number of analyzed SNPs = 0

[MooseyGoosey]

I've been trying several phenotypes (same VCF data), but for every single one I get 0 SNPs analyzed and thus GEMMA is unable to calcuate any meaningful values/SNPs. Is there something I am missing? There are no errors throughout the run, and the run completes, just with the output files blank.

GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020
Reading Files ...

number of total individuals = 150

number of analyzed individuals = 150

number of covariates = 1

number of phenotypes = 1

number of total SNPs/var = 7288009

number of analyzed SNPs = 0

================================================== 100%
**** INFO: Done.
Starting with Pb analysis..
Output will be saved in ./gwas_out/Pb_data/Output/Linear_Model/Pb/Pb_20230614_052857/
Calculating linear model..
Linear model calculated successfully
GEMMA executed successfully on Pb

GEMMA completed successfully (Duration: 45.5 seconds)

Analyzing GEMMA results

Starting post-processing of Pb..
Summarizing p-values..
Variants with the best p_wald score saved in ./gwas_out/Pb_data/Output/Linear_Model/Pb/Pb_20230614_052857/best_p-values
Creating Manhattan plot of p_wald..
GEMMA couldn't calculate any meaningful values!
Creating QQ-plot..
GEMMA couldn't calculate any meaningful values!
Analysis of Pb completed

Analysis of GEMMA results completed successfully