Off topic:What would cause you to have no phenotype data?

Question

[tmrhyd]

I have a VCF file that I am running through PLINK to get PED and MAP files, and then .assoc files, so I can get Manhattan plots. Whenever I try to get any files from PLINK it says there are no phenotypes present. It is a plant genome.

What could be causing this? I started with Fastq files, ran BWA on them to align them with the reference, and then marked duplicates in sandblaster, converted sam to bam, and then sorted and indexed it, and ran it through freebayes to get the VCF.

everything is the right size file, and ran normally. What might be the problem?

Why would someone have no phenotypes?