[DAS] Need help about ProServer error

陈岗 danielchen06 at gmail.com
Tue Jun 12 07:47:15 UTC 2012

Hi All

I follow ProServer tutorial Part 3 (
http://www.ebi.ac.uk/~aj/das_workshop_2012/proserver/tutorial3.html ), try
to get the gene-exon data, but an error occurs. The SQl sentence is
correct, I tried it on MySQL server.  what is the problem?

Bad data source exonsdb (error processing command: 'features')

The error was: 'Error running query: DBD::mysql::st execute failed:
called with 3 bind variables when 0 are needed at
blib/lib/Bio/Das/ProServer/SourceAdaptor/Transport/dbi.pm line 77.

Args were: Bio::Das::ProServer::SourceAdaptor::Transport::dbi=HASH(0xbc99e8)
select sr.name AS chromosome,
       g.stable_id AS g_id, g.seq_region_start AS g_start,
g.seq_region_end AS g_end,
       t.stable_id AS t_id, t.seq_region_start AS t_start,
t.seq_region_end AS t_end,
       e.stable_id AS e_id, e.seq_region_start AS e_start,
e.seq_region_end AS e_end
from   seq_region sr, coord_system c,gene g,transcript t,
exon_transcript et, exon e
where sr.seq_region_id = g.seq_region_id
and g.gene_id = t.gene_id
and t.transcript_id = et.transcript_id
and sr.name = 'Y'
and sr.coord_system_id = c.coord_system_id
and c.name = 'chromosome'
and c.version = 'GRCh37'
and g.seq_region_end >= 1
and g.seq_region_start <= 59373566
and e.exon_id = et.exon_id
 Y 2800000 2900000
 at blib/lib/Bio/Das/ProServer/SourceAdaptor/EnsExon.pm line 38.'

Best Regards


Gang Chen
Taicang Institute For Life Science Information
Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province,

More information about the DAS mailing list