Issue with input files

[hw85241]

Using the chr_len.txt, chr_siz.txt, and peanut.gff files provided from the testData folder, errors arise when using my own .vcf and .hapmap files as input (note, the .vcf and .hapmap files correspond to peanut and chromosome names have been modified to match those as listed in the testData files.

When supplying a .vcf, the following error messages arises:
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': undefined columns selected
In addition: There were 20 warnings (use warnings() to see them)

When supplying a .hapmap, the following error messages arises:
Error in if (h1[[1]][1] == "#CHROM") { :
missing value where TRUE/FALSE needed
In addition: There were 23 warnings (use warnings() to see them)

Attached are images of the input files.