SMOKE EDGAR missing variables

Hi everyone,

I am using SMOKE-4.8.1 to process hg area inventory. I have three emission variables in the input emission files, however my output files only have one variable.
I checked all intermediate files, in the scenario directory, i found that for one sector on one day, i have two atmp files, named, for example atmp.hg_cement.US12NE.2010045.1.ncf and atmp.hg_cement.US12NE.2010045.2.ncf. In file 1 there are two variables and in file 2 there is one variable. My output file only have one variable that is same as file 2. Does this have something to do with the missing variables?