error message in pcr.seqs using new silva version 132 reference file

Commands in mothur
1

Hi,
I tried running pcr.seqs on the new silva version 132 reference file to get the V4 region of the 16S rRNA gene, and encountered this error message:

[ERROR]: seqs are not aligned. When using start and end your sequences must be aligned.

Here is how I ran the command:

pcr.seqs(fasta=silva.nr_v132.align, start=11894, end=25319, keepdots=F)

I used the same start and end coordinates described in the silva v132 README page.

Any ideas what this error message means and how I can correct it? Does it have to do with the coordinates I used for start and end?

Thank you!

2

I am not able to reproduce that with our current version. Could you try upgrading?

3

Upgrading did the trick. Thanks!