I am getting a headache trying to read your post. Please edit your post and change your <end code> to </CODE>.

I fear you do not understand how chdir works in Perl. After calling chdir, you must call getcwd() again to refresh your $current_dir variable. Please run this program and let us know what it prints:

# change_directory.pl

use warnings;
use strict;
use Cwd;

my $current_dir = getcwd();

#list the Timepoint directories
my @TP_dir = glob("T*");

for my $dir (@TP_dir) {
   my $fulldir = "$current_dir/$dir";
   if (-d $fulldir) {
      chdir($fulldir) or die "error: chdir '$fulldir': $!";
      my $currdir = getcwd();
      print "cd worked: currdir is now '$currdir'\n";
   }
   else {
      print "oops: '$fulldir' is not a dir\n";
   }
}
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