Error in creating variation graph

[priyambial123]

Hello,

I tried to create a variation graph using the vcf data from this link: https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/vcf/nstd162.GRCh38.variant_call.vcf.gz. Please find the below command and error message

svjedi-graph.py -v nstd162.GRCh38.variant_call.vcf -r "/reference/human_GRCh38_no_alt_analysis_set.fasta" -q "/m64156_230613_232726.hifi_reads.fastq.gz" -q "/m64156_230504_074854.hifi_reads.fastq.gz" -p vcf

Constructing variation graph...
Traceback (most recent call last):
  File "/svjedi/bin/construct-graph.py", line 636, in <module>
    main(sys.argv[1:])
  File "/svjedi/bin/construct-graph.py", line 188, in main
    if end_on_chr >= len(d_chrom[chrom]) - 1 or start_on_chr >= len(d_chrom[chrom]) - 1:
                         ~~~~~~~^^^^^^^
KeyError: '1'
Mapping reads on graph...
[ERROR] failed to load the graph from file 'test1.gfa'
Filtering alignment file...
Traceback (most recent call last):
  File "/svjedi/bin/filter-alignments.py", line 631, in <module>
    main(sys.argv[1:])
  File "/svjedi/bin/filter-alignments.py", line 112, in main
    with open(gfa_file, "r") as graph_file:
         ^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'test1.gfa'
Genotyping SVs...
Traceback (most recent call last):
  File "/svjedi/bin/predict-genotype.py", line 424, in <module>
    main(sys.argv[1:])
  File "/svjedi/bin/predict-genotype.py", line 77, in main
    with open(aln_dict_file, 'r') as file:
         ^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'test1_informative_aln.json'

Thank you

[clemaitre]

Hi,

Thank you for reporting this issue for SVJedi-graph. However, this is the repository for another tool: SVJedi. Could you put it on the correct SVjedi-graph github repository, so that other SVJedi-graph users can benefit from the answers: https://github.com/SandraLouise/SVJedi-graph/issues.

Best, Claire

[priyambial123]

Thank you. Okay, I will post it in SVjedi-graph github repository

[clemaitre]

Thank you !