I am trying to remove rare OTUs using the remove.rare command. Since I generated my list with a count table, I also included that in the command.
It has been running for about two days now. My list was based on unique sequences (not clustered based on 0.03), as I am working with data where SNPs are important for allele designation.
Is there any way to increase the speed of this process? I notice I cannot designate how many processors to use, and looking at the task manager it looks like it is only using one.
Any help is greatly appreciated.