vg giraffe - Signal 6 occurred. VG has crashed about vg HOT 1 OPEN

@glennhickey The Cactus-Minigraph pipeline won't leave any absurdly long nodes, right?

I'm not sure how to connect either the error from faster_cap or the error from vg::DozeuInterface::calculate_max_position to the fact that some paths in the graph might be very long.

What looks most suspicious is your indexing. You shouldn't need to make genome.gcsa for Giraffe, and genome.xg here is not going to be usable with genome.gbz because they use different node IDs and have different nodes. But it's possible Giraffe is picking it up anyway; it automatically finds any inputs you don't give it based on filename patterns, so that you can just point it at a graph that has all the indexes next to it, and it can use a .xg file alongside a .gbz if one is available, to save on reconstructing some path position information.

I would try keeping all the files generated from the pruned/mod-ed graphs in a different directory. You can also run Giraffe with --progress and it should tell you what it is loading, which might help you figure out if it is loading anything it shouldn't be using.

from vg.