The error is linked to the presence of options -s and -t that imply some statistics on outputs.

## get some statistics about mapped reads if options{'s'} and options{'t'} are supplied
if($options{'s'} and $options{'t'}){
    read_stats();
}

The part of the script that generates the error is the following. Maybe someone with more experience than me in perl can check it and add more comments. The variable $count2 is present only in this part of the code.

sub read_stats{
    my %hash;
    my $count;
    my %k2;
    my $total;

    open IN,"$options{'s'}" or die "No reads file in fasta format given\n";
    while(<IN>){
        if(/^>*((\S\S\S)\S+_x(\d+))/){
            next if($hash{$1});
            $hash{$1} = 1;
            $count+=$3;
            $k2{$2}+=$3;
        }
    }
    close IN;
    my %hash2;
    my $count2;
    my %k22;

    print STDERR "Mapping statistics\n";
    open IN, "$options{'t'}" or die "No mapping file given\n";
    while(<IN>){
        if(/^>*((\S\S\S)\S+_x(\d+))/){
            next if($hash2{$1});
            $hash2{$1} = 1;
            $count2+=$3;
            $k22{$2}+=$3;
        }
    }

    print STDERR "\n#desc\ttotal\tmapped\tunmapped\t%mapped\t%unmapped\n";
    print STDERR "total: ",$count,"\t",$count2,"\t",$count-$count2,"\t";
    printf STDERR "%.3f\t%.3f\n",$count2/$count,1-($count2/$count);
    foreach(sort keys %k2){
        print STDERR "$_: ",$k2{$_},"\t",$k22{$_},"\t",$k2{$_}-$k22{$_},"\t";
        printf STDERR "%.3f\t%.3f\n",$k22{$_}/$k2{$_},1-($k22{$_}/$k2{$_});
    }
}