Greetings:
Seem to be having some issues classifying my sequences. I am using the Silva SSURef_115 as a reference and a taxonomy file generated in ARB from this same reference database - everything seems to be in correct formatting: no spaces with lines ending in “;”
When I run the command, I receive the old, “’‘xxxxx’ is in your template file and is not in your taxonomy file…” Any thoughts would be much appreciated 
Many thanks.
This has generally been happening because there are spaces in the sequence string. Can you post the lines above and below the problem sequence from both the taxonomy and fasta files?
Hi Friends,
The issue (I think) has been resolved following the suggestions of a previous post:
http://mothur.ltcmp.net/t/using-new-silva-taxonomy-file-with-classify-seqs/1101/1
I removed the “>” at the beginning of all the lines in the taxonomy file and Mothur seems to be Mothuring as expected - finger crossed.
Many thanks Pat for the reply.