In the latest Windows GUI release (1.31.2), 64 bit, File: Preferences does not bring up the preferences box.
In the same release, align.seqs may have a bug. Using silva.bacteria.fasta as the reference file, when I hit run the name of the file disappears from the box and I get an error message that align.seqs requires a reference file. It does not matter what directory the reference file is in. Also occurs with other reference files such as core_set_aligned.imputed.fasta. The same error occurred in the previous release of the GUI. I’m not sure if this is really a bug or my error, as I am brand new to mothur.
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.
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: