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

ian Longden ianl at ebi.ac.uk
Fri Aug 26 16:00:45 BST 2011


On Fri, Aug 26, 2011 at 3:46 PM, Damian <dfermin at umich.edu> wrote:
>
> I changed the registry settings to point it to ensembldb.ensembl.org and
> Version 62 worked. I got the same things you did.
> I set the registry settings back to our local host and the problem
> reappeared.
>
> So should I reinstall the API or reinstall version 62 core?

hmmm.
The API obviously works as you can get data from the ensembl site. So
it might be worth
reinstalling 62 version of core for human.

It might be worth having a quick look at your internal database and
compare counts for a few tables between that and the ensembl version.

i.e.
mysql -hensembldb.ensembl.org -uanonymous -P5306
homo_sapiens_core_62_37g -e 'select count(1) from exon'
+----------+
| count(1) |
+----------+
|  1128110 |
+----------+

try this for a few tables like gene, transcript, dna,  seq_region,
exon_transcript..

Just to make sure it is this but it might be quicker just to reinstall..

-Ian.

>
> Damian
>
>
> On 08/26/2011 10:39 AM, ian Longden wrote:
>>
>> Change 63 to 62.
>> I did this and got:-
>>
>>> ENSE00002226834
>>
>>
>> CTGACCCCGACCCCCGCATATACCAGCAACGGTGCGCCCGGGGGCCTGACCCCGACCACCGCATATACCAGCAACGGTGCGCCCGGGGGCCTGACCCCGACCCCCGCATATACCAGCAACG
>>
>>> ENSE00002270664
>>
>>
>> CAACAGTGCGCCCGGGGGGCCTGACCCCGACCACCGCATATACCAGCAAAGATGCGCCCGGGGGCCTGACCCCGACCACCGCATATACCAGCAACGGTGCGCCCGGGGGCCTGACCCCGACCCCCGCATATACCAGCAACGGTGCGCCCGGGGGCCTGACCCCGACCACCGCATATACCAGCAACGGTGCGCCCGGGGGCCTGACCCCGACCCCCGCATATACCAGCAACGCCCGGGGGCCTGACCCCGACCCCCGCATATACCAGCAACGGTGCGCCCGGGGGCCTGACCCCGACCCCCGCATATACCAGCAAAGGTGCGCCCGGGGGCCT
>>
>>> ENSE00002216223
>>
>>
>> CAACGCCCGGGGGCCTGACCCCGACCCCCGCATATACCAGCAACGGTGCGCCCGGGGGCCTGACCCCGACCCCCGCATATACCAGCAAAG
>>
>>
>> I am guessing you have 62 version of the API installed, in which case
>> if you do not set a db_version, you will automatically load the 62
>> databases.
>>
>> So try two things 1) connect to our server to see if that works okay
>>                           2) connect to your local copy and see if it
>> works
>>
>> This will hopefully tell us if there is a problem with your local copy
>> or wether the API is wrong at your end.
>>
>> -Ian.
>>
>>
>> -Ian
>>
>>
>>
>> On Fri, Aug 26, 2011 at 3:27 PM, Damian<dfermin at umich.edu>  wrote:
>>>
>>> Hi Ian.
>>> Thanks for the quick reply.
>>>
>>> I'm using Ensembl Human Core 62_37g.
>>>
>>> We have to stick to this version because all our previous work was done
>>> with
>>> it.
>>>
>>> Your code changes do indeed work but only with the 63 release.
>>> Is there a way to identify these problem cases in 62 and to skip them?
>>>
>>> if(defined($gene)) doesn't work for me since the gene object is indeed
>>> returned.
>>>
>>> Damian
>>>
>>>
>>>
>>> On 08/26/2011 10:16 AM, ian Longden wrote:
>>>>
>>>> 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
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Dev mailing list    Dev at ensembl.org
>>>>> List admin (including subscribe/unsubscribe):
>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>
>>> --
>>>
>>> ------------------------------------------------------------------------------
>>> 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
>>>
>>> ------------------------------------------------------------------------------
>>>
>>>
>>
>
> --
> ------------------------------------------------------------------------------
> 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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