make.contigs() puts everything in scrap file


I am trying to follow Mothur MiSeq sop. I want to remove primers from my sequences while running make.contigs. My oligos file looks like this:

However make.contigs puts all my sequences in *.scrap.contigs.fasta.
How can I get around this problem?

Thanks in advance for helping me out.

This happens because mothur cannot find the primers on the sequences. Can you manually check a few sequences in your fastq files and see if they’re there? If you aren’t providing barcode information then mothur looks for the primer at the very beginning of the sequence.