SegAlign crashes while running cactus on Terra

[hloucks]

Glenn Hickey wanted me to report this issue I'm seeing while running ComparativeGenomicsToolkit/cactus on Terra. It looks like there is an issue in SegAlign causing the crash. I've attached the full log of errors I'm seeing when running.

Cactus_allerrors_20221014.txt

[glennhickey]

To further clarify: this is a crash in segalign_repeat_masker that happens on a 5.7Gb mollusk genome. run_segalign does seem to work on this genome, at least when aligning to human. It does not seem to be exceeding either system or video memory limits from my tests. We can share the genome on request.

[gsneha26]

Can you share the genome files? I need to investigate the error outside of the container run logs.

[glennhickey]

I emailed a link to you.