ERROR:magma when MAGMA analysis is enabled and GWAS file appears correctly formatted

[Yan'e Lu]

Hi FUMA team,

I encountered a repeated issue when submitting a GWAS file for MAGMA analysis using SNP2GENE. I have ensured that MAGMA analysis was enabled, and I have carefully checked the file formatting, but I still receive the following error:

"An error occurred during the process of your job (job ID: 609011, job title: FUMA_Sleep efficiency). The specific error message is 'ERROR:magma'. The instructions suggest that this may happen if the rsID or p-value columns are incorrectly labeled or if the file format is invalid."

Here are the details of my submission:

• Job ID: 609011

• Job title: FUMA_Sleep efficiency

• MAGMA analysis: Enabled

• File format: .txt (uncompressed)

• Delimiter: Tab (verified using R fwrite(..., sep = "\t", quote = FALSE))

• Header row: SNP, CHR, BP, A1, A2, BETA, SE, P

• Number of SNPs in file: Only 3

• No row indices, no quotation marks, no missing columns or values

I’ve reviewed the troubleshooting documentation and previous forum threads. The column names and values appear to follow FUMA’s formatting requirements. There are no extra headers, no comment characters (#), and positions are integers using hg19 coordinates.

That said, I suspect the root of the problem may be that the file contains only 3 SNPs, which may be insufficient for MAGMA to perform gene-level regression.

Could you please help clarify the following:

1. Is there a minimum number of SNPs required for MAGMA to work?

2. Can MAGMA be applied to very small filtered SNP sets (e.g., from pleiotropy analysis), or is full GWAS input required?

3. Are there alternative ways to conduct MAGMA-based gene prioritization or gene set enrichment with such limited SNP sets?

I would appreciate any suggestions you can provide to help me resolve this issue.

Best regards,

Yan'e Lu

[Tanya Phung]

Hello, 

The error of your job is: 
ERROR - reading gene annotation file: found no genes containing SNPs in genotype data

For your information, if you are interested in studying 3 SNPs, FUMA is not a suitable tool for this, because we expect genome-wide data. 

For your other MAGMA specific questions,  you can consult the MAGMA manual and/or send a message to the developers of MAGMA, as I do not support MAGMA. 
MAGMA manual: https://cncr.nl/research/magma/

Best,
Tanya