#chimera.bellerophon
# chimera.bellerophon is very slow, so this batch test will take a very long time. (~7000 secs / ~2 hours)
# chimera.fasta is stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta from MISeq_SOP
# chimera.count is stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table from MISeq_SOP
# NOTE: download TestReferences and TestFiles and put in same location as mothur executable
set.dir(input=./TestFiles, output=./chimera.bellerophon, tempdefault=./TestReferences)
set.logfile(name=chimera.bellerophon.logfile)
chimera.bellerophon(fasta=chimera.fasta)
chimera.bellerophon(fasta=chimera.fasta, filter=t)
quit()
