[ensembl-dev] Re： Re： Re： Can't connect to ensembl database

[Michael Schuster]

Dear Grace,

Would it be possible that you are overriding the -port in the load_registry_from_db call? The registry cannot find any Compara, ancestral or GO database and that suggests to me that you are connecting to a database instance, but not the correct one. Ensembl databases beyond release 42 are on ensembldb.ensembl.org port 5306. If you would not specify a port, then the API will connect to the correct instance depending on version information.

Hope that helps,
Michael


> Hi Abel,
> 
> Here is what I get:
> 
> [GraceCheng at bxiew Desktop]$ DBD::mysql::db selectall_arrayref failed: fetch() without execute() at /src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 1418.
> Will only load v58 databases
> Bio::EnsEMBL::Variation::DBSQL::DBAdaptor module not found so variation databases will be ignored if found
> Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor module not found so functional genomics databases will be ignored if found
> No Compara databases found
> No ancestral database found
> No GO database found 
> 
> Thanks,
> Grace
> 
> 寄件人﹕ Abel Ureta-Vidal <abel at eaglegenomics.com>
> 收件人﹕ Grace Cheng <himwo at yahoo.com.hk>
> 副本(CC) dev ensembl <dev at ensembl.org>
> 傳送日期﹕ 2010/8/5 (四) 3:11:46 AM
> 主題： Re: [ensembl-dev] Re： Re： Can't connect to ensembl database
> 
> What do you get with -verbose?
> 
> Abel
> 
> On 4 Aug 2010, at 19:49, Grace Cheng wrote:
> 
>> Hi Abel,
>> 
>>  
>> Thanks for your help. I get the things below:
>> 
>>  
>> [GraceCheng at bxiew Desktop]$ grep API_VERSION /src/ensembl/modules/Bio/EnsEMBL/Registry.pm
>> my $API_VERSION = 58;
>>   return $API_VERSION;
>>   if ( $database_version != $API_VERSION ) {
>>         $API_VERSION, $database_version
>>  
>> 
>> That mean I am in the right version, v58? I am really stuck in this point........
>> 
>>  
>> Grace
>> 
>> 
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> 
> __
> Abel Ureta-Vidal
> Eagle Genomics Ltd | E: abel at eaglegenomics.com
> http://www.eaglegenomics.com
> 
> 
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--
Michael Schuster
Ensembl Genome Browser
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire CB10 1SD
United Kingdom

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