ASV: Make.Biom Many Instances of the Same Genus

[jgcx]

Hello Mothur Community,

What explanation, if any, sheds light on why many instances of the same genus appear within one sample when conducting the ASV approach and creating a BIOM file? Here are the commands used below and a snapshot of the many instances of the same genus in one sample.

Batch File Commands
set.logfile(name=Testing123LogFile)
fastq.info(fastq=Testing123.fastq)
get.current()
summary.seqs(fasta=current, processors=32)
trim.seqs(fasta=current, oligos=CXMicroMothurOligos.txt, maxambig=0, maxhomop=6, bdiffs=0, pdiffs=0, minlength=265, keepfirst=285, flip=F, processors=32)
summary.seqs(fasta=current, count=current, processors=32)
unique.seqs(fasta=current, count=current)
summary.seqs(fasta=current, count=current, processors=32)
align.seqs(fasta=current, reference=silva.v4.fasta, processors=32)
summary.seqs(fasta=current, count=current)
screen.seqs(fasta=current, count=current, summary=current, optimize=start-end, criteria=95, processors=32)
summary.seqs(fasta=current, count=current, processors=32)
filter.seqs(fasta=current, vertical=T, trump=.)
summary.seqs(fasta=current, count=current, processors=32)
unique.seqs(fasta=current, count=current)
summary.seqs(fasta=current, count=current, processors=32)
get.current()
pre.cluster(fasta=current, count=current, diffs=2, processors=32)
summary.seqs(fasta=current, count=current, processors=32)
get.current()
chimera.vsearch(fasta=current, count=current, dereplicate=t)
get.current()
summary.seqs(fasta=current, count=current, processors=32)
classify.seqs(fasta=current, count=current, template=silva.nr_v138_1.align, taxonomy=silva.nr_v138_1.tax, cutoff=80, processors=8)
get.current()
remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-unknown-Eukaryota)
summary.seqs(fasta=current, count=current)
get.current()
summary.tax(taxonomy=current, count=current)
get.current()
rename.file(fasta=current, count=current, taxonomy=current, prefix=FinalCurationComplete)
make.shared(count=FinalCurationComplete.count_table)
classify.otu(list=current, count=current, taxonomy=FinalCurationComplete.taxonomy, label=ASV)
count.groups(shared=current)
get.current()
make.biom(shared=FinalCurationComplete.asv.shared, constaxonomy=FinalCurationComplete.asv.ASV.cons.taxonomy)
quit()

Commands Outside of Mothur to Make BIOM File
#biom convert -i FinalCurationComplete.asv.ASV.biom -o FinalCurationComplete.asvtable.txt --to-tsv --header-key taxonomy

[pschloss]

Recall that ASVs and OTUs are typically at a fine scale than a genus. If we loosely think of these as strains or species, then it is reasonable to expect to see multiple instances of populations from the same genus.