Maping big sequences

For my work I get some slices of 100 kb from real chromosomes, but I forget to insert in the fasta comment the name and coordinates for each sequences, now I need to know this information for each one, so I tried to map using blast, but in the server a weird error marks "Segmentation fault" (I format the full genome ~3 Gb).

I think in the Perl solution and this is the code:

#!/usr/bin/perl -w
use strict;

=head1 NAME

mapSeq2Chr.pl

=head1 DESCRIPTION

Perl script to find and get the position of each sequence in a
multifasta file into a big sequence (a chromosome).
 
The comparation is direct, so it only works with sequences in same
direction (typical 5' -> 3').
 
Output is a simple text file with the name of the sequence, the name
of the big sequence and the positions where match.
 
Note we match every line with a fasta comment (defined with ">") but
the last sequence is omitted, I add a ">" as last line with:

echo ">" >> fasta

=cut

$ARGV[2] or die "usage: perl mapSeq2Chr.pl CHR SEQ MAP\n";

# Global variables
my ($chr_file) = shift @ARGV; # Fasta file with chromosome
my ($seq_file) = shift @ARGV; # Fasta file with sequences
my ($map_file) = shift @ARGV; # Output file
my ($seq)      =          ''; # Sequence to map
my ($name)     =          ''; # Fasta comment
my ($chr)      =          ''; # Genomic sequence
my ($first)    =         'y'; # Flag for first line

print "Reading genome sequences ...\n";
open C, "$chr_file" or die "Cannot open $chr_file\n";
while (<C>) {
 next if (/>/);
 chomp;
 $chr .= $_;
}
close C;
print "   loaded $chr_file with ", length $chr, " bases\n";

open F,  "$seq_file" or die "Cannot open $seq_file\n";
open O, ">$map_file" or die "Cannot open $map_file\n";
print "Mapping sequences ...\n";
while (<F>) {
 chomp;
 if ($first eq 'y') {
  s/>//;
  $name = $_;
  $first = 'n';
 }
 elsif (/>/) {
  s/>//;
  if ($chr =~ /$seq/) {
   print "   $name mapped in $chr_file ";
   print O "$name\t$chr_file\t";
   
   # We use @- to look for multiple matches
   foreach my $match (@-) {
    print O "$match:";
    print "$match ";
   }
   print O "\n";
   print "\n";
  }
  else {
   print "   $name not match in $chr_file\n";
  }
  $name = $_;
  $seq  = '';
 }
 else {
  $seq .= $_;
 }
}
close F;
close O;
print "Done\n";

=head1 AUTHOR

Juan Caballero (linxe _at_ glib.org.mx)

=head1 LICENSE

Perl Artistic License (http://dev.perl.org/licenses/artistic.html)

=cut