Hi Ensiyeh,
Please consider moving to the latest WRF-CMAQ release which uses WRFv4.1.1 and CMAQv5.3. A tarball with build and run scripts and a README file with instructions is available here (Google Drive): https://drive.google.com/drive/folders/1ru64xxZeRcE5buQ9fygV9jUHAQ9aDnL7
One day benchmark input and output datasets are available to download from here (Google Drive): https://drive.google.com/drive/folders/1apg7_LXU4Kpzx5EZgdc07Q3UTTpL-jah
The tarball and benchmark input data are also available from the EPA anonymous ftp server: ftp://newftp.epa.gov/exposure/CMAQ/V5_3/WRF-CMAQ_Coupled_Model/
The benchmark output data is not there yet but will be uploaded sometime next week.