The cluster.split command is not providing a list file and is removing groups at the end. I have repeated the command with taxlevel=4 and taxlevel=6 and the same thing keeps happening. I do not have a mock community so did not perform any of the commands concerning the removal of a mock community. Once the cluster.split command is completed it displays the number of seconds it took to complete, in my case it was about 47,000 seconds, but no output files get listed and it is then stuck with no mothur> showing. I know it is not a computer RAM and space issue b/c the whole time the command was running only 20%-35% of the RAM was being used and I am using a 4TB storage device.
Below are the commands used up to the cluster.split command.
fastq.info(fastq=R_2021_10_05_12_00_01_user_S51010052021_Chip.fastq)
summary.seqs(fasta=,R_2021_10_05_12_00_01_user_S51010052021_Chip.fasta, processors=8)
trim.seqs(fasta=R_2021_10_05_12_00_01_user_S51010052021_Chip.fasta, oligos=CXMicroMothurOligos.txt, maxambig=0, maxhomop=6, bdiffs=0, pdiffs=0, minlength=265, keepfirst=285, flip=F, processors=8)
summary.seqs(fasta=current, processors=8)
get.current()
unique.seqs(fasta=current)
get.current()
summary.seqs(fasta=current, name=current, processors=8)
count.seqs(name=current, group=current)
get.current()
#pcr.seqs(fasta=silva.nr_v138_1.align,start=11895,end=25318,keepdots=F,processors=32)
#rename.file(input=silva.nr_v138_1.pcr.align,new=silva.v4.fasta)
#summary.seqs(fasta=silva.v4.fasta)
#get.current()
align.seqs(fasta=current, reference=silva.v4.fasta, processors=2)
summary.seqs(fasta=current, count=current, processors=8)
get.current()
summary.seqs(fasta=current, count=current, processors=8)
screen.seqs(fasta=current, count=current, summary=current, start=1967, optimize=end, criteria=95, processors=8)
summary.seqs(fasta=current, count=current, processors=8)
filter.seqs(fasta=current, vertical=T, trump=.)
summary.seqs(fasta=current, count=current, processors=8)
unique.seqs(fasta=current, count=current)
summary.seqs(fasta=current, count=current, processors=8)
get.current()
pre.cluster(fasta=current, count=current, diffs=2)
summary.seqs(fasta=current, count=current, processors=8)
chimera.vsearch(fasta=current, count=current, dereplicate=t)
remove.seqs(accnos=current, fasta=current)
summary.seqs(fasta=current, count=current, processors=8)
classify.seqs(fasta=current, count=current, template=silva.nr_v138_1.align, taxonomy=silva.nr_v138_1.tax, cutoff=80, processors=8)
remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-unknown-Eukaryota)
summary.seqs(fasta=current, count=current, processors=8)
summary.tax(taxonomy=current, count=current)
get.current()
rename.file(fasta=current, count=current, taxonomy=current, prefix=10_05_2021CurationComplete)
cluster.split(fasta=current, count=current, taxonomy=current, taxlevel=6, cutoff=0.30)