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while (my $line = <DATA>) {
    chomp $line;
...
    unless $line =~ /\S/;
    ...
}

my $dir = "$base_dir/$filepath"
do { mkpath $dir; print "Made $dir\n"; } unless -d $dir;

warn "Line: ==$line==";
my ($filename, $filepath) = split '\t', $line;
warn "filename: '$filename' --- filepath: '$filepath'";