error related to MetaXcan
0
0
Entering edit mode
3 months ago
rheab1230 ▴ 30

Hello everyone, I am running gwas_parsing.py 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_parsing.py \ -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/gwas_parsing.py", line 311, in <module> run(args) File "/work/08259/stampede2/i/summary-gwas-imputation/src/gwas_parsing.py", 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/GWAS.py", 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/GWAS.py", 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/GWAS.py", 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 • 142 views
ADD COMMENT

Login before adding your answer.

Traffic: 2521 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6