(PLINK): Can't convert .ped .map into .bim .fam .bed. Why?

Question

[Roland]

Hi.

I have a .ped and .map that I have previously created from a .vcf. Note that this VCF was NOT created by aligning reads to a reference genome, but rather by de novo (using the "STACKS" pipeline). I need this .ped .map files in .bim .fam .bed formats, but I can't get it to work.

This is the code I'm using and the error I get:

plink --file my_data --make-bed --out pleasework

And the error:

Error: Invalid chromosome code '27' on line 59 of .map file. (This is disallowed for humans. Check if the problem is with your data, or if you forgot to define a different chromosome set with e.g. --chr-set.)

Any suggestions? I don't have any chromosome data as I haven't aligned my reads to a reference genome.