This is a huge guess here, but I feel that this is due to a #define ENOENT 2 /* No such file or directory */ that may have been encountered.

You may be in a directory that you think you are but aren't, or possibly trying to work on a file from a location where it doesn't exist. Can you change:

system($program,$outfile) == 0
  or die "$program $outfile failed: $?";
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...to:

print -x $program . "\n";
open my $fh, '<', $outfile or die $!;
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...within the exact same code and see if you get an error?