[ensembl-dev] Core API quits with no error messages

[ian Longden]

What version of the API are you using?
ENSG00000256461 has been archived and is not in release 63 so that
could be part of it.

also add -verbose => 1 to the load_registry_form_db to see which
databases it is connecting to.

So i modified your script to use our server as a test
#######################################################
use Bio::EnsEMBL::Registry;

my $reg = 'Bio::EnsEMBL::Registry';

$reg->load_registry_from_db(
       -host => 'ensembldb.ensembl.org',
       -user => 'anonymous',
       -db_version => 63,
       -verbose => 1
);


my $GA = $reg->get_adaptor('Human', 'Core', 'Gene');

my $gene = $GA->fetch_by_stable_id('ENSG00000256461');

if(defined($gene)){

  my @exons = @{ $gene->get_all_Exons() };

  foreach my $e (@exons) {
    print ">" . $e->stable_id() . "\n";
    print $e->seq->seq . "\n\n";
  }
}
else{
  print "Gene could not be found\n";
}

exit;
##################################################################
which gave me the list of databases and also the message:-
Gene could not be found

-Ian Longden
EnsEMBL Developer.


On Fri, Aug 26, 2011 at 2:36 PM, Damian <dfermin at umich.edu> wrote:
> Hello.
>
>
> I don't know how to debug this problem with the Core API in perl.
>
> Here is the code:
> ####################################################
> use Bio::EnsEMBL::Registry;
>
> my $reg = 'Bio::EnsEMBL::Registry';
> $reg->load_registry_from_db(
>        -host => '127.0.0.1',
>        -user => 'nesviLab'
> );
>
>
> my $GA = $reg->get_adaptor('Human', 'Core', 'Gene');
>
> my $gene = $GA->fetch_by_stable_id('ENSG00000256461');
>
> my @exons = @{ $gene->get_all_Exons() };
>
> foreach my $e (@exons) {
>    print ">" . $e->stable_id() . "\n";
>    print $e->seq->seq . "\n\n";
> }
>
> exit;
>
> ####################################################
>
>
> When I run this code, the output is the first exon of the array and that's
> it:
>>ENSE00002226834
>
> The sequence of the exon is never written out.
> The script does not throw an error and the program does exit.
> Running 'top' on my computer shows that the script is not even using up CPU
> cycles.
>
> This only happens with genes on chromosome 1. The above code runs to
> completion with any genes from chromosomes 2..Y
> Any idea what's going on? Any and all help is greatly appreciated.
>
> I'm running the Ensembl Core version 62 on RHEL 5.4 (64bit).
> Perl version: 5.8.8
> MySQL version: 5.0.77
>
> Damian
>
> --
> ------------------------------------------------------------------------------
> Damian Fermin, Ph.D.
> Pathology Department
> University of Michigan
> 4237 Medical Science I
> 1301 Catherine
> Ann Arbor, MI 48109-0602
> 734.615.0302
>
> "There is No Gene for the Human Spirit"
>        -- GATTACA
> ------------------------------------------------------------------------------
>
>
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