I am running a MiSeq analysis on 11 samples of 18S rDNA (Eukarya) following MiSeqSOP (Mothur v.1.42) on a 16 processors server (64GB RAM). As it has happened to me before, I know that with my pair of primers we amplify lots of diversity (from algae to insects), so the dist. file should always be very big, even when running it with cutoff=0.03.
However, in this experiment it is extremely big for such a small number of samples. It took 61 hours to complete the command (
dist.seqs(fasta=current, cutoff=0.03, output=lt)) and, consequently, the cluster command is taking very long too.
Is there anything I could change in my commands to reduce the size of the dist file?
output=lt since I want to get representative sequences afterwards and in my experience this is the best output to do so.
Thank you very much