Align.seqs question

I run align seqs.(fasta=runtwo.trim.contigs.good.unique.fasta, reference=silva.v4.fasta) as per the MiSeq SOP.

In the protocol, it says that this should take a matter of seconds, and it does, to give the message ‘It took 7 seconds etc’ DONE

Then the output on the screen seems to continue on producing sequential sequnce numbers, presuming it’s aligning?

Is this normal or should it finish this command quicker?

Thank you so much

Are you running it with multiple processors?