I am trying to do GWAS in GAPIT but it is showing the following error again and again. I have been trying to figure out this problem. Can anyone explain what is the reason behind it.

Error in merge.data.frame(PWIP$PWIP, GI[, c("SNP", "effect")], by.x = "SNP",  : 
  negative length vectors are not allowed
In addition: There were 18 warnings (use warnings() to see them)
Called from: merge.data.frame(PWIP$PWIP, GI[, c("SNP", "effect")], 
    by.x = "SNP", by.y = "SNP")
Browse[1]>

Details of my data:

At first,I have tried to do association using genotype data in HapMap format, then I thought the problem would be in HapMap file. To check it, I have converted it into numerical format, and tried again but still doesn't work.