Try this it works for me.

#!/usr/bin/perl -w

use strict;
use warnings;
#open(FILE, "twentySeq1e-10.out") or die("Cannot open file");
my $gi;
while(<DATA>){
    if(/^# Query: gi.([0-9]+)/) {$gi = $1;} 
    if(/^# 0 hits found/){print "$gi\n";}
}
__DATA__
# BLASTP 2.2.28+
# Query: gi|338220664|gb|EGP06123.1| hypothetical protein GEW_00005 [P
+asteurella multocida subsp. gallicida str. Anand1_poultry]
# Database: nr-25sep
# Fields: query id, subject id, % identity, alignment length, mismatch
+es, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 2 hits found
gi|338220664|gb|EGP06123.1|    gi|45383702|ref|NP_989542.1|    45.15  
+  206    96    7    3    204    28    220    1e-51     170
gi|338220664|gb|EGP06123.1|    gi|15419940|gb|AAK97214.1|    44.17    
+206    98    7    3    204    28    220    5e-50     166
# BLASTP 2.2.28+
# Query: gi|338220666|gb|EGP06125.1| hypothetical protein GEW_00015 [P
+asteurella multocida subsp. gallicida str. Anand1_poultry]
# Database: nr-25sep
# 0 hits found
# BLASTP 2.2.28+
# Query: gi|338220651|gb|EGP06111.1| hypothetical protein GEW_00275 [P
+asteurella multocida subsp. gallicida str. Anand1_poultry]
# Database: nr-25sep
# 0 hits found
[download]

RESULT

Process started >>>
338220666
338220651
<<< Process finished. (Exit code 0)
[download]

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