Thank you to all the Monks for your valuable edits / modifications/ complete re-writes. I learned some things about reducing memory usage and ridding useless variables etc. Appreciate it!

Since none of your suggestions were working either, I write a short script to see the length distribution explicitly, and there was sequences from input file # 1 that were 0 (zero) in length as well as longer than the longest sequence in input file # 2. This will cause my scrip tp search without terminating. And this was also confirmed by hdb's script because it exits with an error message after error-checking

Anti-climactically, the error in the input files that were being fed to me was the reason that my original script that was working stopped working. In the end, a good lesson for me, and useful to get pointers about scripting I wouldnt have otherwise gathered from you all. So thank you all, again!