{"action":"created","issue":{"url":"https://api.github.com/repos/ENCODE-DCC/chip-seq-pipeline2/issues/22","repository_url":"https://api.github.com/repos/ENCODE-DCC/chip-seq-pipeline2","labels_url":"https://api.github.com/repos/ENCODE-DCC/chip-seq-pipeline2/issues/22/labels{/name}","comments_url":"https://api.github.com/repos/ENCODE-DCC/chip-seq-pipeline2/issues/22/comments","events_url":"https://api.github.com/repos/ENCODE-DCC/chip-seq-pipeline2/issues/22/events","html_url":"https://github.com/ENCODE-DCC/chip-seq-pipeline2/issues/22","id":360365080,"node_id":"MDU6SXNzdWUzNjAzNjUwODA=","number":22,"title":"Failed to access ‘*.jsd.qc’ (ENCSR936XTK test sample)","user":{"login":"dcdxy","id":43275460,"node_id":"MDQ6VXNlcjQzMjc1NDYw","avatar_url":"https://avatars0.githubusercontent.com/u/43275460?v=4","gravatar_id":"","url":"https://api.github.com/users/dcdxy","html_url":"https://github.com/dcdxy","followers_url":"https://api.github.com/users/dcdxy/followers","following_url":"https://api.github.com/users/dcdxy/following{/other_user}","gists_url":"https://api.github.com/users/dcdxy/gists{/gist_id}","starred_url":"https://api.github.com/users/dcdxy/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dcdxy/subscriptions","organizations_url":"https://api.github.com/users/dcdxy/orgs","repos_url":"https://api.github.com/users/dcdxy/repos","events_url":"https://api.github.com/users/dcdxy/events{/privacy}","received_events_url":"https://api.github.com/users/dcdxy/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":24,"created_at":"2018-09-14T16:04:31Z","updated_at":"2018-11-26T16:48:55Z","closed_at":null,"author_association":"NONE","body":"When attempting to run AQUAS on the test sample datasets (ENCSR936XTK FASTQs), I receive:\r\n\r\n`[2018-09-13 15:32:39,95] [error] WorkflowManagerActor Workflow 0846c6f1-989d-4622-8512-b1aebfb5ea97 failed (during ExecutingWorkflowState): Job chip.fingerprint:NA:1 exited with return code 1 which has not been declared as a valid return code.`\r\n\r\nwhich seems to arise from\r\n\r\n`ln: failed to access ‘*.jsd.qc’: No such file or directory`.\r\n\r\nAny suggestions would be greatly appreciated. Thank you!\r\n\r\n**Details:**\r\nI installed AQUAS on a SGE cluster.\r\n**Cromwell:** cromwell-34\r\n**Conda:** conda 4.3.30\r\n\r\n[debug_22.tar.gz](https://github.com/ENCODE-DCC/chip-seq-pipeline2/files/2384060/debug_22.tar.gz)"},"comment":{"url":"https://api.github.com/repos/ENCODE-DCC/chip-seq-pipeline2/issues/comments/441711359","html_url":"https://github.com/ENCODE-DCC/chip-seq-pipeline2/issues/22#issuecomment-441711359","issue_url":"https://api.github.com/repos/ENCODE-DCC/chip-seq-pipeline2/issues/22","id":441711359,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0MTcxMTM1OQ==","user":{"login":"dcdxy","id":43275460,"node_id":"MDQ6VXNlcjQzMjc1NDYw","avatar_url":"https://avatars0.githubusercontent.com/u/43275460?v=4","gravatar_id":"","url":"https://api.github.com/users/dcdxy","html_url":"https://github.com/dcdxy","followers_url":"https://api.github.com/users/dcdxy/followers","following_url":"https://api.github.com/users/dcdxy/following{/other_user}","gists_url":"https://api.github.com/users/dcdxy/gists{/gist_id}","starred_url":"https://api.github.com/users/dcdxy/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dcdxy/subscriptions","organizations_url":"https://api.github.com/users/dcdxy/orgs","repos_url":"https://api.github.com/users/dcdxy/repos","events_url":"https://api.github.com/users/dcdxy/events{/privacy}","received_events_url":"https://api.github.com/users/dcdxy/received_events","type":"User","site_admin":false},"created_at":"2018-11-26T16:48:55Z","updated_at":"2018-11-26T16:48:55Z","author_association":"NONE","body":"I receive again the same error (comments on September 25) on a different dataset:\r\n\r\n```\r\n[2018-11-26 11:13:35,00] [error] WorkflowManagerActor Workflow 11f011ae-0014-470d-\r\n9fc7-cb896683bf60 failed (during ExecutingWorkflowState): Job chip.xcor:2:1 exited \r\nwith return code 1 which has not been declared as a valid return code. See \r\n'continueOnReturnCode' runtime attribute for more details.\r\n[...]\r\nln: failed to access ‘*.cc.plot.pdf’: No such file or directory\r\nln: failed to access ‘*.cc.plot.png’: No such file or directory\r\nln: failed to access ‘*.cc.qc’: No such file or directory\r\nln: failed to access ‘*.cc.fraglen.txt’: No such file or directory\r\n```\r\nPlease find the tarball below.\r\n[debug_22_4.tar.gz](https://github.com/ENCODE-DCC/chip-seq-pipeline2/files/2616538/debug_22_4.tar.gz)\r\n"}}
{"actor":{"display_login":"dcdxy"}}