[ensembl-dev] Question on using ensembl-compara to extract homology alignment

[William Spooner]

Can you try updating your Perl DBI and DBD::mysql modules to the latest versions from CPAN? This looks a lot like a problem we had a few years back with those modules.

Best,

Will

On 29 Jul 2011, at 20:40, Jianguo Lu wrote:

> Hello, 
> 
> I used this command to do the homology alignment and got some error information. I am sure there is the GenomeDBAdaptor in my computer. Could you help me to fix this problem? Appreciate it!
> 
> Best Regards,
> Jianguo Lu
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> perl getHomologyAlignment.pl -dbhost ensembldb.ensembl.org -dbname ensembl_compara_51 -dbuser anonymous -dbport 5306 -sp sapiens -g ENSG00000004059
> 
> -------------------- WARNING ----------------------
> MSG: Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor cannot be found.
> Exception Bareword "SQL_VARCHAR" not allowed while "strict subs" in use at /home/catfish/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm line 278.
> Bareword "SQL_VARCHAR" not allowed while "strict subs" in use at /home/catfish/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm line 279.
> Bareword "SQL_INTEGER" not allowed while "strict subs" in use at /home/catfish/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm line 280.
> Bareword "SQL_TINYINT" not allowed while "strict subs" in use at /home/catfish/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm line 281.
> Bareword "SQL_VARCHAR" not allowed while "strict subs" in use at /home/catfish/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm line 282.
> Bareword "SQL_VARCHAR" not allowed while "strict subs" in use at /home/catfish/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm line 283.
> Compilation failed in require at (eval 46) line 3.
> 
> 
> FILE: Bio/EnsEMBL/Registry.pm LINE: 502
> CALLED BY: EnsEMBL/DBSQL/DBAdaptor.pm  LINE: 713
> ---------------------------------------------------
> 
> -------------------- WARNING ----------------------
> MSG: Could not find GenomeDB adaptor in the registry for DEFAULT compara
> 
> FILE: EnsEMBL/DBSQL/DBAdaptor.pm LINE: 719
> CALLED BY: EnsEMBL/Compara/Member.pm  LINE: 488
> ---------------------------------------------------
> Can't call method "fetch_by_dbID" on an undefined value at /home/catfish/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/Member.pm line 489.
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--
William Spooner
whs at eaglegenomics.com
http://www.eaglegenomics.com