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frankvogt / vcf2gwas

Python API for comprehensive GWAS analysis using GEMMA
GNU General Public License v3.0
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vcf2gwas error after updating to new version #9

Closed vinod1981 closed 2 years ago

vinod1981 commented 2 years ago

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,

frankvogt commented 2 years ago

Hi Vinod, What is the command you used to run the analysis?

vinod1981 commented 2 years ago

Hi Frank, I have updated the question. Thanks,

frankvogt commented 2 years ago

Hi Vinod, Thanks! Just update again, the bug is fixed in the latest version. Sorry for the inconvenience