align.seqs error--How should I troubleshoot?

Right now I’m following the MiSeq SOP using my own data. When I run align.seqs, I’m getting this:

mothur > align.seqs(fasta=TZ_Treatmenttrim.contigs.good.fasta, reference=gg_v4.fasta)

Using 8 processors.

Reading in the /Users/katinker/Desktop/WorkingCockroach/Comparison_Mothur/gg_v4.fasta template sequences… [ERROR]: template is not aligned, aborting.
It took 0 to read 0 sequences.

I’m not really sure what my problem is. I downloaded the most recent .fasta file from green genes, but perhaps something is going on with it? Any ideas?


FWIW, when I run align.seqs with the silva reference database it works perfectly.

Your gg_v4.fasta file isn’t aligned - it has to be aligned to generate an alignment.