Your output begins with a blank line because the string you are splitting is -type signsample -PHI_file ../12x3X1V1.PHI   -PHI_LIBRARY_LIST PHI_LIB.list. The string starts with a hyphen, so the first split element is a null string.

As a second note, you should get in the habit of using or in place of || for the phrase or die if you don't want to get Burned by precedence rules.

Update: Prior to that split, the matching @arr element is variation_input_db -type signsample -PHI_file ../12x3X1V1.PHI   -PHI_LIBRARY_LIST PHI_LIB.list, so perhaps you meant s/variation_input_db\s*\-//g;?