AWallBuilder:

You should show some sample input, the actual output and expected output to make it simpler for us to see the error. As it is, we need to either:

• Be lucky and spot the error immediately.
• Write the code to a file and execute it, making up data as we go along and guessing about the output you want, or
• Give up and go to the next question.

Also, if you indent your code to show the structure, it makes things a bit easier for us to see how it works. It should also help you when you're creating/modifying/debugging it. It even makes some errors pretty obvious, like so:

#!/usr/bin/perl -w

my $Num_Bact_Virus_Chimera=0;
my $Num_Bact_Bact_Chimera=0;
my $Num_Virus_Virus_Chimera=0;
my $outfile='MC38_ChimeraTable.txt';
my $MG_Num=1;

open(OUT, ">$outfile") || die "Can't open outputfile $!\n";

print OUT join("\t",qw (
                        MG_Num Num_Bact_Virus_Chimeras 
                        Num_Bact_Bact_Chimera
                        Num_Virus_Virus_Chimera
                    ), "\n") ;

while ($MG_Num <= 72) {

   @files=</outputMC38/*.MG$MG_Num.*>;

   foreach $file (@files) {

      if ($file=qr/HybridViralBactContigsList.txt/){
         $Num_Bact_Virus_Chimera = qx/wc -l $file/;
         $Num_Bact_Virus_Chimera=$Num_Bact_Virus_Chimera-1;
      }

      if ($file=qr/HybridOnlyBactContigsList.txt/){
         $Num_Bact_Bact_Chimera= qx/wc -l $file/;
         $Num_Bact_Bact_Chimera=$Num_Bact_Bact_Chimera-1;
      }

      if ($file=qr/HybridOnlyVirusContigsList.txt/){
         $Num_Virus_Virus_Chimera=qx/wc -l $file/;
         $Num_Virus_Virus_Chimera=$Num_Virus_Virus_Chimera-1;
      }

      print OUT
         join("\t", $MG_Num,$Num_Bact_Virus_Chimera,
                    $Num_Bact_Bact_Chimera,
                    $Num_Virus_Virus_Chimera,
                    "\n");
   }
}
$MG_Num=$MG_Num+1;
[download]

Now that the code has some visual structure, one error immediately sticks out: Your while loop is checking when $MG_Num reaches 72, but you don't modify $MG_Num inside your loop. You only change it after the end of your while loop. I'm sure that's only one of your errors, but as you don't have sample data, expected and actual output and the error message, I'll just stop here.... ;^)

...roboticus