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EBISPOT / goci

GWAS Catalog Ontology and Curation Infrastructure
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Investigate why submission is failing validation #1343

Closed karatugo closed 2 weeks ago

karatugo commented 3 weeks ago

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

https://www.ebi.ac.uk/gwas/deposition/submission/665f293ed222f500010ec51f

karatugo commented 3 weeks ago

Investigate the following error --> https://github.com/EBISPOT/goci/issues/1344

After validation request, I see the following logs.

[2024-06-05 14:17:45,669: WARNING/ForkPoolWorker-29] Running NextFlow command...
[2024-06-05 14:17:45,853: WARNING/ForkPoolWorker-29] Error in submitting job:
[2024-06-05 14:17:45,853: WARNING/ForkPoolWorker-29] ERROR: Cannot find 'curl' nor 'wget' utility --  please install one of them

This causes validation fail.

karatugo commented 3 weeks ago

@earlEBI I restarted validation manually.

File header error for the file Weight_M_k1_k2_k3_sumstats.tsv.gz

CHR POS Tested_Allele   Other_Allele    BETA    SE  AF_Tested   PVALUE  SNP
1   717587  G   A   -0.000909902    0.0114664   0.984489    0.94    rs144155419
1   731718  T   C   -0.00402037 0.0040427   0.879571    0.32    rs58276399
...
earlEBI commented 3 weeks ago

@karatugo Thanks Karatug - so the submission pages' error reports are broken?

karatugo commented 3 weeks ago

@earlEBI They are not correct as I rerun manually. Please ignore them.

earlEBI commented 3 weeks ago

The user resubmitted and it's gone through.