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.
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
$ head $PHENOTYPES
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