$Euk is not initilized in your code before being used in:

but I assume it was supposed to be:

Then the following, slightly modified script should do roughly what you want:

use strict;
use warnings;

my $infile=$ARGV[0];
open (IN,$infile) or die "cannot open $infile";

my %count_Bact; my %count_undef; my %count_ProphVir; my %count_Euk;

my %processed;

while (my $line=<IN>) {
        chomp $line;
        next if ($line =~/^#/) ;
        my ($geneid,$cons_flag)=split(/\t/,$line);
        my @geneid_columns=split(/_/,$geneid);
        my $contig=join("_",$geneid_columns[0],$geneid_columns[1],$gen
+eid_columns[2],$geneid_columns[3]);
        if ($cons_flag eq "Bact"){
                $count_Bact{$contig} ++;
        }
        if ($cons_flag eq "undef"){
                $count_undef{$contig} ++;
        }
        if ($cons_flag eq "Proph_Vir" || $cons_flag eq "Vir" || $cons_
+flag eq "Proph"){
                $count_ProphVir{$contig} ++;
        }
        if ($cons_flag eq "Euk"){
                $count_Euk{$contig} ++ ;
        }
        $processed{$contig}++;
}
close (IN);

my @counts = (\%count_Bact, \%count_undef, \%count_ProphVir, \%count_E
+uk);

for my $contig (keys %processed) {
        print join (' ', $contig,  map { $_->{$contig} || 0}  @counts)
+ , "\n";
}
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