{"action":"created","issue":{"url":"https://api.github.com/repos/Oshlack/STRetch/issues/45","repository_url":"https://api.github.com/repos/Oshlack/STRetch","labels_url":"https://api.github.com/repos/Oshlack/STRetch/issues/45/labels{/name}","comments_url":"https://api.github.com/repos/Oshlack/STRetch/issues/45/comments","events_url":"https://api.github.com/repos/Oshlack/STRetch/issues/45/events","html_url":"https://github.com/Oshlack/STRetch/issues/45","id":387170177,"node_id":"MDU6SXNzdWUzODcxNzAxNzc=","number":45,"title":"error on bam files","user":{"login":"hrafehi","id":34467267,"node_id":"MDQ6VXNlcjM0NDY3MjY3","avatar_url":"https://avatars3.githubusercontent.com/u/34467267?v=4","gravatar_id":"","url":"https://api.github.com/users/hrafehi","html_url":"https://github.com/hrafehi","followers_url":"https://api.github.com/users/hrafehi/followers","following_url":"https://api.github.com/users/hrafehi/following{/other_user}","gists_url":"https://api.github.com/users/hrafehi/gists{/gist_id}","starred_url":"https://api.github.com/users/hrafehi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hrafehi/subscriptions","organizations_url":"https://api.github.com/users/hrafehi/orgs","repos_url":"https://api.github.com/users/hrafehi/repos","events_url":"https://api.github.com/users/hrafehi/events{/privacy}","received_events_url":"https://api.github.com/users/hrafehi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-12-04T08:26:22Z","updated_at":"2018-12-04T23:34:05Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI had the following error when trying to run sTRetch on bam files:\r\n\r\n[]\t======================================== Stage str_targets =========================================\r\nERROR: An output containing or ending with '.bed' was referenced.\r\n\r\nHowever such an output was not in the outputs specified by an enclosing transform / filter / produce statement.\r\n\r\nValid outputs according to the enclosing block are: 24644-1-fixed.slop.bam \r\n\r\nThanks\r\n\r\nHaloom"},"comment":{"url":"https://api.github.com/repos/Oshlack/STRetch/issues/comments/444300554","html_url":"https://github.com/Oshlack/STRetch/issues/45#issuecomment-444300554","issue_url":"https://api.github.com/repos/Oshlack/STRetch/issues/45","id":444300554,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0NDMwMDU1NA==","user":{"login":"hrafehi","id":34467267,"node_id":"MDQ6VXNlcjM0NDY3MjY3","avatar_url":"https://avatars3.githubusercontent.com/u/34467267?v=4","gravatar_id":"","url":"https://api.github.com/users/hrafehi","html_url":"https://github.com/hrafehi","followers_url":"https://api.github.com/users/hrafehi/followers","following_url":"https://api.github.com/users/hrafehi/following{/other_user}","gists_url":"https://api.github.com/users/hrafehi/gists{/gist_id}","starred_url":"https://api.github.com/users/hrafehi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hrafehi/subscriptions","organizations_url":"https://api.github.com/users/hrafehi/orgs","repos_url":"https://api.github.com/users/hrafehi/repos","events_url":"https://api.github.com/users/hrafehi/events{/privacy}","received_events_url":"https://api.github.com/users/hrafehi/received_events","type":"User","site_admin":false},"created_at":"2018-12-04T23:34:05Z","updated_at":"2018-12-04T23:34:05Z","author_association":"NONE","body":"I updated STRetch to the most recetn version and that error isnt occuring any more, now I get hte following error:\r\n\r\nbpipe.PipelineStage\t[191]\tSEVERE\t|10:26:03 Cleaning up outputs due to error \r\nbpipe.PipelineStage\t[191]\tSEVERE\t|10:26:03 Cleaning up outputs due to error \r\nbpipe.PipelineCategory\t[191]\tSEVERE\t|10:26:03 Pipeline segment in thread Thread-171 failed with internal error: groovy.util.ConfigObject \r\n"}}
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