Inquiry about FUMA "ERROR: magma" with small dataset

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Yu Zhu

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Jan 21, 2026, 7:49:05 AMJan 21

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Experienced "ERROR: magma" during FUMA analysis (Job ID: 699999). Input file format is correct (P-values, CHR, BP, A1, A2 verified), but the file contains only 3 SNPs.

Could this failure be due to the limited number of SNPs? Is there a minimum SNP requirement for FUMA? Any guidance on resolving this or alternative approaches is appreciated.

Tanya Phung

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Jan 22, 2026, 3:59:23 PMJan 22

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Hi,

I answered a similar question here: https://groups.google.com/g/fuma-gwas-users/c/DBe4n_-BOEo/m/yIZtVoePDAAJ