[ensembl-dev] Bulk download of Microarray Probe mapping via MySQL

[Alex Holman]

Hi Thomas and Nathan,

Thanks for your input. I'm still having a couple of issues.

When I run the command you pasted above:

perl ../ensembl_scripts/dump_array_annotations.pl \
 -user anonymous \
 -port 3306 \
 -host ensembldb.ensembl.org \
 -dbname homo_sapiens_funcgen_72_37 \
 -dnadb_user anonymous\
 -dnadb_port 3306 \
 -dnadb_host useastdb.ensembl.org \
 -dnadb_name homo_sapiens_core_72_37 \
 -arrays HuGene-1_0-st-v1 \
 -features

I still get a whole cascade of errors, which I have included below under the header # Error list 1.  However, my guess is that the root issue is in one of the first errors thrown:

Could not connect to database homo_sapiens_funcgen_72_37 as user anonymous using [DBI:mysql:database=homo_sapiens_funcgen_72_37;host=ensembldb.ensembl.org;port=3306] as a locator:

It seems to me that the script is having trouble making the initial database connection.  This is strange to me, because I can get the script to work on the virtual box version, after I install mysql with: 'sudo apt-get install mysql-client-core-5.5'.

At this point, I'm not sure what would be functionally different between the two boxes, mine (mac 10.8, mysql client version 5.6.12, ensembl-api v.72) and the virtual box (ubuntu probably netbook edition, mysql client version 5.5.31, ensembl-api v.72).  On my machine I can successfully connect to the ensembl servers directly with 'mysql --user='anonymous' -hensembldb.ensembl.org --port=3306 homo_sapiens_funcgen_72_37'
Any thoughts on what the issue might be?

Thanks,
-Alex-


# Error list 1
---------------
dhcp-155-52-120-81:test_Ensembl_script alex$ perl ../ensembl_scripts/dump_array_annotations.pl \
>  -user anonymous \
>  -port 3306 \
>  -host ensembldb.ensembl.org \
>  -dbname homo_sapiens_funcgen_72_37 \
>  -dnadb_user anonymous\
>  -dnadb_port 3306 \
>  -dnadb_host useastdb.ensembl.org \
>  -dnadb_name homo_sapiens_core_72_37 \
>  -arrays HuGene-1_0-st-v1 \
>  -features
Setting name at /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm line 344.
Could not connect to database homo_sapiens_funcgen_72_37 as user anonymous using [DBI:mysql:database=homo_sapiens_funcgen_72_37;host=ensembldb.ensembl.org;port=3306] as a locator:

-------------------- EXCEPTION --------------------
MSG: Cannot run 'select meta_value from meta where meta_key =?' with params 'species.production_name' due to error: 
-------------------- EXCEPTION --------------------
MSG: Could not connect to database homo_sapiens_funcgen_72_37 as user anonymous using [DBI:mysql:database=homo_sapiens_funcgen_72_37;host=ensembldb.ensembl.org;port=3306] as a locator:

STACK Bio::EnsEMBL::DBSQL::DBConnection::connect /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:321
STACK Bio::EnsEMBL::DBSQL::DBConnection::db_handle /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:675
STACK Bio::EnsEMBL::DBSQL::DBConnection::prepare /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:706
STACK (eval) /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/Utils/SqlHelper.pm:999
STACK Bio::EnsEMBL::Utils::SqlHelper::_base_execute /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/Utils/SqlHelper.pm:996
STACK Bio::EnsEMBL::Utils::SqlHelper::_execute /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/Utils/SqlHelper.pm:952
STACK Bio::EnsEMBL::Utils::SqlHelper::execute_simple /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/Utils/SqlHelper.pm:303
STACK Bio::EnsEMBL::Utils::SqlHelper::execute_single_result /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/Utils/SqlHelper.pm:496
STACK Bio::EnsEMBL::Utils::ConfigRegistry::pre_funcgen_hook /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm:345
STACK Bio::EnsEMBL::Utils::ConfigRegistry::gen_load /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm:148
STACK Bio::EnsEMBL::DBSQL::DBAdaptor::new /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm:148
STACK Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor::new /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/DBAdaptor.pm:153
STACK Bio::EnsEMBL::Funcgen::Utils::DBAdaptorHelper::create_DBAdaptor_from_params /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/Utils/DBAdaptorHelper.pm:385
STACK Bio::EnsEMBL::Funcgen::Utils::DBAdaptorHelper::create_Funcgen_DBAdaptor_from_options /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/Utils/DBAdaptorHelper.pm:282
STACK toplevel ../ensembl_scripts/dump_array_annotations.pl:114
Date (localtime)    = Fri Jul 19 12:04:16 2013
Ensembl API version = 73
---------------------------------------------------

STACK Bio::EnsEMBL::Utils::SqlHelper::_base_execute /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/Utils/SqlHelper.pm:1007
STACK Bio::EnsEMBL::Utils::SqlHelper::_execute /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/Utils/SqlHelper.pm:952
STACK Bio::EnsEMBL::Utils::SqlHelper::execute_simple /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/Utils/SqlHelper.pm:303
STACK Bio::EnsEMBL::Utils::SqlHelper::execute_single_result /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/Utils/SqlHelper.pm:496
STACK Bio::EnsEMBL::Utils::ConfigRegistry::pre_funcgen_hook /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm:345
STACK Bio::EnsEMBL::Utils::ConfigRegistry::gen_load /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm:148
STACK Bio::EnsEMBL::DBSQL::DBAdaptor::new /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm:148
STACK Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor::new /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/DBAdaptor.pm:153
STACK Bio::EnsEMBL::Funcgen::Utils::DBAdaptorHelper::create_DBAdaptor_from_params /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/Utils/DBAdaptorHelper.pm:385
STACK Bio::EnsEMBL::Funcgen::Utils::DBAdaptorHelper::create_Funcgen_DBAdaptor_from_options /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/Utils/DBAdaptorHelper.pm:282
STACK toplevel ../ensembl_scripts/dump_array_annotations.pl:114
Date (localtime)    = Fri Jul 19 12:04:16 2013
Ensembl API version = 73
---------------------------------------------------
dhcp-155-52-120-81:test_Ensembl_script alex$