For Scalar value @fields1[1] better written as $fields1[1], change @fields1[1] to $fields1[1].

Failed to open "./input.txt" for writing: No such file or directory comes from your attempt to open a file that doesn't exist for reading. Maybe you want to skip that directory?

for my $subdir ( sort @subdirs ) {
   chdir($dir);

   ...

   my $in_fh1;
   if (!open $in_fh1, '<', $infile1) {
      goto NEXT if $!{ENOENT};
      die qq{Failed to open "$infile1" for reading: $!};
   }

   ...

NEXT:
   chdir('..');
}
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