Thanks everyone, Okay, as cranky as roboticus sounded the indenting DID help, and so did the wc -l < $file. The script is working fine now.

#!/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=</g/bork6/mende/MGSimulation/hybridcontigs/outputMC38/*.MG$MG
+_Num.*>;

  foreach $file (@files) {

    if ($file=~/HybridViralBactContigsList/){

    $Num_Bact_Virus_Chimera=qx/wc -l < $file/;
    $Num_Bact_Virus_Chimera=$Num_Bact_Virus_Chimera-1;

    }

    if ($file=~/HybridOnlyBactContigsList/){

    $Num_Bact_Bact_Chimera=qx/wc -l < $file/;
    $Num_Bact_Bact_Chimera=$Num_Bact_Bact_Chimera-1;
    }

    if ($file=~/HybridOnlyVirusContigsList/){

    $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]

Output file

MG_Num  Num_Bact_Virus_Chimeras Num_Bact_Bact_Chimera   Num_Virus_Viru
+s_Chimera
1       0       3502    0
2       0       3356    4
3       0       3363    17
4       1       3374    41
5       2       3499    93
6       0       3498    89
7       0       4005    0
8       1       4415    4
9       0       3986    17
10      4       4382    41
11      3       4381    80
12      1       4415    80
13      0       1       0
14      0       0       4
15      0       0       16
16      0       0       44
17      0       1       86
18      0       1       87
19      0       3133    0
20      0       3301    3
21      0       3120    9
[download]