Hi Colin and Zayed
We were able to get this to run by using a queue with larger memory nodes along with "h_vmem=50G -l h_stack=20M" args. Your ideas about tweaking the memory footprint trough SGE were definitely correct. Using a smaller index would likely have proved this as well. I'll continue to pare this down to see what the optimal settings will be for various sets. Thank you for all your help.