Hi Banisha,
Make sure the two numbers on the first line match to (a) the number of sequences and (b) the number of bases.
The “3117” at the top of your file looks wrong, so PAML doesn’t know where the first sequence ends.
Also – it looks like your sequences are not aligned. Your input sequence file should be codon-aligned, otherwise your results will make no sense. There is more information here https://github.com/abacus-gene/paml-tutorial/tree/main/positive-selection/00_data
All the best,
Janet