You might find that the pcr.seqs command is more suited to this. It works in a similar fashion, you provide an oligos file with your primer sequences and the fasta file to trim from.
That would be the most straight forward method, but I’ve found sometimes that using pcr.seqs discards a number of sequences (when it can’t find your primer targets in the sequence). An alternative approach, which would be a bit more complicated, is that you could align a few representative V2 sequences and then use their alignment space as a filtering criteria for the rest of your data.
For example, if you copy an E. coli V2 sequence into a fasta file, you could run the commands: