{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/82","labels_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/82/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/82/comments","events_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/82/events","html_url":"https://github.com/arq5x/lumpy-sv/issues/82","id":76595057,"number":82,"title":"Parameter required for id","user":{"login":"panummi","id":12455347,"avatar_url":"https://avatars.githubusercontent.com/u/12455347?v=3","gravatar_id":"","url":"https://api.github.com/users/panummi","html_url":"https://github.com/panummi","followers_url":"https://api.github.com/users/panummi/followers","following_url":"https://api.github.com/users/panummi/following{/other_user}","gists_url":"https://api.github.com/users/panummi/gists{/gist_id}","starred_url":"https://api.github.com/users/panummi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/panummi/subscriptions","organizations_url":"https://api.github.com/users/panummi/orgs","repos_url":"https://api.github.com/users/panummi/repos","events_url":"https://api.github.com/users/panummi/events{/privacy}","received_events_url":"https://api.github.com/users/panummi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2015-05-15T05:02:18Z","updated_at":"2015-09-03T12:56:46Z","closed_at":null,"body":"Hi,\r\nI'm running LUMPY express, and I get message: \"Parameter required for id\". What is the parameter mentioned? Also, I've noticed that even though I run LUMPY express, it prints out options for traditional LUMPY (-g, -e, -w ...). What should I do?"},"comment":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/comments/137431117","html_url":"https://github.com/arq5x/lumpy-sv/issues/82#issuecomment-137431117","issue_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/82","id":137431117,"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":"2015-09-03T12:56:46Z","updated_at":"2015-09-03T12:56:46Z","body":"great thanks. It looks like lumpyexpress is unable to extract the sample ID from your BAM header and I have a feeling it's related to different flavors of awk. Could you send me the first ~10000 lines of each of your 3 BAM files so I can confirm? My email is colbychiang [at] wustl [dot] edu\r\n\r\nIt's possible that running the following before your lumpyexpress command will work, but send me your BAMs if you don't mind regardless:\r\n```\r\nalias awk=gawk\r\n```"}}