The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
running wdl on google genomics
Hi I followed the example and removed a couple of tasks in the following: https://cloud.google.com/genomics/v1alpha2/gatk
I got the following error message. I have rerun this a couple of times and the message seems to be somewhat esoteric. Any idea what went wrong here?
gcloud alpha genomics operations describe <runID> --format='yaml(done, error, metadata.events)' done: true error: code: 10 message: |- 11: Docker run failed: command failed: 2017-07-25 19:50:27,396 sys_util INFO: CROMWELL->/cromwell/cromwell.jar 2017-07-25 19:50:27,396 sys_util INFO: CROMWELL_CONF->/cromwell/jes_template.conf 2017-07-25 19:50:27,401 discovery INFO: URL being requested: GET https://www.googleapis.com/discovery/v1/apis/storage/v1/rest 2017-07-25 19:50:27,432 discovery INFO: URL being requested: GET https://www.googleapis.com/storage/v1/b/ccgd-test/o?fields=nextPageToken%2Citems%28name%29&prefix=example-lane-v4%2Foutputs&alt=json&maxResults=2 2017-07-25 19:50:27,432 transport INFO: Attempting refresh to obtain initial access_token 2017-07-25 19:50:27,531 cromwell_driver INFO: Started Cromwell 2017-07-25 19:50:27,531 wdl_runner INFO: starting 2017-07-25 19:50:33,594 cromwell_driver INFO: Failed to connect to Cromwell (attempt 1): ('Connection aborted.', error(104, 'Connection reset by peer')) 2017-07-25 19:50:39,625 cromwell_driver INFO: Failed to connect to Cromwell (attempt 2): ('Connection aborted.', error(104, 'Connection reset by peer')) ERROR: Job status from Cromwell was not 'Submitted', instead 'fail' . See logs at gs://ccgd-test/example-lane-v4/logging metadata: events: - description: start startTime: '2017-07-25T19:49:48.601466303Z' - description: pulling-image startTime: '2017-07-25T19:49:48.602007220Z' - description: localizing-files startTime: '2017-07-25T19:50:26.067038416Z' - description: running-docker startTime: '2017-07-25T19:50:26.067093941Z' - description: fail startTime: '2017-07-25T19:50:47.787272621Z'