Unexpected error: DataFrame.drop() takes from 1 to 2 positional arguments but 3 were given

[halkelchen]

This is my command:

!python /Users/halk/MetaXcan/software/SPrediXcan.py \ --model_db_path /Users/halk/Downloads/eqtl/mashr/mashr_Whole_Blood.db \ --covariance /Users/halk/Downloads/eqtl/mashr/mashr_Whole_Blood.txt.gz \ --gwas_file /Users/halk/cleandatawithsnps.txt \ --gwas_file_pattern ".*txt" \ --snp_column SNPID \ --effect_allele_column EA \ --non_effect_allele_column NEA \ --zscore_column Z \ --pvalue_column P \ --output_file output/spredixcan_TWAS_whole_blood.csv

and this is the out with the error I am receiving:

INFO - Processing GWAS command line parameters INFO - Building beta for /Users/halk/cleandatawithsnps.txt and /Users/halk/Downloads/eqtl/mashr/mashr_Whole_Blood.db INFO - Reading input gwas with special handling: /Users/halk/cleandatawithsnps.txt INFO - Processing input gwas INFO - Aligning GWAS to models INFO - Trimming output INFO - Successfully parsed input gwas in 32.18299175502034 seconds INFO - Started metaxcan process INFO - Loading model from: /Users/halk/Downloads/eqtl/mashr/mashr_Whole_Blood.db INFO - Loading covariance data from: /Users/halk/Downloads/eqtl/mashr/mashr_Whole_Blood.txt.gz INFO - Processing loaded gwas INFO - Started metaxcan association INFO - 0 % of model's snps used INFO - Unexpected error: DataFrame.drop() takes from 1 to 2 positional arguments but 3 were given

Anyone know how to fix this?

[Fnyasimi]

Hi @halkelchen could you share the sample of GWAS you are using to reproduce the error for further troubleshooting?

On the other note can you check your enviroment has the required version of python has defined here?

[1667857557]

Same issue