mothur

Issue in ASV make.shared

I performed ASV analysis as the pipeline discribed in Miseq SOP:

pre.cluster(fasta=test2.unique.good.filter.unique.fasta, name=test2.unique.good.filter.names, group=test2.good.groups, diffs=15)
chimera.uchime(fasta=test2.unique.good.filter.unique.precluster.fasta, count=test2.unique.good.filter.unique.precluster.count_table)
remove.seqs(accnos=test2.unique.good.filter.unique.precluster.denovo.uchime.accnos, fasta=test2.unique.good.filter.unique.precluster.fasta, count=test2.unique.good.filter.unique.precluster.count_table, dups=T)
classify.seqs(fasta=test2.unique.good.filter.unique.precluster.pick.fasta, count=test2.unique.good.filter.unique.precluster.pick.count_table, reference=/home/disk2/DATABAE/QIIME2/silva-138-99-seqs.fasta, taxonomy=/home/disk2/DATABAE/QIIME2/silva-138-99.tax, cutoff=80,processors=30)
make.shared(count=test2.unique.good.filter.unique.precluster.pick.count_table)
classify.otu(list=test2.unique.good.filter.unique.precluster.pick.ASV.list,count=test2.unique.good.filter.unique.precluster.pick.count_table,taxonomy=test2.unique.good.filter.unique.precluster.pick.silva_138_99.wang.taxonomy,label=ASV)
I noticed that make.shared step output wrong *shared file.
For example, Otu09245 size in file RNA.unique.good.pcr.filter.unique.precluster.pick.ASV.ASV.cons.taxonomy is 36370, however, in RNA.unique.good.pcr.filter.unique.precluster.pick.ASV.shared is 1.

Anyone encounter this issue?

It looks like the *.ASV.shared file may not include the redundant sequences in the counts. We have made several improvements to the ASV workflow in our latest release, Releases · mothur/mothur · GitHub. Can you upgrade and if the problem persists send your input files and logfile to mothur.bugs@gmail.com?

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.