Nitrogen markers with ShortBRED Identify

We are trying to use ShortBRED to develop markers for nitrogen cycling using the NCycDB database. However, NCycDB is ten times larger than CARD and the program runs two weeks without finishing. Any suggestions on how to make a nitrogen-cycling marker set?

Sorry for the late reply. Do you have a sense of where the program is getting stuck? I would not expect any parts of the ShortBRED marker identification process to take this long.

How many input nitrogen cycling sequences do you have? And what are you using as a sequence background?

Thanks so much for this reply.
The NCyc95 database has approximately 85,000 sequences. We filter markers against UniRef90.