ERROR: magma

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刘焕

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Apr 11, 2024, 8:35:24 AMApr 11
to FUMA GWAS users
Dear FUMA support,

I face this error ERROR: magma for job id  472411  . Could you please help me in fixing this issue?

Thanks a lot.

Best regards
FUMA user

fuma.ctglab

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Apr 15, 2024, 10:38:17 AMApr 15
to FUMA GWAS users
Dear user, 

You input a file that has SNP, effect_allele, and non_effect_allele. Because your file did not have chromosome and position, FUMA extracted chromosome and position information from dbSNP version 146. 
In your case, it seemed that you specified 2 columns that seemingly have the same alleles for effect_allele and non_effect_allele columns, specifically:

eacol = A1.x
neacol = A1.y

The first 10 variants of your file has the following information: 
SNP     A1.x    A1.y
rs10    C       C
rs1000000       A       A
rs10000010      C       C
rs10000012      G       G
rs10000013      A       A
rs10000017      T       T
rs1000002       T       T
rs10000023      T       T
rs1000003       G       G

FUMA will try to match variant rs10 with effect allele C and non_effect_allele C to the reference genome. This is not possible. 
Please double-check. 

Thank you,
FUMA

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