make.file(inputdir=seqs, type=gz, prefix=stability) make.contigs(file=current, processors=16) summary.seqs(fasta=stability.trim.contigs.fasta) screen.seqs(fasta=stability.trim.contigs.fasta,group=stability.contigs.groups,summary=stability.trim.contigs.summary,maxambig=0,maxlength=160) unique.seqs(fasta=stability.trim.contigs.good.fasta) count.seqs(name=stability.trim.contigs.good.names,group=stability.contigs.good.groups) summary.seqs(count=stability.trim.contigs.good.count_table) summary.seqs(fasta=Fish_12S_rDNA_align_070519.fas) align.seqs(fasta=stability.trim.contigs.good.unique.fasta,reference=Fish_12S_rDNA_align_070519.fas,flip=t) summary.seqs(fasta=stability.trim.contigs.good.unique.align,count=stability.trim.contigs.good.count_table) screen.seqs(fasta=stability.trim.contigs.good.unique.align,count=stability.trim.contigs.good.count_table,summary=stability.trim.contigs.good.unique.summary,minlength=120,maxlength=152,maxhomop=7,start=1,end=155) summary.seqs(fasta=stability.trim.contigs.good.unique.good.align,count=stability.trim.contigs.good.good.count_table) pre.cluster(fasta=seqs/stability.trim.contigs.good.unique.good.align,count=seqs/stability.trim.contigs.good.good.count_table, diffs=0) chimera.vsearch(fasta=seqs/stability.trim.contigs.good.unique.good.precluster.align,count=seqs/stability.trim.contigs.good.unique.good.precluster.count_table, dereplicate=t) remove.seqs(fasta=stability.trim.contigs.good.unique.good.precluster.align,accnos=seqs/stability.trim.contigs.good.unique.good.precluster.denovo.vsearch.accnos,name=seqs/stability.trim.contigs.good.names) summary.seqs(fasta=seqs/stability.trim.contigs.good.unique.good.precluster.pick.align,count=seqs/stability.trim.contigs.good.unique.good.precluster.denovo.vsearch.pick.count_table) classify.seqs(fasta=seqs/stability.trim.contigs.good.unique.good.precluster.pick.align,count=seqs/stability.trim.contigs.good.unique.good.precluster.denovo.vsearch.pick.count_table,reference=seqs/Fish_12S_rDNA_align_070519.fas,taxonomy=seqs/Fish_12S_rDNA_taxonomy_070519.txt,cutoff=80) dist.seqs(fasta=seqs/stability.trim.contigs.good.unique.good.precluster.pick.align,cutoff=0.01) cluster(column=seqs/stability.trim.contigs.good.unique.good.precluster.pick.dist,count=seqs/stability.trim.contigs.good.unique.good.precluster.denovo.vsearch.pick.count_table,cutoff=0.01) make.shared(list=seqs/stability.trim.contigs.good.unique.good.precluster.pick.opti_mcc.list,count=seqs/stability.trim.contigs.good.unique.good.precluster.denovo.vsearch.pick.count_table) classify.otu(list=seqs/stability.trim.contigs.good.unique.good.precluster.pick.opti_mcc.list,count=seqs/stability.trim.contigs.good.unique.good.precluster.denovo.vsearch.pick.count_table,taxonomy=seqs/stability.trim.contigs.good.unique.good.precluster.pick.Fish_12S_rDNA_taxonomy_070519.wang.taxonomy) count.groups(shared=seqs/stability.trim.contigs.good.unique.good.precluster.pick.opti_mcc.shared)