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glennhickey avatar glennhickey commented on June 27, 2024

Here's a more manageable example

wget -q http://public.gi.ucsc.edu/~hickey/debug/chr14.gfa.gz
gzip -d chr14.gfa.gz
vg validate chr14.gfa
graph: valid
gfaffix chr14.gfa --output_refined chr14.gfaffix.gfa --dont_collapse "GRCh38*" > /dev/null
vg validate chr14.gfaffix.gfa
graph invalid: missing edge between 547163th step (2438295:0) and 547164th step (2433572:0) of path HG00673.1.JAHBBZ010000004.1
graph invalid: missing edge between 547164th step (2433572:1) and 547163th step (2438295:0) of path HG00673.1.JAHBBZ010000004.1
graph: invalid

Interestingly, this happens in the presence of a huge node:

grep ^S chr14.gfaffix.gfa | grep 2438295 | wc
831317

Chopping the graph seems to help:

vg mod -X 1000 chr14.gfa > chr14.chop.gfa
gfaffix chr14.chop.gfa --output_refined chr14.chop.gfaffix.gfa --dont_collapse "GRCh38*" > /dev/null
vg validate chr14.chop.gfaffix.gfa
graph: valid

from gfaffix.

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