I’ve just encountered the same problem, using the Mac GUI (v1.31.2 for OS10.8).
To add a little context - it happens with the demo Schloss dataset, as well as my own
It happens with whatever reference file I’m specifying - whether it’s the silva.v4.fasta, employed in the tutorial down stream of pcr.seqs trimming, or if I try and use the whole untrimmed silva.bacteria.fasta file.
Mothur returns no logfile, and the Mothur output window is blank (if previously cleared). Only the warning popup mentioned above returns, along with a notification the pipeline is stopping.
Will try rerunning pcr.seqs again, but the output from that (silva.v4.fasta) looked like it matched the tutorial from the summary.seqs output.
Thanks for posting more details about the issue. I will look into it.
I found the source of the problem. The preferences file was overwriting the reference file you selected. It will be fixed in our next release. I have also fixed the preference option on the file menu. As a workaround until we release, you can add the references you would like by modifying the .\mothurGUI\pref\userPreferences.txt file. It should look like:
You can add the full path for your align.seqs reference.
Thanks for reporting this bug.