A very quick method of finding out issues can be introducing temporary 'print' statements in the code. So you could print the value of $FastaSeqOfDataBase after it is assigned a value in the code snippet you pasted. Then see if the value is still undef.

The log message you've pasted suggests that your code is over 500 lines long, so I guess to one extent it might be difficult for you to put a lot of other background information here.