Distance between vcf position and chrom start is smaller than read length. #83
Description
2024-06-22 10:50:05,945 ERROR VCF to JSON conversion failed.
2024-06-22 10:50:05,946 ERROR Traceback (most recent call last):
2024-06-22 10:50:05,946 ERROR File "/home/Dongxianggui/anaconda3/envs/paragraph2/bin/multigrmpy.py", line 52, in load_graph_description header, records, event_list = convert_vcf_to_json(args, alt_paths=True)
2024-06-22 10:50:05,946 ERROR File "/home/Dongxianggui/anaconda3/envs/paragraph2/lib/python3/grm/vcf2paragraph/init.py", line 133, in convert_vcf_to_json header, records, block_ids = parse_vcf_lines(args.input, args.read_length, args.split_type)
2024-06-22 10:50:05,946 ERROR File "/home/Dongxianggui/anaconda3/envs/paragraph2/lib/python3/grm/vcf2paragraph/init.py", line 209, in parse_vcf_lines raise Exception("Distance between vcf position and chrom start is smaller than read length.")
2024-06-22 10:50:05,946 ERROR Exception: Distance between vcf position and chrom start is smaller than read length.
2024-06-22 10:50:05,946 ERROR Traceback (most recent call last):
2024-06-22 10:50:05,946 ERROR File "/home/Dongxianggui/anaconda3/envs/paragraph2/bin/multigrmpy.py", line 261, in run graph_files = load_graph_description(args)
2024-06-22 10:50:05,946 ERROR File "/home/Dongxianggui/anaconda3/envs/paragraph2/bin/multigrmpy.py", line 52, in load_graph_description header, records, event_list = convert_vcf_to_json(args, alt_paths=True)
2024-06-22 10:50:05,946 ERROR File "/home/Dongxianggui/anaconda3/envs/paragraph2/lib/python3/grm/vcf2paragraph/init.py", line 133, in convert_vcf_to_json header, records, block_ids = parse_vcf_lines(args.input, args.read_length, args.split_type)
2024-06-22 10:50:05,946 ERROR File "/home/Dongxianggui/anaconda3/envs/paragraph2/lib/python3/grm/vcf2paragraph/init.py", line 209, in parse_vcf_lines raise Exception("Distance between vcf position and chrom start is smaller than read length.")
2024-06-22 10:50:05,946 ERROR Exception: Distance between vcf position and chrom start is smaller than read length.
Traceback (most recent call last):
File "/home/Dongxianggui/anaconda3/envs/paragraph2/bin/multigrmpy.py", line 353, in
main()
File "/home/Dongxianggui/anaconda3/envs/paragraph2/bin/multigrmpy.py", line 349, in main
run(args)
File "/home/Dongxianggui/anaconda3/envs/paragraph2/bin/multigrmpy.py", line 261, in run
graph_files = load_graph_description(args)
File "/home/Dongxianggui/anaconda3/envs/paragraph2/bin/multigrmpy.py", line 52, in load_graph_description
header, records, event_list = convert_vcf_to_json(args, alt_paths=True)
File "/home/Dongxianggui/anaconda3/envs/paragraph2/lib/python3/grm/vcf2paragraph/init.py", line 133, in convert_vcf_to_json
header, records, block_ids = parse_vcf_lines(args.input, args.read_length, args.split_type)
File "/home/Dongxianggui/anaconda3/envs/paragraph2/lib/python3/grm/vcf2paragraph/init.py", line 209, in parse_vcf_lines
raise Exception("Distance between vcf position and chrom start is smaller than read length.")
Exception: Distance between vcf position and chrom start is smaller than read length.
Hello, author, I want to know how to solve this situation.