JOB ID: 640703, help request, error code:magma

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wided boukhalfa

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Jul 14, 2025, 7:09:36 AMJul 14

to FUMA GWAS users

Dear FUMA team,

I am reaching out to request your assistance regarding my job "640703." I keep receiving a failed job email with an error code related to magma.

I have resubmitted the job several times with different inputs—specifically, I eliminated the missing SNPs and p-values. Additionally, I removed the CHR and BP columns to avoid including non-matching positions with the rsID, since the association analysis was conducted on a VCF file aligned to the hg38 assembly.

Could you please help me resolve this issue?

Thank you in advance for your support.

Tanya Phung

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Jul 16, 2025, 7:31:26 AMJul 16

to FUMA GWAS users

Hi,

This is the error of your magma job:

ERROR - reading p-value file: no valid p-values found for any SNPs in the data

Also, after pre-processing by FUMA there were only 40 snps left. Is this what you expect?

Did you check that the rsID in your file matches with the rsID that FUMA uses for reference? you can check it in the download page (scroll towards the end): https://fuma.ctglab.nl/downloadPage