I’m working through the Schloss MiSeq_SOP for Illumina data and I keep getting an error on the dist.seqs command near the end of the SOP as I prepare to make phylogenetic trees. When I give mothur the command dist.seqs(fasta=final.fasta, output=phylip, processors=2) I get the error:
Unable to open final.fasta
I go back to look and see if final.fasta has been generated in the folder and there is no such file.
What am I doing wrong? I followed the SOP exactly, I believe.