Google Genomics jobs never ending

Question

We were using Google Genomics ReadGroupSets to store our alignment data (BAM files) and it was running amazingly, until yesterday...

Yesterday (08/29/2016) our import jobs (Method: readgroupsets.import) started the "running" status, but until now did not achieve "done" or error message.

Is anyone else getting the same problem?

e.g.: Job running for 1 day and no error msg is displayed.

$ gcloud alpha genomics operations describe identifier

done: false
metadata:
  '@type': type.googleapis.com/google.genomics.v1.OperationMetadata
  clientId: ''
  createTime: '2016-08-30T01:08:57.000Z'
  events: []
  projectId: xxxxxxx
  request:
    '@type': type.googleapis.com/google.genomics.v1.ImportReadGroupSetsRequest
    datasetId: 'xxx'
    partitionStrategy: PER_FILE_PER_SAMPLE
    referenceSetId: ''
    sourceUris:
    - gs://xxx/yyy/zzz.bam
name: operations/identifier

Yesterday we also had temporary problems in getting "public links" from objects in Google Storage, but this one is ok now.

edit: I also tried to trigger the import job using the gcloud cli, pointing to another dataset and to another cloud project but the jobs still stay in "running".

edit2: I'm using Google Genomics for ~3 months and have successfully imported more than 400 alignments. Only this week I'm having problems.

edit3: Solved. All my jobs successfully ended.

@paul-grosu I resubmit the jobs and this time in events appear an expected msg (no referenceSetId) but the job is running for 2h. These import jobs usually were taking no more than 40 min. — Lucas Taniguti, Aug 31 '16 at 15:02
Hi Lucas, I worked off the OperationMetadata API docs and CH's reply the other day for the recommendation. but Melissa just let us know the issue is originating from a different part of the path. I replied to the Google Groups message to synchronize to single thread. Hopefully it will be fixed soon. Paul — Paul Grosu, Aug 31 '16 at 17:25
Hi Lucas, CH and Melissa were able to fix it and now the queue is progressing through the backlog. — Paul Grosu, Aug 31 '16 at 23:03
Hello Paul, thank you for the support. Our import jobs are now successfully done. — Lucas Taniguti, Sep 01 '16 at 16:37
Hello Lucas, Gladly and I am happy to hear that everything is working properly now, though all the hard work was done by Melissa and CH, and they would definitely deserve most of the credit :) Thank you, Paul — Paul Grosu, Sep 02 '16 at 04:15

score 1 · Answer 1 · answered Aug 31 '16 at 16:49

1

Sorry about that. ReadGroupSets Imports are currently not working, see https://groups.google.com/forum/#!topic/google-genomics-discuss/aWV8NjAbaFg

answered Aug 31 '16 at 16:49

Melissa

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Thank you for the information. It would be very nice to see the service status in some place [like this](https://status.cloud.google.com/). – Lucas Taniguti Aug 31 '16 at 17:20
No worries Melissa, thank you for looking into it. I replied on Google Groups to synchronize the information into one place. Thanks, ~p – Paul Grosu Aug 31 '16 at 17:26

score 0 · Answer 2 · answered Aug 31 '16 at 00:14

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There was a backlog yesterday afternoon, and I'm not seeing that your even got the started stage. I would cancel the operation and resubmit it again.

Paul

answered Aug 31 '16 at 00:14

Paul Grosu

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Google Genomics jobs never ending

2 Answers2