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connection reset by peer, defining memory is not working

afriedenafrieden Cambridge, MAMember

Hi WDL Team,
I am currently trying to run a pipeline using some small data. I have set the memory CLI to 5,10, and 20 but to no avail:

gcloud alpha genomics pipelines run \
--pipeline-file workflows/wdl_pipeline.yaml \
--zones us-central1-f \
--memory 20 \
--logging gs://ccgd-test/aggTest/logging \
--inputs-from-file WDL=/path/to/aggregationLevel.wdl \
--inputs-from-file WORKFLOW_INPUTS=/path/to/aggregationLevel.inputs.test.json \
--inputs-from-file WORKFLOW_OPTIONS=/path/to/PublicPairedSingleSampleWf_170412.options.json \
--inputs WORKSPACE=gs://ccgd-test/aggTest/workspace \
--inputs OUTPUTS=gs://ccgd-test/aggTest/outputs

Getting the following error:

error:
 code: 10
 message: |-
  11: Docker run failed: command failed: 2017-07-28 19:47:17,952 sys_util INFO: CROMWELL->/cromwell/cromwell.jar
  2017-07-28 19:47:17,952 sys_util INFO: CROMWELL_CONF->/cromwell/jes_template.conf
  2017-07-28 19:47:17,956 discovery INFO: URL being requested: GET https://www.googleapis.com/discovery/v1/apis/storage/v1/rest
  2017-07-28 19:47:17,994 discovery INFO: URL being requested: GET https://www.googleapis.com/storage/v1/b/ccgd-test/o?fields=nextPageToken%2Citems%28name%29&prefix=aggTest%2Foutputs&alt=json&maxResults=2
  2017-07-28 19:47:17,994 transport INFO: Attempting refresh to obtain initial access_token
  2017-07-28 19:47:18,089 cromwell_driver INFO: Started Cromwell
  2017-07-28 19:47:18,089 wdl_runner INFO: starting
  2017-07-28 19:47:24,145 cromwell_driver INFO: Failed to connect to Cromwell (attempt 1): ('Connection aborted.', error(104, 'Connection reset by peer'))
  ERROR: Job status from Cromwell was not 'Submitted', instead 'fail'
  . See logs at gs://ccgd-test/aggTest/logging

Logs don't seem to be any more useful. Any thoughts on what is going on?

Answers

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