Hi All,

I am having trouble with the chimera.uchime
This is the command I am running
chimera.uchime(fasta=Dnitro.good.unique.good.filter.unique.precluster.fasta, count=Dnitro.good.unique.good.filter.unique.precluster.count_table, dereplicate=t)

I am expecting the following outputs

Output File Names:

The problem is I am not getting the count table output file. It is not being generated. This is causing me issues later in my analysis. Does anyone know why the count table is not being generated as an output? I have used this command before on a different data set and it worked fine. I do not understand why it is not working now.


In my experience you only ever get the chimeras and accnos file. You then just remove the chimeric sequences from your data with:

remove.seqs(fasta=current, count=current, accnos=Dnitro.good.unique.good.filter.unique.precluster.uchime.accnos)

Does your count table have group data? If not, mothur can’t use the dereplicate option and will not create a new count table.