Chimera/Uchime problem

Commands in mothur
1

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?

2

Hey G.

First, be sure to check out this: http://blog.mothur.org/2014/09/11/Why-such-a-large-distance-matrix%3F/. 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?

Pat