Running the chimera.vsearch command produces only the vsearch.chimeras file and a vsearch.accnos file. The subsequent classify.seq command (after removing chimeras and summarizing) requires the file:

I haven’t produced this file with the vsearch command and the post chimera.vsearch commands such as summary.seqs and classify.seqs are using the file: filename.trim.contigs.good.unique.good.filter.unique.precluster.count_table,

which is the same count file used for the chimera.vsearch command. I believe this is causing mismatches between my count and fasta files. Am I missing a step that would produce the “filename.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table” file?


A new count table is only created when your count table contains group information and dereplicate=T. Most often the issue you are seeing is caused when you run the chimera.vsearch command with a count table that does not contain group data. In this case instead of processing by group, all the sequences are considered to be from the same group, and the dereplicate parameter defaults to F.