in reply to Re^2: Help with pattern matching and calling wc -l
in thread Help with pattern matching and calling wc -l

$Num_Bact_Virus_Chimera=$Num_Bact_Virus_Chimera-1;

Maybe you should check that $Num_Bact_Virus_Chimera contains what you think it does. See print:

print "Got '$Num_Bact_Virus_Chimera' lines.