From what I understand this is a timestamp issue, but I have triple checked my emissions inputs netcdfs for 2019244 (attached) and they have the correct start time of 2019244:000000 and I have tested running straight from the second day and the GR_EMIS_001 is read in fine and runs for 2019244.
The CMAQ run script that EPA distributes is set up for multiple executions of the model, with each run being 24 hours. You have set NSTEPS to 1440000, or 144 hours, equal to 6 days. It is possible to do a single execution for 6 days (or far longer), but you need to have all your meteorology, emissions, IC/BCs, etc., available in the files specified by the run script. Here your gridded emissions file for September 1 contains only 24 time steps, and CMAQ does not know to look for the next file.
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