No tested/printed variants

[idolawoye]

Hi! I am trying to run pyseer on a dataset using the vcf file and the distance matrix from the gene_absence_presence file. However, I am not getting any tested/printed variants. Is there something I need to do differently?

When I run: pyseer --phenotypes resistance.pheno --pres gene_presence_absence.Rtab --distances mash.tsv --save-m mash_mds --max-dimensions 10 > amikacin_COGs.txt

I get this: Read 174 phenotypes Detected binary phenotype Structure matrix has dimension (174, 174) Analysing 174 samples found in both phenotype and structure matrix 21834 loaded variants 7025 pre-filtered variants 14809 tested variants 14807 printed variants

However, when I run: pyseer --phenotypes resistance.pheno --vcf filtered.snps.vcf.gz --load-m mash_mds.pkl --lineage --print-samples > amikacin_SNPs.txt

This is what I get: Read 174 phenotypes Detected binary phenotype Loaded projection with dimension (174, 96) Analysing 174 samples found in both phenotype and structure matrix Writing lineage effects to lineage_effects.txt 287347 loaded variants 287347 pre-filtered variants 0 tested variants 0 printed variants

Therefore the amikacin_SNPs.txt file is empty.

Thanks

[idolawoye]

I just realized my VCF format was the issue