ValueError

[Guanchao Wang]

Hi All,

I am trying out running SprediXcan on harmonized gwas results, and this just for Kidney_Cortex tissue. But I am receiving an error I have not seen before.  Anyone knows what this means, am I missing some arguments in the script? Any help is appreciated!

File "/accre/arch/easybuild/software/MPI/GCC/8.2.0/OpenMPI/3.1.4/SciPy-bundle/2019.03/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 3087, in _can_reindex
    raise ValueError("cannot reindex from a duplicate axis")
ValueError: cannot reindex from a duplicate axis

My scrips specified are as follwing:

python  ~/MetaXcan/software/SPrediXcan.py \
--gwas_file /panfs/accrepfs.vampire/nobackup/g_cohen_lab/gcwang/eGFR_TWAS/Output/"$input" \
--snp_column gwas_snp \
--non_effect_allele_column gwas_non_effect_allele \
--effect_allele_column gwas_effect_allele \
--zscore_column zscore \
--beta_column beta \
--model_db_path /panfs/accrepfs.vampire/home/wangg11/SprediXcan/data/mashr_v8/mashr_Kidney_Cortex.db \
--covariance /panfs/accrepfs.vampire/home/wangg11/SprediXcan/data/mashr_v8/mashr_Kidney_Cortex.txt.gz \
--keep_non_rsid \
--additional_output \
--throw \

Best,

Guanchao