MCIP is the Meteorology-Chemistry Interface Processor for CMAQ. Its purpose is to take meteorological output from WRF and process it into the form needed for input to CMAQ.
Your simulation is from WRF-Chem. This is a version of WRF which includes chemistry. Once you’ve run WRF-Chem, there is no need to run CMAQ.
You should either run WRF-Chem, or run WRF, followed by MCIP and CMAQ. Alternatively, you can run a “coupled” version of WRF-CMAQ. This is described in the user guide.
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