search

human-pangenomics / hpp_pangenome_resources

94 stars 3 forks source link

Segfault with odgi when trying to convert chrom graphs from mgc #25

Closed dubssieg closed 4 months ago

dubssieg commented 4 months ago

Greetings, and thanks for this work.

The chromosome graphs for minigraph-cactus are available both in .vg and .og format, but as far as I know, only the .og version is the full, non-clipped, non-filtered graph. However, when I try to do any manipulation on them using odgi (0.8.6) like converting those to .gfa using odgi view -g -i $INPUT > $OUTPUT, I get a segfault in return. Is there any place where I can find the full graphs from mgc in .gfa, or a .og that can be read by odgi?

Thanks in advance.

glennhickey commented 4 months ago

I just ran odgi view on https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph-cactus/hprc-v1.1-mc-grch38/hprc-v1.1-mc-grch38.chroms/chrY.full.og using both odgi version 0.8.4 and 0.8.6 and it ran fine. Can you tell me exactly which file you are having trouble with?

dubssieg commented 4 months ago

Just tried on the file you provided, got a core dump as well. I guess it is an issue with my installation of odgi, will investigate and let know if I find any workaround/fix for anyone having the same issue.

Thanks a lot for your quick reply!

dubssieg commented 4 months ago

Tried on another machine, it seems the issue is between Fedora (or at least my machine) and odgi. The only strange point is that I never had such issues with odgi on any other graph. Worked just fine on another system, so closing! Have a nice day.