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

[Jianguo Lu]

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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