When I incorporate allfiles=t into my trim.seqs command, I end up with an error message saying that mothur couldn’t open a file. It was a fasta file, and was named after my first barcode ID in my oligo file. The error message happened after a long while, and it looks like all the right files were created, so I’m not sure if there is actually a problem. My input is:
mothur > trim.seqs(fasta=reads1f.fna, oligos=eftag.txt, maxambig=0, minlength=150, maxlength=300, qfile=qual1f.qual, qaverage=20, maxhomop=6, allfiles=t)
Also, should there be a group file made for each barcode when using allfiles=t? I have twenty barcodes, and two group files: one which I think covers the entire fasta file, and another that is zero bytes in size, and is named after the first barcode in my oligo file.
Thanks
Neil