Does sample_ACCTGG.fq exist when the attempt to rename is made? Try 
if ( -e $file ) {
  rename ($file, $new) or die "Can not change $file to $new, $!\n";
}
else {
  print "$file isn't there to be renamed $new\n";
}

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In reply to Re: change files names bug by keszler
in thread change files names bug by Yuma248

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