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Protein prophet import fails

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Protein prophet import fails roland.luethy  2007-05-23 11:30
Status: Closed
 
Importing data fails during loading the .prot.xml file with the following error message:

23 May 2007 00:15:07,874 INFO : Starting to load ProteinProphet file /stf/scratch/cluster/cpas/U54_A431/WholeCellLysate/Iressa_2h/xtandem/SILAC_K_Xpress/A431_TotExtract_SILAC_Frac37to48.prot.xml
23 May 2007 00:15:08,062 INFO : Resolved referenced PepXML file to /stf/scratch/cluster/cpas/U54_A431/WholeCellLysate/Iressa_2h/xtandem/SILAC_K_Xpress/A431_TotExtract_SILAC_Frac37to48.pep.xml
23 May 2007 00:15:08,126 INFO : A431_TotExtract_SILAC_Frac37to48.pep.xml has already been loaded so it does not need to be reloaded
23 May 2007 00:15:11,746 ERROR: Failed when importing group 350
23 May 2007 00:15:11,750 FATAL: Exception during load
org.labkey.api.exp.XarFormatException: org.labkey.api.exp.ExperimentException: java.sql.BatchUpdateException: Batch entry 614 INSERT INTO PeptideMembershipsTemp619180532 VALUES (TIGGGDDSFNTFFSETGAGK, 2, 2259101, 1.0, 0.0, 0, 2, 0.42, 2, 1, 0, 2006.8857) was aborted. Call getNextException to see the cause.
    at org.labkey.experiment.XarReader.loadDataFile(XarReader.java:986)

The complete log file is attached. The failure seems data dependent, since some files in the same directory import correctly.

We are using Labkey server Version 2.0 on Linux.

Any suggestions?
Thanks

Roland
 
 
jeckels responded:  2007-05-23 17:50
The error log indicates that the problem happened when failure happened when loading protein group 350, but unfortunately the full error didn't get logged. Can you post the XML from the ProteinProphet file (/stf/scratch/cluster/cpas/U54_A431/WholeCellLysate/Iressa_2h/xtandem/SILAC_K_Xpress/A431_TotExtract_SILAC_Frac37to48.prot.xml) for group numbers 349 and 350?

Thanks,
Josh
 
roland.luethy responded:  2007-05-25 09:57
Josh,

    We had a bunch of other runs which loaded fine and I tried to re-load the files that failed before, but now I don't get the error anymore. Maybe you should close this issue for now.

Thanks

Roland
 
jeckels responded:  2007-05-25 09:59
OK, thanks for the update. Please let us know if you see the problem again.

Thanks,
Josh