Dear Monks,
I have written the following code that works OK (i.e. prints the correct results):

use stricts;
use warnings;

my $total_entry_non_barrel='';
my $aligns_non_barrel='';
my @split_aligns_non_barrel=();
my $separate_hit_non_barrel='';
my @split_hit_non_barrel=();
my $hit_line_non_barrel='';
my $hit_name_non_barrel='';
my $protein_non_barrel='';
my $stat_line_non_barrel='';
my @split_stats_non_barrel=();
my $score_non_barrel='';
my $conditional_evalue_non_barrel='';
my $env_start_non_barrel='';
my $env_end_non_barrel='';
my $i=0;
my $k=0;

$/="//\n";
while(<>)
{
    $total_entry_non_barrel=$_;
    if($total_entry_non_barrel=~/^Query:\s+(.*?)\s\[L=(\d+)\]/m)
    {
        $protein_non_barrel=$1; 
    }

    if ($total_entry_non_barrel!~/No hits detected/)    
    {
        if($total_entry_non_barrel=~/Domain annotation for each model:
+(.*)Internal pipeline statistics summary:/s)
        {
            $aligns_non_barrel=$1; 
            @split_aligns_non_barrel=split(">> ", $aligns_non_barrel);

            for($i=0; $i<=$#split_aligns_non_barrel; $i++)
            {
                $separate_hit_non_barrel=$split_aligns_non_barrel[$i];
                @split_hit_non_barrel=split(/\n/, $separate_hit_non_ba
+rrel);
                $hit_line_non_barrel=$split_hit_non_barrel[0];
                if($hit_line_non_barrel=~/^(.*?)\s+/)
                {
                    $hit_name_non_barrel=$1;
                }

                #keep score, c-Evalue, env-start, env-end for each hit
                for($k=3; $k<=$#split_hit_non_barrel; $k++)
                {
                    $stat_line_non_barrel=$split_hit_non_barrel[$k];
                    @split_stats_non_barrel=split(/\s+/, $stat_line_no
+n_barrel);
                    $score_non_barrel = $split_stats_non_barrel[3];
                    $conditional_evalue_non_barrel = $split_stats_non_
+barrel[5];
                    $env_start_non_barrel = $split_stats_non_barrel[13
+];
                    $env_end_non_barrel = $split_stats_non_barrel[14];
                }

                if($hit_name_non_barrel=~/^PF\d+/)        #it is a PFA
+M-A hit, keep it if score >=TC
                {
                    if($score_non_barrel>=$hash_pfamA_tc{$hit_name_non
+_barrel})
                    {
                        print $hit_name_non_barrel, "\t", $score_non_b
+arrel, "\t", $conditional_evalue_non_barrel, "\t",$env_start_non_barr
+el , "\t", $env_end_non_barrel, "\n"; 
                    }
                }

                elsif($hit_name_non_barrel=~/^PB\d+/)    #it is a Pfam
+B hit, keep it if Evalue<=1e-6
                {
                    if($conditional_evalue_non_barrel<=0.000001)
                    {
                        print $hit_name_non_barrel, "\t", $score_non_b
+arrel, "\t", $conditional_evalue_non_barrel, "\t",$env_start_non_barr
+el , "\t", $env_end_non_barrel, "\n"; 
                    }
                }
            }
        }
    }
    print "##\n";
}
$/="\n";
[download]

However, when I run it, I get the warning:

Use of uninitialized value $hit_line_non_barrel in pattern match (m//)
+ at ttt.pl line 735
[download]

which is the line:

if($hit_line_non_barrel=~/^(.*?)\s+/)
[download]

in my program. What am I doing wrong?
Also, is there some tips you could tell me/re-write some commands etc that could make my code run faster?