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EBISPOT / goci

GWAS Catalog Ontology and Curation Infrastructure
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Investigate why submission is failing validation #1340

Closed eks-ebi closed 2 weeks ago

eks-ebi commented 4 weeks ago

This submission is failing validation, but the cause of the failure is unclear.

https://www.ebi.ac.uk/gwas/deposition/submission/665086c4d222f500010e2aba

karatugo commented 4 weeks ago

Restarted the validation and it failed due to mandatory columns being missing. For example, check the header of the file reformatted_residDist.results_240224.tsv.

chromosome  base_pair_location  p_value variant_id
karatugo commented 3 weeks ago

Also see https://github.com/EBISPOT/goci/issues/1342

eks-ebi commented 3 weeks ago

@karatugo Is it only that one file (reformatted_residDist.results_240224.tsv) that has an error? I actually expect an error in that file because it is a non-standard GWAS design. But the other files need to meet all of the validation requirements - can you tell if the others look ok?

karatugo commented 3 weeks ago
karatugo commented 3 weeks ago

@eks-ebi I've rerun the validation, excluding this specific file. But we're still encountering md5sum errors with several files, including "Merged_micronuciformis.tsv", "Merged_Veillonellaceae.tsv", and "Merged_ASV0009.tsv" etc.

For instance, the md5sum for "Merged_micronuciformis.tsv" from our private FTP is 650aa6dedeff99a4b54182e1bc3dd2a0, but in the template, it is d6665937d97682f915b3331b4fd364b5.

eks-ebi commented 3 weeks ago

ok great, thanks Karatug! I'll go back to the authors and ask them to check the md5sums.

karatugo commented 2 weeks ago

Submission is complete now.