`duplicate rank` error in `vg find` when extracting a graph subregion

[AndreaGuarracino]

1. What were you trying to do? I was trying to extract a subregion from a graph encoded in a GFA format file.

2. What did you want to happen? I want to obtain a GFA format file with the graph subregion plus the paths' portions covering that subregion.

3. What actually happened? I get this error error[load_proto_to_graph]: duplicate rank 5944 in path hg38_chr2

4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here: -

5. What data and command can the vg dev team use to make the problem happen?

input=hppy1+chm13+h38-chr2.fa.gz.pggb-s4000-l12000-p98-n6-a0-K16-k29-w180000-j10000-e10000-I0.5-R0.2.smooth.renamed.gfa
path_ref=hg38_chr2

vg convert --gfa-in $input -x > $input.xg
vg find -p ${path_ref}:91597913-96188605 -x $input.xg > $input.${path_ref}_91597913_96188605.vg
vg view $input.${path_ref}_91597913_96188605.vg > $input.${path_ref}_91597913_96188605.gfa

Here the input used.

6. What does running vg version say? vg: variation graph tool, version v1.30.0 "Carentino"

[glennhickey]

I'd suggest 2 things:

• specifying a context size with -c to pull in nodes adjacent to your path. it defaults to 0 in vg find which probably won't give what you want
• using vg chunk instead of vg find. (the relevant options remain the same). vg chunk is more careful to not make path fragments that will cause trouble downstream

[AndreaGuarracino]

Thank you @glennhickey! Using -c with vg find didn't work, but using vg chunk plus -c I was able to get the graph's chunk.

Does it mean that vg find is going to be deprecated?

[heringerp]

Is there any update on this issue?

I'm having the same problem (except that I'm using -N instead of -p for the selection) and unfortunately I cannot use vg chunk as I'm trying to extract a list of nodes (with context) and vg chunk will extract each node into a separate chunk (I want a single graph without duplication and containing the paths).