Hello,

I know this is a very old post but I have just been trying to solve this exact problem. I have a genome that is made up of lots of scaffolds (not a model organism) and so I recieved the error message you report for all my scaffolds.

I found the solution by following this tutorial http://evomics.org/learning/population-and-speciation-genomics/2016-population-and-speciation-genomics/fileformats-vcftools-plink/ section 2.3.

To summarise you need to make your own chromosome map that vcftools uses to make the .ped format. Do this by running the following code:

1. Create chromosome map

bcftools view -H filename.vcf | cut -f 1 | uniq | awk '{print $0"\t"$0}' > filename.chrom-map.txt

2. Make ped file using this chromosome map

vcftools --vcf filename.vcf --plink --chrom-map filename.chrom-map.txt --out filename