You appear to be having trouble boiling the problem down to code that reliably reproduces the problem. I actually don't see how you wind up with a value of undef for a key of %count. There is probably something that you are not showing us.

This is an advanced concept, but it is possible to have a subroutine executed when a Perl warning happens. You can add this code below to your code. At the first warning message, this code should dump the subroutine's input parameters to match_query. match_query($indexfile,$queryseq) and then exit.

The results of this are what we want. When the error happens, what are the values of $index_file and $queryseq? From that, this error can be replicated.

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

$SIG{'__WARN__'} = \&stop_n_report; #add this

my $indexfile = {
                  'GCTCAGGA' => '4',
                  'AGCGTAGC' => '5',
                 }; 
                 
my $queryseq='something';

my $undef_val;      #simulation of your code
print "$undef_val"; #simulation of your code to produce an error

sub stop_n_report  ## add this
{
   print "some kind of warning detected: @_\n";
   print "Dumping input data\n";
   print "Dumping indexfile:\n";
   print Dumper $indexfile;
   print "query=$queryseq\n";
   exit;
}

__END__
some kind of warning detected: Use of uninitialized value $undef_val i
+n string at C:\Projects_Perl\testing\sigwarn.pl line 16.

Dumping input data
Dumping indexfile:
$VAR1 = {
          'GCTCAGGA' => '4',
          'AGCGTAGC' => '5'
        };
query=something
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