perform variant detection on second-generation sequencing data based on the pan-genome constructed using Minigraph-Cactus

[C-YONG]

1. What were you trying to do? I want to perform variant detection on second-generation sequencing data based on the pan-genome constructed using Minigraph-Cactus 2. What did you want to happen? I want to use vg::Surjector to convert a GAM file to a BAM file

      vg surject \
      --threads 10 \
      --x /mnt/c/pan-genome/Minigraph-Cactus/pangenome1/fugu.d2.xg \
      --bam-output \
      test/CF8.gam \
      | samtools reheader -c "sed 's/T2T#0#//g'" - \
      | samtools sort --threads 10 -m 20g -O BAM
      > test/CF8.bam

3. What actually happened? The software gave me a warning during the conversion process.

warning[vg::Surjector]: Refusing to perform very large alignment against 110436 bp strand split subgraph for read E150003405L1C001R02201761464/1; suppressing further warnings.

I would like to ask if this issue will have an impact, and how to resolve it.