vg augment forwardize_breakpoints error about vg HOT 1 OPEN

I think your problem is that autoindex imports the GFA, and then you map to that, and then you re-import the GFA again to make a different graph, and try to interpret the mappings against the second graph. The node IDs are not the same between the two graphs; vg has several ways of importing GFAs and they don't always name the nodes in the result the same way.

You should bge able to use the same .xg file you used for mapping as the input to vg augment. If it doesn't like that, you can use vg convert to convert the .xg to .vg (which won't change the node IDs) and then use that file with vg augment.

You can check if vg thinks a file of reads is interpretable against a particular graph with vg validate [graph] -a [gam].

The problem should also go away if you make sure vg doesn't need to do any node ID modifications to your GFA graph: give all the S lines numerical names starting at 1, and make sure that the edges don't specify any overlaps, and that none of the nodes are too long. 32 bp is definitely a safe limit, and I think 1024 bp might be the real upper limit.

from vg.