privacy}","received_events_url":"https://api.github.com/users/yilunhuangyue/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-03-16T03:22:37Z","updated_at":"2016-03-16T03:26:05Z","closed_at":null,"body":"hello，I have install falcon, and i have trid the example from https://github.com/PacificBiosciences/FALCON/wiki/Setup%3A-Running;\r\nthe program ended without error message,but the log file is \r\n\r\n2016-03-16 02:50:02,837 - pypeflow.controller - INFO - _refreshTargets() finished with no thread running and no new job to submit\r\n2016-03-16 02:50:02,837 - pypeflow.controller - INFO - _refreshTargets() finished with no thread running and no new job to submit\r\n\r\nAnd the 2-asm-falcon file contains files such as a_ctg_all.fa and p_ctg.fa, I am not sure if it is the assembly result.\r\n\r\nbesides,I want to assembly a plant genome, the genome size is about 400M. what parameters should be changed in the cfg file?\r\n\r\nThanks a lot for any help!"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/comments/197134375","html_url":"https://github.com/PacificBiosciences/FALCON/issues/308#issuecomment-197134375","issue_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/308","id":197134375,"user":{"login":"pb-jchin","id":1071734,"avatar_url":"https://avatars.githubusercontent.com/u/1071734?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-jchin","html_url":"https://github.com/pb-jchin","followers_url":"https://api.github.com/users/pb-jchin/followers","following_url":"https://api.github.com/users/pb-jchin/following{/other_user}","gists_url":"https://api.github.com/users/pb-jchin/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-jchin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-jchin/subscriptions","organizations_url":"https://api.github.com/users/pb-jchin/orgs","repos_url":"https://api.github.com/users/pb-jchin/repos","events_url":"https://api.github.com/users/pb-jchin/events{/privacy}","received_events_url":"https://api.github.com/users/pb-jchin/received_events","type":"User","site_admin":false},"created_at":"2016-03-16T03:26:05Z","updated_at":"2016-03-16T03:26:05Z","body":"There is no universal parameters for all genome (yet?) Anyway, depending on the read length distribution and the complexity of the repeats in the genome, there will be different choice to optimize for making the assembly. If you get >20x read > 10kb, I would suggest using length cutoff ~10kb. If not, you will need to include more reads."}}