Chimera/Uchime problem

I am processing a Miseq run. It has about 11M reads from a 2x300 bp run. After alignment and uniquing, there are about 8M reads. I end up with an alignment file of 148GB. Big. When I run UCHIME to remove chimeras, I end up with an OSX no memory for applications message, and even though I think I have plenty of room on my hard drive, 700+ GB, I eventually find that my Mac freezes and I can’t go further.

Any thoughts on this? Something beyond freeing up more space? Any notion about what kind of space mothur actually needs for UCHIME?

Hey G.

First, be sure to check out this: tl;dr? the 300PE kit is garbage, error rates kill

Second, there really shouldn’t be that much of a memory limitation unless you’re trying to read all of those in at the same time. We normally fraction the samples by group. Are you giving chimera.uchime a count/group file?