Hi I have two vcf files from different sets of individuals

1.vcf file is genotype data and 2.vcf files is wgs data

when I run

QTLtools pca --vcf 1.vcf --scale --center --maf 0.05 --distance 50000 --out 1.genotypes.output
QTLtools pca --vcf 2.vcf --scale --center --maf 0.05 --distance 50000 --out 2.genotypes.output

separately on each file I am able get pcas but when I run QTLtools pca on merged vcf file. I dont get any pcs. I get this message. Can anyone help me with this?

bcftools merge 1.vcf 2.vcf > 1.2.vcf

QTLtools pca --vcf 1.2.vcf --scale --center --maf 0.05 --distance 50000 --out 1.2.genotypes.output

Reading genotype data in [test.vcf.gz]
  * File format detected: VCF
  * Read 100000 lines
  * 0 variants included
  * 126480 variants excluded by user

EXITED: Cannot find genotypes in target region!