{"action":"created","issue":{"url":"https://api.github.com/repos/CPTR-ReSeqTB/UVP/issues/4","repository_url":"https://api.github.com/repos/CPTR-ReSeqTB/UVP","labels_url":"https://api.github.com/repos/CPTR-ReSeqTB/UVP/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/CPTR-ReSeqTB/UVP/issues/4/comments","events_url":"https://api.github.com/repos/CPTR-ReSeqTB/UVP/issues/4/events","html_url":"https://github.com/CPTR-ReSeqTB/UVP/issues/4","id":376193365,"node_id":"MDU6SXNzdWUzNzYxOTMzNjU=","number":4,"title":"rm: cannot remove ‘Results/test/kraken/kraken.txt’: No such file or directory","user":{"login":"matnguyen","id":22606034,"node_id":"MDQ6VXNlcjIyNjA2MDM0","avatar_url":"https://avatars0.githubusercontent.com/u/22606034?v=4","gravatar_id":"","url":"https://api.github.com/users/matnguyen","html_url":"https://github.com/matnguyen","followers_url":"https://api.github.com/users/matnguyen/followers","following_url":"https://api.github.com/users/matnguyen/following{/other_user}","gists_url":"https://api.github.com/users/matnguyen/gists{/gist_id}","starred_url":"https://api.github.com/users/matnguyen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matnguyen/subscriptions","organizations_url":"https://api.github.com/users/matnguyen/orgs","repos_url":"https://api.github.com/users/matnguyen/repos","events_url":"https://api.github.com/users/matnguyen/events{/privacy}","received_events_url":"https://api.github.com/users/matnguyen/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-10-31T23:06:27Z","updated_at":"2018-11-14T22:54:21Z","closed_at":"2018-11-14T15:18:29Z","author_association":"NONE","body":"It seems that UVP is trying to remove a file that has already been moved. This is what I see in the log file:\r\n\r\n```\r\n---[ mv ]---\r\nCommand: \r\nmv Results/test QC\r\n\r\n---[ rm ]---\r\nCommand: \r\nrm Results/test/kraken/kraken.txt\r\n\r\nStandard Error: \r\nrm: cannot remove ‘Results/test/kraken/kraken.txt’: No such file or directory\r\n```\r\n\r\nI am running UVP with the --keepfiles flag"},"comment":{"url":"https://api.github.com/repos/CPTR-ReSeqTB/UVP/issues/comments/438849778","html_url":"https://github.com/CPTR-ReSeqTB/UVP/issues/4#issuecomment-438849778","issue_url":"https://api.github.com/repos/CPTR-ReSeqTB/UVP/issues/4","id":438849778,"node_id":"MDEyOklzc3VlQ29tbWVudDQzODg0OTc3OA==","user":{"login":"matnguyen","id":22606034,"node_id":"MDQ6VXNlcjIyNjA2MDM0","avatar_url":"https://avatars0.githubusercontent.com/u/22606034?v=4","gravatar_id":"","url":"https://api.github.com/users/matnguyen","html_url":"https://github.com/matnguyen","followers_url":"https://api.github.com/users/matnguyen/followers","following_url":"https://api.github.com/users/matnguyen/following{/other_user}","gists_url":"https://api.github.com/users/matnguyen/gists{/gist_id}","starred_url":"https://api.github.com/users/matnguyen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matnguyen/subscriptions","organizations_url":"https://api.github.com/users/matnguyen/orgs","repos_url":"https://api.github.com/users/matnguyen/repos","events_url":"https://api.github.com/users/matnguyen/events{/privacy}","received_events_url":"https://api.github.com/users/matnguyen/received_events","type":"User","site_admin":false},"created_at":"2018-11-14T22:54:21Z","updated_at":"2018-11-14T22:54:21Z","author_association":"NONE","body":"Kraken runs properly and the outputs are present. It is just that the files that are in Results/test (which include the kraken.txt) are moved to the QC directory. UVP then tries to remove Results/test/kraken/test.txt which has already been moved to QC."}}
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