Problem with Classify.seqs

mothur bugs
1

Hi
I am having persistent problem with classify.seq command. I have been repeated getting the following error. I have been using mothur v.1.28.0. I appreciate any suggestions from you.
src@zcluster:Abundant$ /usr/local/mothur/latest/mothur > classify.seqs(fasta=c5check.fasta, template=nogap.bacteria.fasta, taxonomy=silva.bacteria.silva.tax)
-bash: syntax error near unexpected token `(’

Thanks
Srini

2

You need to be inside mothur to call this command. From the terminal open mothur and then once inside mothur type:

classify.seqs(fasta=c5check.fasta, template=nogap.bacteria.fasta, taxonomy=silva.bacteria.silva.tax)

Incidentally, I’d strongly encourage you to use the rdp reference training set for classification and only use silva for alignments.

3

Thanks! It worked. I was having problems when I process more than one files from same folder. Seems like Intemediate files (trainset9_032012.rdp.trainset9_032012.rdp.8mer.numNonZero, trainset9_032012.rdp.trainset9_032012.rdp.8mer.prob, trainset9_032012.rdp.tree.train) are being generated with exactly same names.