Pcr.seqs nomatch=keep not giving expected output

Hi,
I’m running pcr.seqs in mothur v. 1.48 on a custom database using the following command

pcr.seqs(fasta=custom_db.align, processors=8, keepdots=F, keepprimer=T, seed=8947961, start=1044, end=13862)

which leads to roughly 1/6 of my sequences to end up in the bad.accnos file. I assume this is because their start > requested start and/or end < requested end?

I was under the impression setting nomatch=keep would keep these sequences in the pcr.align file, but what it actually does is print the full 50.000bp sequence (instead of position 1044-13.862) to the scrap.pcr.align. Is this the intended behaviour? Is there a way to allow sequences with leading/trailing dots to not be rejected?

The nomatch parameter is only used by mothur when you are using an oligos file. You can use the chops.seqs command to trim while allowing for leading/trailing gaps.

First trim from 13862:
chop.seqs(fasta=current, keep=front, countgaps=true, numbases=13862)

To trim to position 1044 (13862-1043):
chop.seqs(fasta=current, keep=back, countgaps=true, numbases=12819)