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EBISPOT
Reharmonise updated sumstats for GCST90268462 to GCST90268500
GCST90268462 - GCST90268500 have been updated manually (replaced on staging).
New harmonised files need to be generated for these studies.
@karatugo Just to make sure I understand: I recently manually replaced the summary statistics for these studies with corrected versions supplied by the author. The old summary statistics files had already been harmonised, so I deleted the old harmonised versions. I would now like new harmonised files to be created for the new summary statistics that I have added.
Are you saying that we can just wait, and this task will be picked up automatically by the harmonisation pipeline?
@eks-ebi Sorry for the misunderstanding. I didn't realize the old harmonised files were deleted. I thought they hadn't been created yet. In that case, they would automatically enter the harmonisation pipeline. But, since they were already generated and then deleted, we need to reharmonise them. I'll take care of it.
Submitted to codon-slurm.
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
62990405 standard goci1258 gwas_lsf R 3:30 1 hl-codon-10-03
The job in SLURM failed, submitted using LSF.
92613079 gwas_ls RUN standard codon-login hl-codon-44 *sf.config Mar 18 12:49
LSF job is likely to fail, do first https://github.com/EBISPOT/goci/issues/1257
https://github.com/EBISPOT/goci/issues/1257 done.
Submitted a SLURM job now.
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
383374 standard goci1258 spotbot R 0:13 1 hl-codon-10-01
I have contacted Yue for assistance in debugging the issue, as similar failures are occurring frequently.
[1a/b4a5a3] process > NFCORE_GWASCATALOGHARM:GWAS... [100%] 39 of 39, failed: 39
- [x] Copy harmonised files from
/nfs/ftp/private/gwas_cat/harm_test/success/GCST90268001-GCST90269000/to the public ftp.