vg mod from gam file not working as described

[egoltsman]

1. What were you trying to do?

Following steps to add gene annotations to the graph as described here: https://github.com/vgteam/vg/wiki/VG-RDF,-the-Ensembl-bacteria-E.-coli-genome-hack-attack

2. What did you want to happen? Ultimately, I'd like to try out the RDF functionality and make a few queries using the gene annotations as criteria

3. What actually happened? Calling vg mod -i results in the "deprecated" error pointing the user to vg augment, but the latter bails out on the input:

$vg mod -i foo.gam foo.vg >bar.vg`
[vg mod] error: vg mod -i is deprecated.  please switch to vg augment

$vg augment foo.vg foo.gam > bar.vg
error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph

Is this workflow still supported or is there an alternative way to do it?

I'm working with the latest release - v.1.27.1

Thanks!

[glennhickey]

What do do vg validate foo.vg and vg stats -F foo.vg print?

[ekg]

I suggest building the graph with pggb. https://github.com/pangenome/pggb

On Tue, Oct 20, 2020, 16:22 Glenn Hickey notifications@github.com wrote:

What do do vg validate foo.vg and vg stats -F foo.vg print?

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[egoltsman]

vg validate did expose the problem - thanks for the tip! The paths in the vg graph were botched by my earlier attempt to merge adjacent paths into one, and I ended up with paths that don't have the edges to support it. Once I fixed this everything worked.

Thanks!