Shaghayegh Hosseini | 19 Jul 15:28 2013

MSG: Response Error STACK: Error::throw when trying to download genbank files using GI


I am trying to fetch genebank features,here is the script

use strict;

use warnings;

use Bio::SeqIO;

use Bio::DB::EUtilities;

my $gi="385220095";

my  $factoryID = Bio::DB::EUtilities->new(-eutil => 'efetch',

                                          -db =>'protein',

                                          -rettype=> 'gbwithparts',

                                          -email=> 'x <at>',

                                          -id=>$gi) ;

my $gbfile="$gi.gbk";

$factoryID->get_Response(-file =>$gbfile);

my $seqio_object = Bio::SeqIO->new(-file =>"$gbfile",'protein');

while ( my $seq_object=$seqio_object->next_seq){

    for my $feat_object ($seq_object->get_SeqFeatures) {

        my $sequence_string = $feat_object->spliced_seq->seq;



I have got 2 problems

1. For some GIs I am getting (MSG: seq doesn' t validate, mismatch or MSG:
Got a sequence with no letters in it cannot guess alphabet )which is
 annoying since I have about 2000 GIs  and for half of them this warnings
are there BUT  it  does the job.

2. After  downloading lets say 1000 file I am getting Error (MSG: Response
Error STACK: Error::throw or Bad Gateway)

Please let me know what I have done wrong

This  is the ERROR for First problem

--------------------- WARNING ---------------------

MSG: seq doesn't validate, mismatch is 266299291214720428459636348159


------------- EXCEPTION: Bio::Root::Exception -------------

MSG: Attempting to set the sequence to [266299291214720428459636348159]
which does not look healthy

STACK: Error::throw

STACK: Bio::Root::Root::throw /Bioperl/1.6.1/lib/perl5/Bio/Root/

STACK: Bio::PrimarySeq::seq /Bioperl/1.6.1/lib/perl5/Bio/

STACK: Bio::PrimarySeq::new Bioperl/1.6.1/lib/perl5/Bio/

STACK: Bio::Seq::new /Bioperl/1.6.1/lib/perl5/Bio/

STACK: Bio::SeqFeatureI::spliced_seq