{"action":"opened","issue":{"url":"https://api.github.com/repos/ARTbio/tools-artbio/issues/100","repository_url":"https://api.github.com/repos/ARTbio/tools-artbio","labels_url":"https://api.github.com/repos/ARTbio/tools-artbio/issues/100/labels{/name}","comments_url":"https://api.github.com/repos/ARTbio/tools-artbio/issues/100/comments","events_url":"https://api.github.com/repos/ARTbio/tools-artbio/issues/100/events","html_url":"https://github.com/ARTbio/tools-artbio/issues/100","id":194772214,"number":100,"title":"lumpy paired end input","user":{"login":"mvdbeek","id":6804901,"avatar_url":"https://avatars.githubusercontent.com/u/6804901?v=3","gravatar_id":"","url":"https://api.github.com/users/mvdbeek","html_url":"https://github.com/mvdbeek","followers_url":"https://api.github.com/users/mvdbeek/followers","following_url":"https://api.github.com/users/mvdbeek/following{/other_user}","gists_url":"https://api.github.com/users/mvdbeek/gists{/gist_id}","starred_url":"https://api.github.com/users/mvdbeek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mvdbeek/subscriptions","organizations_url":"https://api.github.com/users/mvdbeek/orgs","repos_url":"https://api.github.com/users/mvdbeek/repos","events_url":"https://api.github.com/users/mvdbeek/events{/privacy}","received_events_url":"https://api.github.com/users/mvdbeek/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-12-10T14:53:48Z","updated_at":"2016-12-10T14:53:48Z","closed_at":null,"body":"Hey @drosofff,\r\n\r\nhave you tried lumpy already with paired-end input?\r\nI'm getting:\r\n```\r\nFatal error: Exit code 1 ()\r\n[bam_sort_core] merging from 25 files...\r\n[bam_sort_core] merging from 31 files...\r\nWarning: only 0 elements in distribution (min: 1000)\r\nWarning: only 0 elements in distribution (min: 1000)\r\nmissing pair end parameters:mean stdev \r\n\r\nProgram: ********** (v 0.2.13)\r\nAuthor:  Ryan Layer (rl6sf@virginia.edu)\r\nSummary: Find structural variations in various signals.\r\n\r\nUsage:   ********** [OPTIONS] \r\n\r\nOptions: \r\n\t-g\tGenome file (defines chromosome order)\r\n\t-e\tShow evidence for each call\r\n\t-w\tFile read windows size (default 1000000)\r\n\t-mw\tminimum weight for a call\r\n\t-msw\tminimum per-sample weight for a call\r\n\t-tt\ttrim threshold\r\n\t-x\texclude file bed file\r\n\t-t\ttemp file prefix, must be to a writeable directory\r\n\t-P\toutput probability curve for each variant\r\n\t-b\toutput BEDPE instead of VCF\r\n\t-sr\tbam_file:<file name>,\r\n\t\tid:<sample name>,\r\n\t\tback_distance:<distance>,\r\n\t\tmin_mapping_threshold:<mapping quality>,\r\n\t\tweight:<sample weight>,\r\n\t\tmin_clip:<minimum clip length>,\r\n\t\tread_group:<string>\r\n\r\n\t-pe\tbam_file:<file name>,\r\n\t\tid:<sample name>,\r\n\t\thisto_file:<file name>,\r\n\t\tmean:<value>,\r\n\t\tstdev:<value>,\r\n\t\tread_length:<length>,\r\n\t\tmin_non_overlap:<length>,\r\n\t\tdiscordant_z:<z value>,\r\n\t\tback_distance:<distance>,\r\n\t\tmin_mapping_threshold:<mapping quality>,\r\n\t\tweight:<sample weight>,\r\n\t\tread_group:<string>\r\n\r\n\t-bedpe\tbedpe_file:<bedpe file>,\r\n\t\tid:<sample name>,\r\n\t\tweight:<sample weight>\r\n\r\n```\r\nI'll have a look if I can figure out what's wrong"}}
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