{"action":"created","issue":{"url":"https://api.github.com/repos/ekg/freebayes/issues/170","labels_url":"https://api.github.com/repos/ekg/freebayes/issues/170/labels{/name}","comments_url":"https://api.github.com/repos/ekg/freebayes/issues/170/comments","events_url":"https://api.github.com/repos/ekg/freebayes/issues/170/events","html_url":"https://github.com/ekg/freebayes/issues/170","id":73583555,"number":170,"title":"Freebayes skips some contigs?","user":{"login":"nicolasnzt","id":12271166,"avatar_url":"https://avatars.githubusercontent.com/u/12271166?v=3","gravatar_id":"","url":"https://api.github.com/users/nicolasnzt","html_url":"https://github.com/nicolasnzt","followers_url":"https://api.github.com/users/nicolasnzt/followers","following_url":"https://api.github.com/users/nicolasnzt/following{/other_user}","gists_url":"https://api.github.com/users/nicolasnzt/gists{/gist_id}","starred_url":"https://api.github.com/users/nicolasnzt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nicolasnzt/subscriptions","organizations_url":"https://api.github.com/users/nicolasnzt/orgs","repos_url":"https://api.github.com/users/nicolasnzt/repos","events_url":"https://api.github.com/users/nicolasnzt/events{/privacy}","received_events_url":"https://api.github.com/users/nicolasnzt/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-05-06T10:28:14Z","updated_at":"2015-05-06T15:24:34Z","closed_at":null,"body":"Hi,\r\nI've similarly issue that the post #168.\r\n\r\nI tried to use freebayes to call variants on a custom genome (with more than 80000 contigs) but I think freebayes skips the analysis of some contigs.\r\nIn my reference file, I’ve 81730 contigs (63232 contigs with reads), but in the freebayes log file (-d option) I can see information about only 5091 contigs.\r\n\r\nConsequently I tried to run freebayes against one only contig (which don’t output previously results) specify “-r MyContig” option. In this case freebayes outputs variants!\r\n\r\nPlease, can you help me to solve this issue?\r\n\r\nBest regards\r\nNicolas\r\n"},"comment":{"url":"https://api.github.com/repos/ekg/freebayes/issues/comments/99513313","html_url":"https://github.com/ekg/freebayes/issues/170#issuecomment-99513313","issue_url":"https://api.github.com/repos/ekg/freebayes/issues/170","id":99513313,"user":{"login":"nicolasnzt","id":12271166,"avatar_url":"https://avatars.githubusercontent.com/u/12271166?v=3","gravatar_id":"","url":"https://api.github.com/users/nicolasnzt","html_url":"https://github.com/nicolasnzt","followers_url":"https://api.github.com/users/nicolasnzt/followers","following_url":"https://api.github.com/users/nicolasnzt/following{/other_user}","gists_url":"https://api.github.com/users/nicolasnzt/gists{/gist_id}","starred_url":"https://api.github.com/users/nicolasnzt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nicolasnzt/subscriptions","organizations_url":"https://api.github.com/users/nicolasnzt/orgs","repos_url":"https://api.github.com/users/nicolasnzt/repos","events_url":"https://api.github.com/users/nicolasnzt/events{/privacy}","received_events_url":"https://api.github.com/users/nicolasnzt/received_events","type":"User","site_admin":false},"created_at":"2015-05-06T15:24:34Z","updated_at":"2015-05-06T15:24:34Z","body":"Hi Erik,\r\nI'm trying to create a small dataset, but when I extract reads corresponding to a subset of contigs  freebayes runs successfully. \r\nDo you think freebayes bugs with a lot of contigs (80000)?\r\n\r\nCheers!\r\nNicolas\r\n\r\n"}}