Hello!
I downloaded the latest Ubuntu version. My Ubunu is at the latest version.
First step I am doing: unique.seqs(fasta=barcode35chop.fasta) and all is going well.
Then I try the following and look at the strange results:
mothur > align.seqs(candidate=current, reference=silva.seed_v138_2.align, search=kmer, ksize=15, flip=true)
[WARNING]: reference is not a valid parameter, ignoring.
The valid parameters are: reference, fasta, search, ksize, match, align, mismatch, gapopen, gapextend, processors, flip, threshold, seed, inputdir, and outputdir.
Using barcode35chop.unique.fasta as input file for the fasta parameter.
[ERROR]: The reference parameter is a required for the align.seqs command, aborting.
Using 7 processors.
[ERROR]: did not complete align.seqs.
Well…