Closed vinod1981 closed 2 years ago
Hi Vinod, What is the command you used to run the analysis?
Hi Frank, I have updated the question. Thanks,
Hi Vinod, Thanks! Just update again, the bug is fixed in the latest version. Sorry for the inconvenience
Hi Frank, When I am running vcf2gwas, I am getting error:
Command line:
/vol/cluster-data/vkumar/miniconda3/envs/myenv/bin/vcf2gwas -v /prj/pflaphy-robot/genotypeGVCF_allsamples_updated/linkimpute/output_all_imputed_final_chr7Mod_js_GT_EA_js.vcf.gz -pf /prj/pflaphy-robot/genotypeGVCF_allsamples_updated/linkimpute/vcf2gwas/soil_pH/EA/soil_pH_EA_updated.csv -ap -cf /prj/pflaphy-robot/genotypeGVCF_allsamples_updated/linkimpute/vcf2gwas/soil_pH/EA/pca_EA_updated_cofactor_chr8.csv -ac -lmm -sv 5 -nl -q 0.01 -o /prj/pflaphy-robot/genotypeGVCF_allsamples_updated/linkimpute/vcf2gwas/soil_pH/pca_with_cof/
Parsing arguments.. Genotype file: output_all_imputed_final_chr7Mod_js_GT_EA_js.vcf.gz Phenotype file(s): soil_pH_EA_updated.csv Covariate file: pca_EA_updated_cofactor_chr8.csv Arguments parsed successfully
Preparing files
Traceback (most recent call last): File "/vol/cluster-data/vkumar/miniconda3/envs/myenv/lib/python3.9/site-packages/vcf2gwas/starter.py", line 348, in
if set(Y).issubset([i+1 for i in list(range(l_covar))]) == False:
TypeError: 'NoneType' object is not iterable
What could be the reason for this?
Thanks,