{"action":"created","issue":{"url":"https://api.github.com/repos/hall-lab/svtyper/issues/21","labels_url":"https://api.github.com/repos/hall-lab/svtyper/issues/21/labels{/name}","comments_url":"https://api.github.com/repos/hall-lab/svtyper/issues/21/comments","events_url":"https://api.github.com/repos/hall-lab/svtyper/issues/21/events","html_url":"https://github.com/hall-lab/svtyper/issues/21","id":129271731,"number":21,"title":"Stopped SVtyper","user":{"login":"sehrrot","id":3627124,"avatar_url":"https://avatars.githubusercontent.com/u/3627124?v=3","gravatar_id":"","url":"https://api.github.com/users/sehrrot","html_url":"https://github.com/sehrrot","followers_url":"https://api.github.com/users/sehrrot/followers","following_url":"https://api.github.com/users/sehrrot/following{/other_user}","gists_url":"https://api.github.com/users/sehrrot/gists{/gist_id}","starred_url":"https://api.github.com/users/sehrrot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sehrrot/subscriptions","organizations_url":"https://api.github.com/users/sehrrot/orgs","repos_url":"https://api.github.com/users/sehrrot/repos","events_url":"https://api.github.com/users/sehrrot/events{/privacy}","received_events_url":"https://api.github.com/users/sehrrot/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-01-27T21:18:41Z","updated_at":"2016-01-27T21:21:42Z","closed_at":null,"body":"Hi,\r\n\r\nThanks for the nice tool. I have been running SVtyper for 1000 Genome WGS samples (~30X) after Lumpy-SV run. \r\n\r\nThe tool worked okay when I ran with chr22. Then, I used it for entire chromosomes, and I found strange behaviour that SVTyper stopped after writing few lines (~100-200 lines including header) of VCF output. \r\n\r\nThen, I did bit more experiments that I did split the VCF file into few chunks (200 lines), given that the run of chr22 was okay and I assumed it could be line number issue, and ran again them but wasn't working. \r\n\r\nI am wondering whether you or other users noticed this issue before.\r\n\r\nThanks\r\nJoon"},"comment":{"url":"https://api.github.com/repos/hall-lab/svtyper/issues/comments/175859477","html_url":"https://github.com/hall-lab/svtyper/issues/21#issuecomment-175859477","issue_url":"https://api.github.com/repos/hall-lab/svtyper/issues/21","id":175859477,"user":{"login":"cc2qe","id":3903682,"avatar_url":"https://avatars.githubusercontent.com/u/3903682?v=3","gravatar_id":"","url":"https://api.github.com/users/cc2qe","html_url":"https://github.com/cc2qe","followers_url":"https://api.github.com/users/cc2qe/followers","following_url":"https://api.github.com/users/cc2qe/following{/other_user}","gists_url":"https://api.github.com/users/cc2qe/gists{/gist_id}","starred_url":"https://api.github.com/users/cc2qe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cc2qe/subscriptions","organizations_url":"https://api.github.com/users/cc2qe/orgs","repos_url":"https://api.github.com/users/cc2qe/repos","events_url":"https://api.github.com/users/cc2qe/events{/privacy}","received_events_url":"https://api.github.com/users/cc2qe/received_events","type":"User","site_admin":false},"created_at":"2016-01-27T21:21:42Z","updated_at":"2016-01-27T21:21:42Z","body":"SVtyper shouldn't stop, but it can be slow for variants where the data is very deep. Did you run LUMPY using the [exclude regions](https://github.com/hall-lab/speedseq#annotations)? also, are you able to identify the problematic variant in your VCF file?"}}