I'm trying to estimate the size of the linkage blocks in the genome of a non-model organism. I have SNPs for multiple individuals and I'm running the Plink1.9 function --blocks. The issue is that Plink results says "0 haploblocks written to plink.blocks". I've tried to limit the analysis to the largest scaffolds or a few individuals and I keep getting this error. Am I missing something? Is this even biologically possible? Is it possibly an issue with my data or filtering of SNPs?
plink --allow-extra-chr --blocks no-pheno-req --vcf SNPs_only-3firstscaffolds.vcf
I would appreciate any insight.