[ensembl-dev] ensj-41 chromosome Y
Alireza Khodabakhshi
alirezak at bcgsc.ca
Mon Apr 16 23:47:05 BST 2012
Hi,
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?
Thanks,
Apr 16, 2012 3:14:37 PM org.ensembl.driver.impl.BaseFeatureAdaptorImpl fetch
WARNING: empty idString for loc =
chromosome_GRCh37:Y:1-10000->chromosome_GRCh37:X:60001-2699520->chromosome_GRCh37:Y:2649521-59034049->chromosome_GRCh37:X:154931044-155270560
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
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