ERROR:magma

[王运航]

Dear FUMA support,

I face this error ERROR: magma for job id  686721  . Could you please help me in fixing this issue?
 

I have attached some of my data for your reference.

head lead_snps_for_fuma.tsv
SNP     CHR     BP      P       BETA    SE      A1      A2      N
rs4938017       11      113433207       8.86650611339758e-13    0.0187320999583054      0.0026209568967457      T       C       33371
rs7629322       3       49584561        1.20488809840217e-11    0.0243197834091945      0.00358718748931201     C       T       33371
rs12466671      2       22360563        1.55719167258161e-11    0.0177348889751041      0.00263032623938734     G       A       33371
rs12963463      18      55431862        3.60713748853661e-11    0.0194161507158016      0.00293322894368923     C       T       33371
rs10736470      11      113547649       3.94163745750614e-10    -0.0171695062375539     0.00274434525307988     G       A       33371
rs10401969      19      19296909        4.60080132164005e-10    0.0770815299217183      0.0123683712244678      C       T       33371
rs1839245       5       120730938       1.24117702991865e-09    0.0171641645215704      0.0028254550778846      G       A       33371
rs4476748       5       120798862       1.51223354860911e-09    0.0190393748192544      0.00315062096275082     G       A       33371
rs11807366      1       73450965        1.55321172578996e-09    0.0154616325556391      0.00256040657695966     A       G       33371

head lead_snps_for_fuma2.tsv
SNP     CHR     BP
rs11807366      1       73450965
rs12028949      1       154169789
rs11596214      10      104694074
rs12575544      11      113048263
rs4938017       11      113433207
rs10736470      11      113547649
rs2052187       17      67838621
rs62084248      17      67878425
rs12963463      18      55431862

Thanks a lot.

Best regards
FUMA user

[Tanya Phung]

Hi, 

I don't know how many variants there were in the file that you submitted to FUMA SNP2GENE because I don't have access to that file. 
However, what I can see from the processed input file is that there were 21 variants. This is not appropriate for MAGMA analysis. 

MAGMA expects genome-wide input. See my explanation here: https://groups.google.com/g/fuma-gwas-users/c/DBe4n_-BOEo/m/yIZtVoePDAAJ

But if there are a lot more variants in your input file, one other issue is that your chromosome:position is in GRCh38 format. FUMA currently accepts GRCh37 format. 

Best,
Tanya