This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
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'