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Graph realignment tools for structural variants
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Distance between vcf position and chrom start is smaller than read length. #38

Closed MaoYafei closed 4 years ago

MaoYafei commented 4 years ago

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 commented 4 years ago

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 commented 1 year ago

coule u solve this problem?

pingxinxing commented 1 month ago

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