Hi Denny,
can you execute the same query in reverse order - by swapping the
dataset order ? what happens when you do this ?
syed
On Thu, 2008-05-29 at 08:02 -0400, Chan, Denny (NIH/NCI) [C] wrote:
> When joining two datasets, the BioMart ran a batch iteration for both
> datasets. But when it reached to the end of first dataset, it still
> tried to query the second dataset with a invalid SQL statement. Here is
> what in the log file
>
>
> ========================================================================
> ====================================================
> BioMart.Dataset.TableSet:735:WARN> QUERY SQL: SELECT main.seqid,
> main.charge FROM cpas2biomart.peptidesview__peptidesview
> __main main LIMIT 50000 OFFSET 9815643
> BioMart.DatasetI:1175:DEBUG> Got no results
> BioMart.DatasetI:1261:DEBUG> Attribute hash
> BioMart.DatasetI:1262:DEBUG> Before hash: 0
> BioMart.DatasetI:1269:DEBUG> After hash: 0
> BioMart.Dataset.TableSet:735:WARN> QUERY SQL: SELECT main.seqid_key,
> main.bestname, main.length, main.mass, main.descript
> ion, main.seqid_key FROM
> cpas2biomart.protsequencesview__protsequences__main main WHERE
> (main.seqid_key = '96305') AND (ma
> in.seqid_key IN('')) LIMIT 400
> DBD::Pg::st execute failed: ERROR: invalid input syntax for integer: ""
> BioMart.Web:2228:DEBUG> Serious error: Error during query execution:
> ERROR: invalid input syntax for integer: ""
> ========================================================================
> ======================================================
>
>
> The first dataset "peptidesview__peptidesview" has 9815643 records.
> The first SQL statement will return zero record, which leads to an empty
> IN clause in the second SQL statement.
>
>
> Does anyone know the fix for this problem?
>
> Thanks,
> Denny Chan
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
