[ensembl-dev] ensj-41 chromosome Y

Alireza Khodabakhshi alirezak at bcgsc.ca
Mon Apr 16 23:47:05 BST 2012

I am using the ensj-41.jar API set to retrieve annotations from the 
ensembl database. However when I try to fetch data for chromosome Y 
using the GeneAdaptor I get the following error. I am using core_66_37 
version (hg19). It works fine for the core_54_36p (hg18). Any help?

Apr 16, 2012 3:14:37 PM org.ensembl.driver.impl.BaseFeatureAdaptorImpl fetch
WARNING: empty idString for loc = 
Error:     Could not fetch from Exon Adaptor.
Error:     Message from Java environment (could be null): Failed to 
execute sql against database homo_sapiens_core_66_37:SELECT e.exon_id, 
e.seq_region_id, e.seq_region_start, e.seq_region_end, 
e.seq_region_strand, e.phase, e.end_phase, esi.stable_id, esi.version, 
esi.created_date, esi.modified_date FROM exon e  LEFT JOIN 
exon_stable_id esi ON esi.exon_id = e.exon_id WHERE e.seq_region_id IN 
()  [41-BCGSC]; nested exception is:
        com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: You 
have an error in your SQL syntax; check the manual that corresponds to 
your MySQL server version for the right syntax to use near ')' at line 1

More information about the Dev mailing list