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  exec = ("BlastTool.cgi", "$date", "$show_filter", "$oldRefFile",
 "$blast_filehandle", "$ref_filehandle", "$email", 
 "$send_email","$show_all", "\@OrigRef", "\@blastLine", 
 "\@species_filter", "\@chromo_filter", 
 "\@advanced_filter") or die;

  my $date = shift @_;
  my $show_filter = shift @_;
...
  my @species_filter = @{shift @_};
  my @chromo_filter = @{shift @_};
  my @advanced_filter = @{shift @_};