[Bioperl-l] Warning while running bioperl StandAloneBlast.

Praveen Surendran praveen_spillai at yahoo.co.in
Tue May 19 08:03:50 EDT 2009


I am getting some warning along with results which says --> "[NULL_CAPTION] Warning: Failed to initialize search. ISAM Error code is -5"
Can someone please let me know what this is all about.

Please find my script below.

use Bio::SeqIO;
use Bio::Tools::Run::StandAloneBlast;
open FILE, ">./blast.txt";
my $Seq_in = Bio::SeqIO->new (-file => $ARGV[0],
                               -format => 'fasta');
my $query = $Seq_in->next_seq();
my $factory = Bio::Tools::Run::StandAloneBlast->new( 'program'  => 'blastn',
    'database' => 'nr',
    _READMETHOD => "Blast" );
my $blast_report = $factory->blastall($query);
my $result = $blast_report->next_result;
while( my $hit = $result->next_hit()) {  
  print FILE "\thit name: ", $hit->name(), " significance: ", $hit->significance(), "\n"; 
  # while( my $hsp = $hit->next_hsp()) {
  # print "E: ", $hsp->evalue(), "frac_identical: ", $hsp->frac_identical(), "\n";    }}
  close FILE  
Kind Regards,
Praveen Surendran.

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