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
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?