Pradeep,
I cannot see anything wrong with your input file, I assume you submitted it with the command: ./megan_bio_emiss < megan_bio_emiss.inp ?
I noticed, however, that you only create the wrfbiochemi file for months 11-12 but start your simulation in November. MEGAN needs also the previous months for calculating biogenic emissions, so at least you should set megan_bio_emiss to run for 10-12.
Gabriele