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running wdl on google genomics

afriedenafrieden Cambridge, MAMember

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'
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