align.seqs for 18s miseq reads

I was using the miseq sop for qualitative analysis of 18S reads. for the alignment I was using the reference file from silva (silva.nr_v123.align). the code is running well but the CPU time limit is reached before the analysis is done. I am trying to run the align.seqs command in a batch mode, but still it runs in an interactive way. any hint?

What is your CPU time limit?