CODEWITHSUNDEEP
google-cloud-storagegoogle-genomics
Lucas Taniguti
Lucas Taniguti

Reputation: 11

Google Genomics jobs never ending

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.

Upvotes: 1

Views: 200

Answers (2)

Melissa
Melissa

Reputation: 952

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

Upvotes: 1

Paul Grosu
Paul Grosu

Reputation: 61

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

Upvotes: 0

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