VG node not present in graph

Hello everyone,

I’m currently working on constructing my first pangenome using VG and could use some help. My approach involves using VCF files from individuals in HGDP and following the steps outlined on their GitHub tutorial: GitHub Tutorial Link. This tutorial fits my needs but wasn’t updated since 2020 .. so I am not sure if that’s still up to date.

Here’s an overview of the commands I’ve employed:

To begin, I generated .vg files for each chromosome and then pruned them:

vg construct -r ref.fa -v sub-chrXX.vcf.gz > pXX.vg
vg prune -t 8 -k 45 -r p${SLURM_ARRAY_TASK_ID}.vg > pruned${SLURM_ARRAY_TASK_ID}.vg

Then, I created various indexes:

vg ids -j $(for i in $(seq 1 22); do echo pruned${i}.vg; done)
vg index -x all.xg $(for i in $(seq 1 22); do echo pruned${i}.vg; done)
vg index -t 8 --temp-dir temp -g wg.gcsa pruned{1..22}.vg -p -Z 32768 2>&1

Everything was going well until I attempted to align some fastq reads using the following command:

vg map -x all.xg -g wg.gcsa -f ERR1423010_1.fastq > test.gam

And I have the following error:

terminate called after throwing an instance of 'std::runtime_error'
what():  Attempted to get handle for node 5777068 not present in graph

I’ve verified the validity of all the .vg files using vg validate, and they were all returned valid.

I’ve been troubleshooting for a couple of days but have yet to identify the source of this issue. I’m using VG v1.48. The tutorial I’m following hasn’t been updated since 2020, so I’m uncertain whether it’s still working the same way they are describing there.
I would greatly appreciate your help as it took me several months just to generate that gsca file :’)

Thank you so much.