Distance between vcf position and chrom start is smaller than read length.

[MaoYafei]

Hi All,

I try to run paragraph to my test dataset. but got an error below:

$ python3 ../../../Tools/paragraph/bin/multigrmpy.py -i ../pbsv_sample_Bonobo_sv.vcf.gz -m sample.txt -r ../ref.fa -o test &
[1] 39497
$ 2020-02-04 16:37:34,250 ERROR VCF to JSON conversion failed.
2020-02-04 16:37:34,303 ERROR Traceback (most recent call last):
2020-02-04 16:37:34,303 ERROR File "../../../Tools/paragraph/bin/multigrmpy.py", line 52, in load_graph_description header, records, event_list = convert_vcf_to_json(args, alt_paths=True)
2020-02-04 16:37:34,303 ERROR File "/net/eichler/vol26/projects/primate_sv/nobackups/Tools/paragraph/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)
2020-02-04 16:37:34,304 ERROR File "/net/eichler/vol26/projects/primate_sv/nobackups/Tools/paragraph/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.")
2020-02-04 16:37:34,304 ERROR Exception: Distance between vcf position and chrom start is smaller than read length.
2020-02-04 16:37:34,305 ERROR Traceback (most recent call last):
2020-02-04 16:37:34,305 ERROR File "../../../Tools/paragraph/bin/multigrmpy.py", line 261, in run graph_files = load_graph_description(args)
2020-02-04 16:37:34,305 ERROR File "../../../Tools/paragraph/bin/multigrmpy.py", line 52, in load_graph_description header, records, event_list = convert_vcf_to_json(args, alt_paths=True)
2020-02-04 16:37:34,305 ERROR File "/net/eichler/vol26/projects/primate_sv/nobackups/Tools/paragraph/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)
2020-02-04 16:37:34,306 ERROR File "/net/eichler/vol26/projects/primate_sv/nobackups/Tools/paragraph/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.")
2020-02-04 16:37:34,306 ERROR Exception: Distance between vcf position and chrom start is smaller than read length.
Traceback (most recent call last):
File "../../../Tools/paragraph/bin/multigrmpy.py", line 353, in
main()
File "../../../Tools/paragraph/bin/multigrmpy.py", line 349, in main
run(args)
File "../../../Tools/paragraph/bin/multigrmpy.py", line 261, in run
graph_files = load_graph_description(args)
File "../../../Tools/paragraph/bin/multigrmpy.py", line 52, in load_graph_description
header, records, event_list = convert_vcf_to_json(args, alt_paths=True)
File "/net/eichler/vol26/projects/primate_sv/nobackups/Tools/paragraph/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 "/net/eichler/vol26/projects/primate_sv/nobackups/Tools/paragraph/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.

Here is my manifest file:

$ cat sample.txt
id path idxdepth
bonobo_10 aln_realigned_reads.bam aln_realigned_reads.bam.json
$ ls aln_realigned_reads.bam
aln_realigned_reads.bam
$ ls aln_realigned_reads.bam.json
aln_realigned_reads.bam.json

Do you have any idea about it?

Thank you so much.

Best,
Yafei

[traxexx]

Hi @MaoYafei Could you please check if your VCF contains a record with POS value smaller than your read length? That should be the reason. The graph alignment needs the flanking to be at least one read-length long. If the variant is too close to the start of the chromosome, there is no way to build a good graph for it.
I will update the error message to make it more precise.

[netwon123]

coule u solve this problem?

[pingxinxing]

Hello, have you solved this problem successfully? What is the solution?