Hello Ben and Huan:
I saw the log files posted here and compared with mine and I observed the same problem with the number of layer in the emission file.
In my case, I only have the surface emission file and when I process it, I obtain this message in the log file
Bad argument LAY1= 49
In my case, I have 50 layers made since wrf simulation. I think CCTM is not processing my emissions, because I did the same action as Huan did.
Can I solve this in CMAQ5.2?? Right now it is very dificult for me to migrate to CMAQ5.3
Hope you can help me, thanks