I tried running this over the weekend but it hung (no kill error but no writes to the logfile in 48hrs.
cluster.split(fasta=fancher.all.trim.contigs.good.unique.good.filter.precluster.pick.pick.fasta, count=fancher.all.trim.contigs.good.unique.good.filter.precluster.denovo.uchime.pick.pick.pick.count_table, taxonomy=fancher.all.trim.contigs.good.unique.good.filter.precluster.pick.pds.wang.pick.taxonomy, splitmethod=classify, taxlevel=5, cutoff=0.15, processors=16, classic=T)
So I killed it and ran
cluster.split(fasta=fancher.all.trim.contigs.good.unique.good.filter.precluster.pick.pick.fasta, count=fancher.all.trim.contigs.good.unique.good.filter.precluster.denovo.uchime.pick.pick.pick.count_table, taxonomy=fancher.all.trim.contigs.good.unique.good.filter.precluster.pick.pds.wang.pick.taxonomy, splitmethod=classify, taxlevel=5, cutoff=0.15, processors=16, classic=T, cluster=f)
cluster.split(file=current, processors=1)
Using fancher.all.trim.contigs.good.unique.good.filter.precluster.pick.pick.file as input file for the file parameter.
Using 1 processors.
Using splitmethod distance.
Reading fancher.all.trim.contigs.good.unique.good.filter.precluster.pick.pick.fasta.6.phylip.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix: ||[ERROR]: 57449 is not in your count table. Please correct.
The making of the distance files seems to work but it chokes on clustering the first distance file. that file is 11GB, I have ~150GB available
all the commands that got me to this point
summary.seqs(fasta=fancher.all.trim.contigs.fasta, processors=16)
screen.seqs(fasta=current, group=fancher.all.contigs.groups, summary=current, maxambig=0, maxlength=280)
summary.seqs(fasta=current)
unique.seqs(fasta=current)
summary.seqs(fasta=current, name=current)
count.seqs(name=current, group=current)
align.seqs(fasta=current, reference=silva.v4.fasta)
summary.seqs(fasta=current, count=current)
screen.seqs(fasta=current, count=current, summary=current, start=8, end=9582, maxhomop=8)
filter.seqs(fasta=current, vertical=T)
summary.seqs(fasta=current, count=current)
pre.cluster(fasta=current, diffs=3, count=current)
summary.seqs(fasta=current, count=current)
dereplicate=f
chimera.uchime(fasta=current, count=current, dereplicate=t)
remove.seqs(fasta=current, accnos=current, count=current)
summary.seqs(fasta=current, count=current)
classify.seqs(fasta=current, count=current, reference=trainset10_082014.pds.fasta, taxonomy=trainset10_082014.pds.tax, cutoff=60)
remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-unknown-Eukaryota)