$ python gwas_summary_imputation.py -by_region_file $DATA/eur_ld.bed.gz -gwas_file harmonized.test.txt.gz -parquet_genotype $DATA/reference_panel_1000G/chr1.variants.parquet -parquet_genotype_metadata $DATA/reference_panel_1000G/variant_metadata.parquet -window 100000 -parsimony 7 -chromosome 1 -regularization 0.1 -frequency_filter 0.01 -sub_batches 10 -sub_batch 0 --standardise_dosages -output harmonized.test_chr1_sb0_reg0.1_ff0.01_by_region.txt.gz
INFO - Beginning process
INFO - Creating context by variant
INFO - Loading study
INFO - Loading variants' parquet file
Traceback (most recent call last):
File "/vf/users/HumanRNAProject/TYL/DNA/GWAS_compile/summary-gwas-imputation/src/gwas_summary_imputation.py", line 97, in
run(args)
File "/vf/users/HumanRNAProject/TYL/DNA/GWAS_compile/summary-gwas-imputation/src/gwas_summary_imputation.py", line 60, in run
results = run_by_region(args)
File "/vf/users/HumanRNAProject/TYL/DNA/GWAS_compile/summary-gwas-imputation/src/gwas_summary_imputation.py", line 40, in run_by_region
context = SummaryImputationUtilities.context_by_region_from_args(args)
File "/vf/users/HumanRNAProject/TYL/DNA/GWAS_compile/summary-gwas-imputation/src/genomic_tools_lib/summary_imputation/Utilities.py", line 229, in context_by_region_from_args
study = load_study(args)
File "/vf/users/HumanRNAProject/TYL/DNA/GWAS_compile/summary-gwas-imputation/src/genomic_tools_lib/summary_imputation/Utilities.py", line 162, in load_study
study = Parquet.study_from_parquet(args.parquet_genotype, args.parquet_genotype_metadata, chromosome=args.chromosome)
File "/vf/users/HumanRNAProject/TYL/DNA/GWAS_compile/summary-gwas-imputation/src/genomic_tools_lib/file_formats/Parquet.py", line 218, in study_from_parquet
_v = pq.ParquetFile(variants)
File "/data/lint6/conda/lib/python3.10/site-packages/pyarrow/parquet/core.py", line 318, in init
self.reader.open(
File "pyarrow/_parquet.pyx", line 1470, in pyarrow._parquet.ParquetReader.open
File "pyarrow/error.pxi", line 91, in pyarrow.lib.check_status
How may I solve this?
$ python gwas_summary_imputation.py -by_region_file $DATA/eur_ld.bed.gz -gwas_file harmonized.test.txt.gz -parquet_genotype $DATA/reference_panel_1000G/chr1.variants.parquet -parquet_genotype_metadata $DATA/reference_panel_1000G/variant_metadata.parquet -window 100000 -parsimony 7 -chromosome 1 -regularization 0.1 -frequency_filter 0.01 -sub_batches 10 -sub_batch 0 --standardise_dosages -output harmonized.test_chr1_sb0_reg0.1_ff0.01_by_region.txt.gz INFO - Beginning process INFO - Creating context by variant INFO - Loading study INFO - Loading variants' parquet file Traceback (most recent call last): File "/vf/users/HumanRNAProject/TYL/DNA/GWAS_compile/summary-gwas-imputation/src/gwas_summary_imputation.py", line 97, in
run(args)
File "/vf/users/HumanRNAProject/TYL/DNA/GWAS_compile/summary-gwas-imputation/src/gwas_summary_imputation.py", line 60, in run
results = run_by_region(args)
File "/vf/users/HumanRNAProject/TYL/DNA/GWAS_compile/summary-gwas-imputation/src/gwas_summary_imputation.py", line 40, in run_by_region
context = SummaryImputationUtilities.context_by_region_from_args(args)
File "/vf/users/HumanRNAProject/TYL/DNA/GWAS_compile/summary-gwas-imputation/src/genomic_tools_lib/summary_imputation/Utilities.py", line 229, in context_by_region_from_args
study = load_study(args)
File "/vf/users/HumanRNAProject/TYL/DNA/GWAS_compile/summary-gwas-imputation/src/genomic_tools_lib/summary_imputation/Utilities.py", line 162, in load_study
study = Parquet.study_from_parquet(args.parquet_genotype, args.parquet_genotype_metadata, chromosome=args.chromosome)
File "/vf/users/HumanRNAProject/TYL/DNA/GWAS_compile/summary-gwas-imputation/src/genomic_tools_lib/file_formats/Parquet.py", line 218, in study_from_parquet
_v = pq.ParquetFile(variants)
File "/data/lint6/conda/lib/python3.10/site-packages/pyarrow/parquet/core.py", line 318, in init
self.reader.open(
File "pyarrow/_parquet.pyx", line 1470, in pyarrow._parquet.ParquetReader.open
File "pyarrow/error.pxi", line 91, in pyarrow.lib.check_status