I had a similar memory problem while trying to cluster ~40K decoys using the 3.0 version of CLUSTER. Have you tried expanding your virtual memory. If you don’t mind letting your computer work for 2-3 days without using it for anything else then create a temp. swap file. I tried to increase the swap space to 20g but that still was not enough and it ran out about half way throwing the same alloc. error. It worked after increasing the swap space to 100g. This was on a linux box but I assume the same would be possible on a mac if you have space on your drive to spare.