vg call Hanging on a Few Samples

[GooLey1025]

Dear vg team,

Thanks for sharing this awesome software!

I’m running vg call for variant calling on a population-scale dataset. While it successfully completes on the majority of my samples (~700), I’ve noticed that 6 specific samples appear to hang indefinitely during the calling step.
The command I’m using is:

vg call $P.tmp/$sample.aug.xg -k $P.tmp/$sample.aln_aug.pack --progress -a  -s $sample -t $threads > $P/$sample.vcf 2> $P.logs/$sample.call.err

For these problematic samples:
• The process starts normally.
• Afer a while, however, it produces no output for days and seems to make no progress.
• The .xg and .pack files were generated successfully, and there are no explicit error messages — it just doesn’t finish.

Do you have any suggestions on how to debug this issue, or common causes that might lead to this kind of stalling behavior?

I’d be happy to provide logs or input files if needed.

Best regards,

logs:

[vg call]: Loading graph 705rice.tmp/yangzhou199demilter195.aug.xg
[vg call]: Loaded graph
[vg call]: Applying overlays if necessary (ie input not in XG format)
[vg call]: Applied overlays
[vg call]: Computing snarls
[vg call]: Computed snarls
[vg call]: Loading pack file 705rice.tmp/yangzhou199demilter195.aln_aug.pack
[vg call]: Loaded pack file
[vg call]: Computing coverage statistics
[vg call]: Computed coverage statistics
[vg call]: Calling top-level snarls
[vg call]: Processed 100000 top-level snarls
[vg call]: Processed 200000 top-level snarls
[vg call]: Processed 300000 top-level snarls
[vg call]: Processed 400000 top-level snarls
[vg call]: Processed 500000 top-level snarls
[vg call]: Processed 600000 top-level snarls
[vg call]: Processed 700000 top-level snarls
......
[vg call]: Processed 6300000 top-level snarls
[vg call]: Processed 6400000 top-level snarls

[adamnovak]

@glennhickey I think you're the current vg call expert.

I don't have advice for debugging this, other than starting vg call under gdb:

gdb vg

And at the gdb prompt:

run call whatever.tmp/samplename.aug.xg ...

And then hitting Ctrl+C when it's stuck and doing bt and info threads to see what it is possibly stuck on. (And you might need a non-stripped, manual build of vg from source for that to be super useful.)