{"action":"created","issue":{"url":"https://api.github.com/repos/ENCODE-DCC/atac-seq-pipeline/issues/43","repository_url":"https://api.github.com/repos/ENCODE-DCC/atac-seq-pipeline","labels_url":"https://api.github.com/repos/ENCODE-DCC/atac-seq-pipeline/issues/43/labels{/name}","comments_url":"https://api.github.com/repos/ENCODE-DCC/atac-seq-pipeline/issues/43/comments","events_url":"https://api.github.com/repos/ENCODE-DCC/atac-seq-pipeline/issues/43/events","html_url":"https://github.com/ENCODE-DCC/atac-seq-pipeline/issues/43","id":369941409,"node_id":"MDU6SXNzdWUzNjk5NDE0MDk=","number":43,"title":"xcor not completing on Sherlock singularity","user":{"login":"knoedlerj","id":44145812,"node_id":"MDQ6VXNlcjQ0MTQ1ODEy","avatar_url":"https://avatars1.githubusercontent.com/u/44145812?v=4","gravatar_id":"","url":"https://api.github.com/users/knoedlerj","html_url":"https://github.com/knoedlerj","followers_url":"https://api.github.com/users/knoedlerj/followers","following_url":"https://api.github.com/users/knoedlerj/following{/other_user}","gists_url":"https://api.github.com/users/knoedlerj/gists{/gist_id}","starred_url":"https://api.github.com/users/knoedlerj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/knoedlerj/subscriptions","organizations_url":"https://api.github.com/users/knoedlerj/orgs","repos_url":"https://api.github.com/users/knoedlerj/repos","events_url":"https://api.github.com/users/knoedlerj/events{/privacy}","received_events_url":"https://api.github.com/users/knoedlerj/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2018-10-14T20:40:52Z","updated_at":"2018-10-16T03:32:13Z","closed_at":null,"author_association":"NONE","body":"I'm running the pipeline with Singularity on Sherlock 2.0 and the xcor job doesn't work on the test data: \r\n\r\n\r\n[2018-10-14 01:26:02,28] [error] WorkflowManagerActor Workflow b3ff0230-746e-42f6-bea3-9a6aafa8ceb2 failed (during ExecutingWorkflowState): Job atac.xcor:0:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.\r\nCheck the content of stderr for potential additional information: /scratch/users/knoedler/atac-seq-pipeline/cromwell-executions/atac/b3ff0230-746e-42f6-bea3-9a6aafa8ceb2/call-xcor/shard-0/execution/stderr.\r\n Traceback (most recent call last):\r\n  File \"/software/atac-seq-pipeline/src/encode_xcor.py\", line 102, in <module>\r\n    main()\r\n  File \"/software/atac-seq-pipeline/src/encode_xcor.py\", line 91, in main\r\n    ta_subsampled, args.speak, args.nth, args.out_dir)\r\n  File \"/software/atac-seq-pipeline/src/encode_xcor.py\", line 53, in xcor\r\n    run_shell_cmd(cmd1)\r\n  File \"/software/atac-seq-pipeline/src/encode_common.py\", line 230, in run_shell_cmd\r\n    os.killpg(pgid, signal.SIGKILL)\r\nOSError: [Errno 3] No such process\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\nJob atac.xcor:1:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.\r\nCheck the content of stderr for potential additional information: /scratch/users/knoedler/atac-seq-pipeline/cromwell-executions/atac/b3ff0230-746e-42f6-bea3-9a6aafa8ceb2/call-xcor/shard-1/execution/stderr.\r\n Traceback (most recent call last):\r\n  File \"/software/atac-seq-pipeline/src/encode_xcor.py\", line 102, in <module>\r\n    main()\r\n  File \"/software/atac-seq-pipeline/src/encode_xcor.py\", line 91, in main\r\n    ta_subsampled, args.speak, args.nth, args.out_dir)\r\n  File \"/software/atac-seq-pipeline/src/encode_xcor.py\", line 53, in xcor\r\n    run_shell_cmd(cmd1)\r\n  File \"/software/atac-seq-pipeline/src/encode_common.py\", line 230, in run_shell_cmd\r\n    os.killpg(pgid, signal.SIGKILL)\r\nOSError: [Errno 3] No such process\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"},"comment":{"url":"https://api.github.com/repos/ENCODE-DCC/atac-seq-pipeline/issues/comments/430088807","html_url":"https://github.com/ENCODE-DCC/atac-seq-pipeline/issues/43#issuecomment-430088807","issue_url":"https://api.github.com/repos/ENCODE-DCC/atac-seq-pipeline/issues/43","id":430088807,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMDA4ODgwNw==","user":{"login":"knoedlerj","id":44145812,"node_id":"MDQ6VXNlcjQ0MTQ1ODEy","avatar_url":"https://avatars1.githubusercontent.com/u/44145812?v=4","gravatar_id":"","url":"https://api.github.com/users/knoedlerj","html_url":"https://github.com/knoedlerj","followers_url":"https://api.github.com/users/knoedlerj/followers","following_url":"https://api.github.com/users/knoedlerj/following{/other_user}","gists_url":"https://api.github.com/users/knoedlerj/gists{/gist_id}","starred_url":"https://api.github.com/users/knoedlerj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/knoedlerj/subscriptions","organizations_url":"https://api.github.com/users/knoedlerj/orgs","repos_url":"https://api.github.com/users/knoedlerj/repos","events_url":"https://api.github.com/users/knoedlerj/events{/privacy}","received_events_url":"https://api.github.com/users/knoedlerj/received_events","type":"User","site_admin":false},"created_at":"2018-10-16T03:32:13Z","updated_at":"2018-10-16T03:32:13Z","author_association":"NONE","body":"Ran everything but atacqc that time; thanks!"}}
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