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
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**** 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
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
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 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