I am having a few problems running this command due to the large amount of unique sequences I have (776,819). I have tried running it on only one processor to decrease RAM usage and I have also tried running it using lower taxonomic levels but it still crashes. I am currently trying to run dist.seqs instead but I am doubtful this is going to be any use as it is taking quite a lot of time to run (although it hasn’t crashed yet after three days).
I have 64 samples run on a MiSeq with 250bp reads of the V2-V3 region. I have been following the MIseq SOP exactly up until this point.
I don’t want to have to use a phylotoype based approach unless I really have to.
Do you have any suggestions? Also, are there any analyses where it is possible to use the taxonomically assigned read data from before clustering into OTUs?