ga4gh / ga4gh/cloud-interop-testing
Execution error on FASP GWAS submission
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- Python
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Description
First attempt to run the GWAS workflow deployed on the DNAStack WES Server.
Using the details posted at the first commit [here](https://github.com/DNAstack/plenary-resources-2020).
Plan A
Can the vcf file be returned from DRS? Perhaps it's in the BioDataCatalyst Thousand genomes dataset.
Yes it's file id dg.4503/dbd55e76-1100-40b3-b420-0eaeee478fbc
The DRS GetObject url for it is
https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/dg.4503/dbd55e76-1100-40b3-b420-0eaeee478fbc
The following gets us a signed URL when called with an access token in the header
https://cgc-ga4gh-api.sbgenomics.com/ga4gh/drs/v1/objects/dg.4503/dbd55e76-1100-40b3-b420-0eaeee478fbc/access/gs
I was then able to submit a job to DNAStack WES passing that signed URL. Code is [here](https://github.com/ianfore/FASPclient/blob/master/FASPScriptGWAS.py)
The run_id was 56d45bee-0022-4a00-ac4d-88e4bb274978
This resulted in an Execution error. See attachment.
[DNAStackGWASRun1_result_json.txt](https://github.com/ga4gh/cloud-interop-testing/files/5112321/DNAStackGWASRun1_result_json.txt)
Perhaps the run logs at DNAStack will give a clue as to the problem.
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