error related to MetaXcan
Entering edit mode
13 months ago
rheab1230 ▴ 80

Hello everyone, I am running script from metaXcan. But I am getting some error. I have followed the tutorial but i am getting error. This is the script: python $GWAS_TOOLS/ \ -gwas_file $AD_DATA/Mari_maternal_AD_GWAS.txt.gz \ -snp_reference_metadata $DATA/reference_panel_1000G/variant_metadata.txt.gz METADATA \ -output_column_map SNP variant_id \ -output_column_map A2 non_effect_allele \ -output_column_map A1 effect_allele \ -output_column_map beta effect_size \ -output_column_map p value \ -output_column_map chr chromosome \ --chromosome_format \ -output_column_map bp position \ -output_column_map effect_allele_freq frequency \ --insert_value sample_size 314278 --insert_value n_cases 60801 \ -output_order variant_id panel_variant_id chromosome position effect_allele non_effect_allele frequency pvalue zscore effect_size standard_error sample_size \ -output $OUTPUT/harmonized_gwas/harmonized_AD_maternal_summary.txt.gz

The error: INFO - Parsing input GWAS Traceback (most recent call last): File "/work/08259/stampede2/i/summary-gwas-imputation/src/", line 311, in <module> run(args) File "/work/08259/stampede2/i/summary-gwas-imputation/src/", line 258, in run enforce_numeric_columns=args.enforce_numeric_columns) File "/work2/08259/stampede2/i/summary-gwas-imputation/src/genomic_tools_lib/file_formats/gwas/", line 18, in load_gwas d = _ensure_columns(d, input_pvalue_fix, enforce_numeric_columns) File "/work2/08259/stampede2/i/summary-gwas-imputation/src/genomic_tools_lib/file_formats/gwas/", line 47, in _ensure_columns _ensure_z(d, input_pvalue_fix) File "/work2/08259/stampede2/i/summary-gwas-imputation/src/genomic_tools_lib/file_formats/gwas/", line 83, in _ensure_z if z is None: raise ReportableException("Couldn't get zscore from GWAS") genomic_tools_lib.Exceptions.ReportableException: Couldn't get zscore from GWAS

PrediXcan TWAS MetaXcan SNP • 301 views

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