Analysis failed with ERROR3
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Sanne Spigt
Jun 1, 2026, 3:56:36 AM (2 days ago) Jun 1
to FUMA GWAS users
Good morning!
I want to run a FUMA analysis on summary statistics from a gsem GWAS. The file contains roughly 7 million SNPs. The zipped file does not reach the upload threshold (the unzipped file does).
When uploading, it gave Error:3. I (and Jeanne) checked the file and all p-values (and other values) seem to be correct. The job does run when only uploading only the SNPs and P-value columns (rather than also including the CHR, MAF, BETA etc.). It also runs when I prefilter SNPs with a P-value > 0.1. This suggests to me that the complete file might be too large?
What do you suggest? I also want to perform MAGMA, which might be influenced when I upload the prefiltered SNPs.
When uploading, it gave Error:3. I (and Jeanne) checked the file and all p-values (and other values) seem to be correct. The job does run when only uploading only the SNPs and P-value columns (rather than also including the CHR, MAF, BETA etc.). It also runs when I prefilter SNPs with a P-value > 0.1. This suggests to me that the complete file might be too large?
What do you suggest? I also want to perform MAGMA, which might be influenced when I upload the prefiltered SNPs.
Hope you can help me out!
Cheers,
Sanne
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