I am using Mothur version 1.46.1, within Ubuntu terminal for Windows10
I ran align.seqs with the silva138 reference alignment and the rrnDB fasta file
align.seqs(fasta=data/raw/rrnDB-5.7_16S_rRNA.fasta, reference=data/references/silva_seed/silva.seed_v138.align, flip=T)
This ran as expected, however pcr.seqs on the resulting .align file gave the error:
pcr.seqs(fasta=data/raw/rrnDB-5.7_16S_rRNA.align, start=1044, end=43116, outputdir=data/v19/)
[ERROR]: seqs are not aligned. When using start and end your sequences must be aligned.
I re-downloaded all the files and tried again with the same result