I’m currently using the 454 SOP to work through my data and on the align.seqs command, I’m getting an error with my current install of mothur v.1.36.0:
mothur > align.seqs(fasta=/users/jw698/tamar/data/Plate2_Lane1.shhh.trim.unique.fasta, reference=silva.nr_v123.align, processors=2) Using 2 processors. Unable to open silva.nr_v123.align. Trying default /cm/shared/apps/mothur/1.36.0/blast/bin/silva.nr_v123.align Reading in the /cm/shared/apps/mothur/1.36.0/blast/bin/silva.nr_v123.align template sequences... DONE. It took 276 to read 172418 sequences. [ERROR]: Could not open /cm/shared/apps/mothur/1.36.0/blast/bin/silva.nr_v123.8mer
I have copied all the Silva reference files from here to the mothur/1.36.0/blast/bin/ directory, but I can’t find any *.8mer files that I might be missing.