align.seqs Sudden trouble...

I am trying to align my .good.unique.fasta to my silva reference file (24850702 seq, 598760 unique seq). I basicly have done copy and paste from previous successfull analysis, but this time it won’t work. The analysis is running and I get the output on the screen:
" It took 9221 secs to align 598760 sequences.

Output File Names:

However, the files contain nothing and no mothur logfile is created. Could this be caused by the large number of sequences? Other options I could try?? :?:

Try fewer processors. Also, make sure you are looking in the right place. It is odd to not find the logfile. This should be generated regardless of whether the program crashes out.