Getting only headers in the output files

[halkelchen]

Hi,
I am not sure what I am doing wrong. I did the quick harmonization and tried to input it into S-predixcan and I keep getting only headers as output, and there should be some overlap. Could someone please help me?

!python MetaXcan/software/M03_betas.py
--snp_map_file /Users/halk/Downloads/data/coordinate_map/map_snp150_hg19.txt.gz
--gwas_file /Users/halk/cleandatabuild37.txt
--snp_column rsID
--non_effect_allele_column NEA
--effect_allele_column EA
--beta_column BETA
--pvalue_column P
--throw
--output Users/halk/quickharmonizedgwas.txt.gz

!python /Users/halk/MetaXcan/software/SPrediXcan.py
--model_db_path /Users/halk/Downloads/eqtl/mashr/mashr_Skin_Sun_Exposed_Lower_leg.db
--model_db_snp_key rsid
--covariance /Users/halk/Downloads/eqtl/mashr/mashr_Skin_Sun_Exposed_Lower_leg.txt.gz
--gwas_file /Users/halk/Downloads/quickharmonizedgwas.txt
--snp_column gwas_snp
--effect_allele_column effect_allele
--non_effect_allele_column non_effect_allele
--zscore_column zscore
--beta_column beta
--throw
--verbosity 9
--output_file output/spredixcan_TWAS_Skin_Sun_Exposed.csv