I just downloaded mothur v.1.32.0 and uchime v4.2.40 as well as the test data for the MiSeq SOP. When running the stability.batch file I get this error:
mothur > chimera.uchime(fasta=current, count=current, dereplicate=t) [WARNING]: no file was saved for count parameter. Using stability.trim.contigs.good.unique.good.filter.precluster.unique.precluster.fasta as input file for the fasta parameter. [ERROR]: You don't have any saved reference sequences and the reference parameter is a required. Using 8 processors. [ERROR]: did not complete chimera.uchime.
I put the entire verbose output here:
I am running on a Debian based Linux server with 32 cores and 128Gb memory.