Hello everyone, I am getting an error while running SPrediXcan.py. I am using whole blood mashr model only.
The command:
python /work2/08259/i/MetaXcan/MetaXcan/software/SPrediXcan.py

--gwas_file $OUTPUT/processed_summary_imputation/imputed_CARDIoGRAM_C4D_CAD_ADDITIVE.txt.gz
--snp_column panel_variant_id
--effect_allele_column effect_allele
--non_effect_allele_column non_effect_allele
--zscore_column zscore
--model_db_path $DATA/models/eqtl/mashr/mashr_Whole_Blood.db
--covariance $DATA/models/eqtl/mashr/mashr_Whole_Blood.txt.gz
--keep_non_rsid
--additional_output
--model_db_snp_key varID
--throw
--output_file $OUTPUT/spredixcan/eqtl/CARDIoGRAM_C4D_CAD_ADDITIVE__PM__Whole_Blood.csv

The error:
INFO - Processing GWAS command line parameters
INFO - Building beta for /scratch/08259/Metaxcan/TestOut_2021v1/processed_summary_imputation/imputed_CARDIoGRAM_C4D_CAD_ADDITIVE.txt.gz and /work2/08259/stampede2/../common_work_files/MetaXcan/data/models/eqtl/mashr/mashr_Whole_Blood.db
INFO - Reading input gwas with special handling: /scratch/08259/Metaxcan/TestOut_2021v1/processed_summary_imputation/imputed_CARDIoGRAM_C4D_CAD_ADDITIVE.txt.gz
Traceback (most recent call last):
File "/work2/08259/i/MetaXcan/MetaXcan/software/SPrediXcan.py", line 65, in <module>
run(args)
File "/work2/08259/i/MetaXcan/MetaXcan/software/SPrediXcan.py", line 29, in run
g = M03_betas.run(M03_args)
File "/work2/08259/i/MetaXcan/MetaXcan/software/M03_betas.py", line 132, in run
b = build_betas(args, model, gwas_format, name, args.snp_map_file)
File "/work2/08259i/MetaXcan/MetaXcan/software/M03_betas.py", line 40, in build_betas
skip_until_header=args.skip_until_header, handle_empty_columns=args.handle_empty_columns, input_pvalue_fix=args.input_pvalue_fix, keep_non_rsid=args.keep_non_rsid)
File "/work2/08259/i/MetaXcan/MetaXcan/software/metax/gwas/GWAS.py", line 97, in load_gwas
d = GWASSpecialHandling.gwas_data_source(source, snps, snp_column_name, skip_until_header, separator, handle_empty_columns)
File "/work2/08259/i/MetaXcan/MetaXcan/software/metax/gwas/GWASSpecialHandling.py", line 43, in gwas_data_source
for i,line in enumerate(file):
File "/home1/08259/miniconda3/envs/imlabtools/lib/python3.7/gzip.py", line 300, in read1
return self._buffer.read1(size)
File "/home1/08259/miniconda3/envs/imlabtools/lib/python3.7/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
File "/home1/08259/miniconda3/envs/imlabtools/lib/python3.7/gzip.py", line 493, in read
raise EOFError("Compressed file ended before the "
EOFError: Compressed file ended before the end-of-stream marker was reached

Can anyone please help me out with this?



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