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191.52user 153.47system 5:49.44elapsed 98%CPU

open SEQ,  '<', $ARGV[0] or die $!; #plain
open MASK, '<', $ARGV[1] or die $!; #hardmask
...
close SEQ;
close MASK;

0.45user 0.07system 0:05.59elapsed 9%CPU

#Seq_name    #Seq_len
2-micron    6318
...
VII    1090946
XV    1091289
IV    1531918