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EBISPOT / gwas-user-requests

Repository to collect user requests and bug reports for the GWAS Catalog
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Harmonise sumstats for 35115689 #54

Closed jdhayhurst closed 2 years ago

jdhayhurst commented 2 years ago

These summary statistics are in the pipeline at the formatting stage but have remained there. We need to figure out why they are not progressing through the pipeline and get them harmonised.

ljwh2 commented 2 years ago

@earlEBI to investigate in the first instance

earlEBI commented 2 years ago

I'm afraid I can't see an obvious reason. gwas-subs suggests they got their submission to go through themselves without help. I checked one file and the headers seem ok...

Screenshot 2022-04-20 at 12 41 44

jdhayhurst commented 2 years ago

I think I've identified and fixed the issue. Snakemake, which is managing this workflow, was exiting as soon as another independent job failed. There was a corrupt file that kept failing the pipeline, so even though these files are fine, they either never started or got terminated by snakemake.