dist.seqs() -- How to deal with 240K input sequences?

Commands in mothur
1

For 16S distance calculation, I am using:
dist.seqs( fasta = file.fasta, cutoff = 0.03, processors=8 )

It turns out that my file.fasta has about 240K sequences ( file size is about 3G ).
At this time, computations have been going on for >10h in our cluster.
I am worried that it may not complete even in 2 days time.

Is there a way to cope with such large no. of sequences.
Your timely input will be a great help. Thanks in advance.

2

Are you using unique.seqs and pre.cluster? You could try cluster.split without running dist.seqs. I suspect you might still have problems, in which case I would suggest consulting this blog post:

http://blog.mothur.org/2014/09/11/Why-such-a-large-distance-matrix/

Pat