It's not easy to tell without access to your specific data.

However, one thing that strikes me as dangerous is:

while(<DATA>)
{
    #...
    if(($x[0] eq 's') && ($x[3] eq 'AGT'))
    {
        $file_position = tell(DATA);
        #...
        while(<DATA>)
        {
            #...
        }
        seek(DATA,$file_position,SEEK_SET);
    }
}
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Which just has "infinite loop" written all over it.  As soon as you're done reading from <DATA>, you jump back to the marked $file_position which you previously saved.

Try putting a print statement in the outer loop, and see if that isn't the problem.