Think about how the contents of the external file containing the file names are going to get into the @filenames array. At present your code has nothing to do that. One way would be:

my $namesFileName = shift; # Get name of the file names file from comm
+and line

open my $inNames, '<', $namesFileName or die "Unable to open $namesFil
+eName: $!\n";
my @filenames = <$inNames>; # Read the file names (one per line)
close $inNames;
chomp @filenames; # Remove the line end character from each entry

...
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or you could replace the for loop with a while loop and eliminate the array:

use strict;
use warnings;

my $namesFileName = shift;   # Get name of the file names file from co
+mmand line

open my $inNames, '<', $namesFileName or die "Unable to open $namesFil
+eName: $!\n";

while (<$inNames>) {
    chomp; # Remove line end character from file name
    open my $dsspIn, '<', $_ or die "Unable to open $_: $!\n";
    ...
}

close $inNames;
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