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broadinstitute / wdl-runner

Easily run WDL workflows on GCP
BSD 3-Clause "New" or "Revised" License
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got "Failed to establish a new connection" when running gatk4-data-processing workflow #9

Open volpato30 opened 5 years ago

volpato30 commented 5 years ago

Hi, I followed and successfully ran the google cloud tutorial. But when I tried to run the data processing workflow I encountered an error message that says:

lib3.connection.HTTPConnection object at 0x7fc007f2fbd0>: Failed to establish a new connection: [Errno 111] Connection refused',)) 2019-07-11 18:42:11,971 cromwell_driver INFO: Failed to connect to Cromwell (attempt 3): HTTPConnectionPool(host='localhost', port=8000): Max retries exceeded with url: /api/workflows/v1 (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fc007f2fc10>: Failed to establish a new connection: [Errno 111] Connection refused',)) 2019-07-11 18:42:16,977 cromwell_driver INFO: Failed to connect to Cromwell (attempt 4): HTTPConnectionPool(host='localhost', port=8000): Max retries exceeded with url: /api/workflows/v1 (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fc007f2fb50>: Failed to establish a new connection: [Errno 111] Connection refused',)) 2019-07-11 18:42:23,296 cromwell_driver INFO: Job submitted to Cromwell. job id: 226db7f3-a007-4b10-8850-7e80dc37ad9a ERROR: Status of job is not Submitted, Running, or Succeeded: Failed

I tried the solution mentioned here and set --memory 5 but that didn't solve my problem.

The command I used for submitting the job is:

gcloud alpha genomics pipelines run \
  --pipeline-file wdl_pipeline.yaml \
  --regions us-central1 \
  --memory 5 \
  --inputs-from-file WDL=${GATK_GOOGLE_DIR}/processing-for-variant-discovery-gatk4.wdl,\
WORKFLOW_INPUTS=${GATK_GOOGLE_DIR}/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json,\
WORKFLOW_OPTIONS=${GATK_GOOGLE_DIR}/generic.google-papi.options.json \
  --env-vars WORKSPACE=${GATK_OUTPUT_DIR}/work,\
OUTPUTS=${GATK_OUTPUT_DIR}/output \
  --logging ${GATK_OUTPUT_DIR}/logging/
willsu commented 4 years ago

@volpato30 I ran into the same issue. Did you happen to get this resolved? Thanks.

tucker-bower-psjh commented 3 years ago

@willsu I, too, have now run into this issue. Did YOU ever get it resolved?

Would be so great if wdl/cromwell would just work as intended for once.

ssllff commented 2 years ago

I ran into the same issue. Any solution available? Thank you!

trum994 commented 2 years ago

I'm also getting the exact same error. Is there a setting in our cromwell server we can modify? [solved: my issue was simply the wrong password but I was only focused at the last error message where it said "max retries exceeded." which made me think something else was wrong ]