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next if -f $subdir;

next unless -d $subdir;

foreach my $subdir ( sort @subdirs ) {

chdir($dir);
next unless -d $subdir;
...

use strict;
use warnings;
...
    chdir $dir . '/' . $subdir;
    system("echo '1 0' | program -f methane.trr -o $result_path/$subdi
+r/outfile.txt");
}