MiSeq SOP with test data fails at uchime step

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.

What now?


After careful reading of that other bug report: MiSeq SOP example batch file fails to complete

I realized that the missing group in screen.seqs in the stability.batch file is indeed the issue where:

screen.seqs(fasta=current, maxambig=0, maxlength=275)

Should be:

screen.seqs(fasta=current, group=current, maxambig=0, maxlength=275)

And then it works!

So there is a bug in the stability.batch file and in the wiki page.


Thanks for reporting this bug, a new version of stability.batch is now up on the wiki.