{"action":"created","issue":{"url":"https://api.github.com/repos/BoevaLab/FREEC/issues/2","repository_url":"https://api.github.com/repos/BoevaLab/FREEC","labels_url":"https://api.github.com/repos/BoevaLab/FREEC/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/BoevaLab/FREEC/issues/2/comments","events_url":"https://api.github.com/repos/BoevaLab/FREEC/issues/2/events","html_url":"https://github.com/BoevaLab/FREEC/issues/2","id":169828078,"number":2,"title":"FREEC was not able to extract reads","user":{"login":"ramaniak","id":6088710,"avatar_url":"https://avatars.githubusercontent.com/u/6088710?v=3","gravatar_id":"","url":"https://api.github.com/users/ramaniak","html_url":"https://github.com/ramaniak","followers_url":"https://api.github.com/users/ramaniak/followers","following_url":"https://api.github.com/users/ramaniak/following{/other_user}","gists_url":"https://api.github.com/users/ramaniak/gists{/gist_id}","starred_url":"https://api.github.com/users/ramaniak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ramaniak/subscriptions","organizations_url":"https://api.github.com/users/ramaniak/orgs","repos_url":"https://api.github.com/users/ramaniak/repos","events_url":"https://api.github.com/users/ramaniak/events{/privacy}","received_events_url":"https://api.github.com/users/ramaniak/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-08-08T01:28:31Z","updated_at":"2016-08-08T14:50:19Z","closed_at":null,"body":"Hello,\r\nI am trying to use FREEC on a paired (Tum/Norm) WGS data set of Illumina paired end bam files. I keep getting the following error\r\n\r\n```\r\nfinished reading T62.sorted.dup.recal.bam\r\nPROFILING [tid=46912512328960]:  T62.sorted.dup.recal.bam read in 8929 seconds [fillMyHash]\r\n990013582 lines read..\r\n0 reads used to compute copy number profile\r\nError: FREEC was not able to extract reads from T62.sorted.dup.recal.bam\r\n\r\nCheck your parameters: inputFormat and matesOrientation\r\nUse \"matesOrientation=0\" if you have single end reads\r\nCheck the list of possible input formats at http://bioinfo-out.curie.fr/projects/freec/tutorial.html#CONFIG\r\n\r\nIf you use sorted SAM or BAM, please set \"mateOrientation=0\"; then FREEC will not try to detect pairs with normal orientation and insert size. Instead, it will keep all pairs from the input file\r\n```\r\nI have repeated the analysis with all possible input options for matesOrientation (FR, RF and 0) and get the same error. I am using BAM for my inputFormat and I am using Control-FREEC v9.3. Any help would be much appreciated.\r\n\r\nThanks\r\nArun"},"comment":{"url":"https://api.github.com/repos/BoevaLab/FREEC/issues/comments/238261681","html_url":"https://github.com/BoevaLab/FREEC/issues/2#issuecomment-238261681","issue_url":"https://api.github.com/repos/BoevaLab/FREEC/issues/2","id":238261681,"user":{"login":"valeu","id":10144507,"avatar_url":"https://avatars.githubusercontent.com/u/10144507?v=3","gravatar_id":"","url":"https://api.github.com/users/valeu","html_url":"https://github.com/valeu","followers_url":"https://api.github.com/users/valeu/followers","following_url":"https://api.github.com/users/valeu/following{/other_user}","gists_url":"https://api.github.com/users/valeu/gists{/gist_id}","starred_url":"https://api.github.com/users/valeu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/valeu/subscriptions","organizations_url":"https://api.github.com/users/valeu/orgs","repos_url":"https://api.github.com/users/valeu/repos","events_url":"https://api.github.com/users/valeu/events{/privacy}","received_events_url":"https://api.github.com/users/valeu/received_events","type":"User","site_admin":false},"created_at":"2016-08-08T14:50:19Z","updated_at":"2016-08-08T14:50:19Z","body":"Actually, FREEC does not understand the fa.fai without the \"chr\" prefixes. Just add them to the fai file and it should work. It is OK not to have \"chr\" in the BAMs"}}
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