Hello
I was trying to query BioMart for Ensembl human genes from within Taverna
and this produced this error:
lookinf for oanatinus_snp
lookinf for oanatinus_snp
lookinf for oanatinus_snp
Apr 4, 2008 3:37:45 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException:
java.lang.IllegalArgumentException: Not supported: indent-number
Exception in thread "Thread-130" java.lang.OutOfMemoryError: Java heap space
at org.jdom.ContentList$FilterList.iterator(ContentList.java:595)
at
org.ensembl.mart.lib.config.DatasetConfigXMLUtils.getOption(DatasetConfigXMLUtils.java:425)
at
org.ensembl.mart.lib.config.DatasetConfigXMLUtils.getFilterDescription(DatasetConfigXMLUtils.java:477)
at
org.ensembl.mart.lib.config.DatasetConfigXMLUtils.getFilterCollection(DatasetConfigXMLUtils.java:415)
at
org.ensembl.mart.lib.config.DatasetConfigXMLUtils.getFilterGroup(DatasetConfigXMLUtils.java:399)
at
org.ensembl.mart.lib.config.DatasetConfigXMLUtils.getFilterPage(DatasetConfigXMLUtils.java:384)
at
org.ensembl.mart.lib.config.DatasetConfigXMLUtils.loadDatasetConfigWithDocument(DatasetConfigXMLUtils.java:343)
at
org.biomart.martservice.MartServiceUtils.getDatasetConfig(MartServiceUtils.java:296)
at
org.biomart.martservice.MartService.getDatasetConfigFromCache(MartService.java:371)
at
org.biomart.martservice.MartService.getDatasetConfig(MartService.java:311)
at
org.biomart.martservice.MartService.getExportables(MartService.java:421)
at
org.biomart.martservice.MartService.getLinkableDatasets(MartService.java:472)
at
org.biomart.martservice.config.ui.MartServiceQueryConfigUIFactory$DatasetLinkComponent$2.run(MartServiceQueryConfigUIFactory.java:2597)
I tried 3 times and got 3 times the error so this seems reproducible.
I normally have no problem doing complex queries on BioMart from within
other workflow tools like Galaxy, so this might be a problem with
Taverna... however the error does not appear when I query the MSD
databaset, so the problem might lie somewhere else?
best regards,
Isabelle
--
Isabelle Phan, D.Phil.
Swiss Institute of Bioinformatics Tel: (+41 22) 379 51 89
CMU - 1, rue Michel Servet Fax: (+41 22) 379 58 58
CH - 1211 Geneva 4 Switzerland email: [EMAIL PROTECTED]
