ValueError: Please make sure to only select phenotypes/covariates featured in the file

[jeremysutherland]

Hello,

I'm having an issue with the basic function of vcf2gwas. When I use the command below I get the following error:

$ vcf2gwas -v filtered.vcf.gz -pf $PHENOTYPES -p 1 -lm

vcf2gwas v0.8.9 

Initialising..

Start time: Thu, 01 Jun 2023 13:57

Parsing arguments..
Genotype file: filtered.vcf.gz
Phenotype file(s): MedicagoGWAS_traits.csv
Traceback (most recent call last):
  File "/home/jeremy/miniconda3/envs/gwas_vcf/lib/python3.9/site-packages/vcf2gwas/starter.py", line 256, in <module>
    X = pheno_switcher(pheno_files_temp, X)
  File "/home/jeremy/miniconda3/envs/gwas_vcf/lib/python3.9/site-packages/vcf2gwas/utils.py", line 268, in pheno_switcher
    raise ValueError(msg)
ValueError: Please make sure to only select phenotypes/covariates featured in the file

$ head $PHENOTYPES

    pred.prop.lobed host.selectivity    vessel.conductance  intercept   pot block
HM015   0.10067165637011    -0.223601828174139  0.0000000044    1   73  A
HM007   0.0129204513655546  0.122816281353039   0.0000000046    1   111 A
HM131   0.0262131975996871  0.140310087620252   0.0000000065    1   647 D

The filtered.vcf.gz file is an indexed vcf file filtered by genotypes in the $PHENOTYPES file (e.g HM015, HM007, ...)

I installed vcf2gwas in a new conda environment and the 'vcf2gwas -v test' command works correctly.

Any ideas?

Thanks in advance