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Stopped running "final_logging"

See original GitHub issue

This may be related to #157 but I don’t want to make assumptions.

A different job (chr20) appears to be complete (it has finished delocalization) but appears to still be running because the “final_logging” could not be found (but still had an exit status of 0!?).

done: false
metadata:
  '@type': type.googleapis.com/google.genomics.v2alpha1.Metadata
  createTime: '2019-05-22T16:35:10.783867Z'
  events:
  - description: |-
      Stopped running "final_logging": environment: line 18: log_info: command not found
      environment: line 18: log_info: command not found
      environment: line 18: log_info: command not found
    details:
      '@type': type.googleapis.com/google.genomics.v2alpha1.ContainerStoppedEvent
      actionId: 8
      exitStatus: 0
      stderr: |
        environment: line 18: log_info: command not found
        environment: line 18: log_info: command not found
        environment: line 18: log_info: command not found
    timestamp: '2019-05-22T23:41:44.276607Z'
  - description: Started running "final_logging"
    details:
      '@type': type.googleapis.com/google.genomics.v2alpha1.ContainerStartedEvent
      actionId: 8
      ipAddress: ''
      portMappings: {}
    timestamp: '2019-05-22T23:41:39.647535Z'
  - description: Stopped running "delocalization"
    details:
      '@type': type.googleapis.com/google.genomics.v2alpha1.ContainerStoppedEvent
      actionId: 7
      exitStatus: 0
      stderr: ''
    timestamp: '2019-05-22T23:41:38.546159Z'

Issue Analytics

State:
Created 4 years ago
Comments:7 (3 by maintainers)

Top GitHub Comments

1reaction

mbookmancommented, Jun 15, 2019

Yes!

1reaction

mbookmancommented, May 23, 2019

Thanks for reporting the problem. The log_info problem was introduced in d3269e53a3dd68063a94b474fc1efd4825130259 and would be for all dsub jobs.

The problem of the VM continuing to run should be unrelated. You’ll see the same error message in the underlying operation for all of your dsub jobs.

If the VM continues to run, you will likely need to terminate it manually and report the problem to Google.