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Dear Corona688,

I really thank you for your help and patience in troubleshooting the problem.
It was indeed a fortran problem and as soon as I installed gfortran, the program started to work....

Dear Corona688,
I first checked with a single operation including other command-line options and then put it into the loop for all the sequences. So far working good :)
Thanks again.
Regards

Dear Corona688, the program is executing successfully using the above commands. Below is the terminal output:

[host@localhost temp]$ ma <<EOF
H_X.fas
auto
n
/home/multalign/dna.tab

n
msf...