no BGZF EOF marker

[xuefenfei712]

Dear ALL
Thankyou for your excellent software, I got a problem when I use it, appreciate for your reply!

command line: multigrmpy.py -i chr1.vcf.gz -m CRR1036.mainfest -o test -M 500 -r genomic.fa --threads 15

Error reported:
2022-05-30 16:25:30,202 ERROR VCF to JSON conversion failed.
2022-05-30 16:25:30,210 ERROR Traceback (most recent call last):
2022-05-30 16:25:30,210 ERROR File "/home/bin/anaconda3/bin/multigrmpy.py", line 52, in load_graph_description header, records, event_list =
convert_vcf_to_json(args, alt_paths=True)
2022-05-30 16:25:30,210 ERROR File "/home/bin/anaconda3/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)
2022-05-30 16:25:30,210 ERROR File "/home/bin/anaconda3/lib/python3/grm/vcf2paragraph/init.py", line 193, in parse_vcf_lines vcf_file =
pysam.VariantFile(vcf_path)
2022-05-30 16:25:30,210 ERROR File "pysam/libcbcf.pyx", line 4015, in pysam.libcbcf.VariantFile.init
2022-05-30 16:25:30,211 ERROR File "pysam/libcbcf.pyx", line 4243, in pysam.libcbcf.VariantFile.open
2022-05-30 16:25:30,211 ERROR File "pysam/libchtslib.pyx", line 365, in pysam.libchtslib.HTSFile.check_truncation
2022-05-30 16:25:30,211 ERROR OSError: no BGZF EOF marker; file may be truncated
2022-05-30 16:25:30,211 ERROR Traceback (most recent call last):
2022-05-30 16:25:30,211 ERROR File "/home/bin/anaconda3/bin/multigrmpy.py", line 261, in run graph_files = load_graph_description(args)
2022-05-30 16:25:30,211 ERROR File "/home/bin/anaconda3/bin/multigrmpy.py", line 52, in load_graph_description header, records, event_list =
convert_vcf_to_json(args, alt_paths=True)
2022-05-30 16:25:30,211 ERROR File "/home/bin/anaconda3/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)
2022-05-30 16:25:30,211 ERROR File "/home/bin/anaconda3/lib/python3/grm/vcf2paragraph/init.py", line 193, in parse_vcf_lines vcf_file =
pysam.VariantFile(vcf_path)
2022-05-30 16:25:30,211 ERROR File "pysam/libcbcf.pyx", line 4015, in pysam.libcbcf.VariantFile.init
2022-05-30 16:25:30,211 ERROR File "pysam/libcbcf.pyx", line 4243, in pysam.libcbcf.VariantFile.open
2022-05-30 16:25:30,211 ERROR File "pysam/libchtslib.pyx", line 365, in pysam.libchtslib.HTSFile.check_truncation
2022-05-30 16:25:30,212 ERROR OSError: no BGZF EOF marker; file may be truncated
Traceback (most recent call last):
File "/home/jianglin/bin/anaconda3/bin/multigrmpy.py", line 353, in
main()
File "/home/jianglin/bin/anaconda3/bin/multigrmpy.py", line 349, in main
run(args)
File "/home/jianglin/bin/anaconda3/bin/multigrmpy.py", line 261, in run
graph_files = load_graph_description(args)
File "/home/jianglin/bin/anaconda3/bin/multigrmpy.py", line 52, in load_graph_description
header, records, event_list = convert_vcf_to_json(args, alt_paths=True)
File "/home/jianglin/bin/anaconda3/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/jianglin/bin/anaconda3/lib/python3/grm/vcf2paragraph/init.py", line 193, in parse_vcf_lines
vcf_file = pysam.VariantFile(vcf_path)
File "pysam/libcbcf.pyx", line 4015, in pysam.libcbcf.VariantFile.init
File "pysam/libcbcf.pyx", line 4243, in pysam.libcbcf.VariantFile.open
File "pysam/libchtslib.pyx", line 365, in pysam.libchtslib.HTSFile.check_truncation
OSError: no BGZF EOF marker; file may be truncated