Segmentation fault (core dumped)

LuyaoRen commented 6 months ago

Hi,

I am trying to use SVarp to detect SV from pangenome graph using this comman line svarp -a sample.gaf -g ref_graph.gfa -f sample.fq.gz -i sample.

ref_graph.gfa was generated by minigraph minigraph -cxggs -t24 T2T-CHM13v2.fasta sample.hap1.fasta sample.hap2.fasta > ref_graph.gfa, alignment was generated by minigraph minigraph -t 24 -cx lr ref_graph.gfa sample.fq.gz > sample_aligned.gaf.

The error message was:


Using wtdbg2 for assembly...
No phase information provided (--phase). SVs will not be phased...

...hallo, merhaba, ola, salaam, hello!!! SVarp is running...

Parameters:
    Minimum read support: 5
    Minimum distance threshold: 100

    Minimum map ratio: 0.9
    Precise clipping (Graphaligner): 0.97
    Alignment score (Graphaligner): 5000

Input files:
    sample_aligned.gaf
    ref_graph.gfa
    sample.fq.gz

Log folder:
    /svarp_log/

Reading the GFA file
Reading the GAF file
Segmentation fault (core dumped)

Can you help me and identify which step I might have gotten wrong? Thank you!

asylvz commented 6 months ago

Can you send me some lines from your GAF and GFA? e.g., cat sample_aligned.gaf |head -n 5000 >dnm.gaf

LuyaoRen commented 6 months ago

Hi, I think I understand the problem now. Based on another issue, it seems that I forgot to include the --vc flag when aligning the sequences to the graph. I've successfully run SVarp and obtained svtigs fasta files. How can I get SV breakpoints next?

Thank you!

asylvz commented 6 months ago

We do not output SV breakpoints but you can use an assembly based SV discovery tool such as SVIM-asm or PAV for this (by giving the svtigs as input).

asylvz / SVarp

Segmentation fault (core dumped) #2