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
