[ensembl-dev] Ensembl plants miss a table

Nick Langridge nickl at ebi.ac.uk
Wed Aug 7 10:17:19 BST 2013

Hi Daniel,

It looks like SQL shown in your error was dropped from the EG codebase 
for version 18-71 and above.
Please check that your eg-plugins/common dir is using 

Specifically, check that the following file is no longer present in your 

You may want to try removing/backing-up you existing eg-plugins/common 
dir and getting a fresh checkout:
cvs co -r branch-ensemblgenomes-19-72 eg-plugins/common

I hope this solves the problem.


On 02/08/2013 04:51, ?? wrote:
> Hi Ensembl developers
> Our plants mirror misses a database 
> table,'ensembl_compara_plants_19_72.gene_tree_member' which doesn't 
> exist on your ftp server.
> MSG: Cannot run '
> 	select dbprimary_acc,count(*) as cnt from gene_tree_root r
> 	join gene_tree_node n using (root_id) join gene_tree_member gm using (node_id)	
> 	join member m using (member_id)
> 	join member_xref mg on (m.gene_member_id=mg.member_id)	
> 	where r.root_id=? and mg.db_name=?
> 	group by dbprimary_acc,db_name order by cnt desc, dbprimary_acc asc
> 	' with params '261020 GO' due to error: DBD::mysql::st execute failed: Table
> 	... 'ensembl_compara_plants_19_72.gene_tree_member' doesn't exist at
> 	... /usr/local/ensembl_plants/ensembl/modules/Bio/EnsEMBL/Utils/SqlHelper.pm line 1003.
> Please check
> Thanks million.
> -- 
> Gang Chen
> Taicang Institute For Life Science Information
> Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province, 
> P.R.China
> Phone: (+86)512-82782588
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