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icgc-argo / workflow-roadmap

Roadmap and management for genomic data processing
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Workflow Run Failure - payload JSON has an invalid value #63

Closed lindaxiang closed 3 years ago

lindaxiang commented 3 years ago

Detailed Description

The issue was caused by payload JSON which has a field populated with invalid value. "oxoQ_score":NaN,

List all runids affected

https://wes.rdpc.cancercollaboratory.org/runs/wes-cb274f93529f4624a03a831e09166f0d

Approach to address this

Fix the tool: https://github.com/icgc-argo/gatk-tools/issues/70 Re-run the job.

Exit criteria

lindaxiang commented 3 years ago

Based on the QC metrics we collected, this input data is single ended dataset, we need to hold on this job for further investigation.

lindaxiang commented 3 years ago

@lepsalex can you re-run this job with latest version of aln-wf: https://github.com/icgc-argo/dna-seq-processing-wfs/releases/tag/1.5.6 The latest version has a fix to handle this type of error.

lepsalex commented 3 years ago

New run: https://wes.rdpc.cancercollaboratory.org/runs/wes-ceea5c8087eb45b4ac041310bd907a12

lindaxiang commented 3 years ago

The job has completed successfully. @lepsalex