different methods for CLEARCUT

Hello again,

I was successfully able to get through the entire Mothur SOP with one file set; however, as I work on this final file set, I am getting caught at the clearcut portion of the SOP.

To clarify, my files all come from the same plate… But I split into a bacteria file and a archaea file at the align.seqs portion. The bacteria file (slightly smaller) worked great, the archaea file seems to get really caught up with clearcut.

I first tried to run the 7.82GP phylip.dist archaea file in clearcut to no avail… Now (after visiting the clearcut wiki) I am trying to run my alignment file:

mothur > clearcut(fasta=HalfPlate01.shhh.trim.unique.good.align.2, DNA=t, verbose=t) (the .2 at the end just specifies to me that is is archaea)

The file itself is 4.68GB which is only .1 GB larger than the bacteria phylip.dist file I ran (which worked like a charm). It has been running for three days.

I was able to complete everything else with for my archaea file excluding the clearcut command, the phylo.diversity, unifrac.weighted, and unifrac.unweighted because they use the output form the clearcut command.

ANY help would be greatly appreciated.