I'm running the Sequest Pipeline just to validate that it is completing the pipeline. So I ran one of the CPASDemo files against a handy database (I think Mouse-Human, not yeast), using default params (not ICAT). I didn't expect good results but I did expect it to complete. I'm getting the error below. I've attached the pep.xml.

Thanks,
Bill

22 Oct 2007 23:36:52,718 DEBUG: Done creating FASTA record
22 Oct 2007 23:36:52,734 INFO : Finished loading protein annotations
22 Oct 2007 23:36:52,734 INFO : Loading took 81 seconds
22 Oct 2007 23:36:52,734 INFO : Loading MS/MS results is 0% complete
22 Oct 2007 23:36:52,765 INFO : Loading MS/MS results is 1% complete
22 Oct 2007 23:36:52,796 INFO : Loading MS/MS results is 2% complete
22 Oct 2007 23:36:52,828 INFO : Loading MS/MS results is 3% complete
22 Oct 2007 23:36:52,875 INFO : Loading MS/MS results is 4% complete
22 Oct 2007 23:36:52,906 INFO : Loading MS/MS results is 5% complete
22 Oct 2007 23:36:52,937 INFO : Loading MS/MS results is 6% complete
22 Oct 2007 23:36:52,968 INFO : Loading MS/MS results is 7% complete
22 Oct 2007 23:36:53,015 INFO : Loading MS/MS results is 8% complete
22 Oct 2007 23:36:53,046 INFO : Loading MS/MS results is 9% complete
22 Oct 2007 23:36:53,078 INFO : Loading MS/MS results is 10% complete
22 Oct 2007 23:36:53,125 INFO : Loading MS/MS results is 11% complete
22 Oct 2007 23:36:53,171 INFO : Loading MS/MS results is 12% complete
22 Oct 2007 23:36:53,203 INFO : Loading MS/MS results is 13% complete
22 Oct 2007 23:36:53,234 INFO : Loading MS/MS results is 14% complete
22 Oct 2007 23:36:53,265 INFO : Loading MS/MS results is 15% complete
22 Oct 2007 23:36:53,312 INFO : Loading MS/MS results is 16% complete
22 Oct 2007 23:36:53,343 INFO : Loading MS/MS results is 17% complete
22 Oct 2007 23:36:53,375 INFO : Loading MS/MS results is 18% complete
22 Oct 2007 23:36:53,406 INFO : Loading MS/MS results is 19% complete
22 Oct 2007 23:36:53,453 INFO : Loading MS/MS results is 20% complete
22 Oct 2007 23:36:53,484 INFO : Loading MS/MS results is 21% complete
22 Oct 2007 23:36:53,515 INFO : Loading MS/MS results is 22% complete
22 Oct 2007 23:36:53,546 ERROR: MS2 data upload failed
java.lang.NumberFormatException: null
    at java.lang.Integer.parseInt(Unknown Source)
    at java.lang.Integer.parseInt(Unknown Source)
    at org.labkey.common.tools.PepXmlLoader$PepXmlPeptide.processStartElement(PepXmlLoader.java:580)
    at org.labkey.common.tools.PepXmlLoader$PepXmlPeptide.load(PepXmlLoader.java:527)
    at org.labkey.common.tools.PepXmlLoader$PepXmlPeptide.getNextPeptide(PepXmlLoader.java:468)
    at org.labkey.common.tools.PepXmlLoader$PeptideIterator.hasNext(PepXmlLoader.java:375)
    at org.labkey.ms2.PepXmlImporter.uploadRun(PepXmlImporter.java:110)
    at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:189)
    at org.labkey.ms2.MS2Manager.uploadRun(MS2Manager.java:411)
    at org.labkey.ms2.MS2Manager.addRun(MS2Manager.java:402)
    at org.labkey.ms2.PepXmlExperimentDataHandler.importFile(PepXmlExperimentDataHandler.java:101)
    at org.labkey.experiment.XarReader.loadDataFile(XarReader.java:1065)
    at org.labkey.experiment.XarReader.loadDoc(XarReader.java:302)
    at org.labkey.experiment.XarReader.parseAndLoad(XarReader.java:105)
    at org.labkey.experiment.api.ExperimentServiceImpl.loadExperiment(ExperimentServiceImpl.java:493)
    at org.labkey.api.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:90)
    at org.labkey.ms2.pipeline.SequestPipelineJob.xinteract(SequestPipelineJob.java:568)
    at org.labkey.ms2.pipeline.SequestPipelineJob.search(SequestPipelineJob.java:329)
    at org.labkey.ms2.pipeline.AbstractMS2SearchPipelineJob.run(AbstractMS2SearchPipelineJob.java:276)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
22 Oct 2007 23:36:53,546 FATAL: Exception during load
java.lang.NumberFormatException: null
    at java.lang.Integer.parseInt(Unknown Source)
    at java.lang.Integer.parseInt(Unknown Source)
    at org.labkey.common.tools.PepXmlLoader$PepXmlPeptide.processStartElement(PepXmlLoader.java:580)
    at org.labkey.common.tools.PepXmlLoader$PepXmlPeptide.load(PepXmlLoader.java:527)
    at org.labkey.common.tools.PepXmlLoader$PepXmlPeptide.getNextPeptide(PepXmlLoader.java:468)
    at org.labkey.common.tools.PepXmlLoader$PeptideIterator.hasNext(PepXmlLoader.java:375)
    at org.labkey.ms2.PepXmlImporter.uploadRun(PepXmlImporter.java:110)
    at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:189)
    at org.labkey.ms2.MS2Manager.uploadRun(MS2Manager.java:411)
    at org.labkey.ms2.MS2Manager.addRun(MS2Manager.java:402)
    at org.labkey.ms2.PepXmlExperimentDataHandler.importFile(PepXmlExperimentDataHandler.java:101)
    at org.labkey.experiment.XarReader.loadDataFile(XarReader.java:1065)
    at org.labkey.experiment.XarReader.loadDoc(XarReader.java:302)
    at org.labkey.experiment.XarReader.parseAndLoad(XarReader.java:105)
    at org.labkey.experiment.api.ExperimentServiceImpl.loadExperiment(ExperimentServiceImpl.java:493)
    at org.labkey.api.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:90)
    at org.labkey.ms2.pipeline.SequestPipelineJob.xinteract(SequestPipelineJob.java:568)
    at org.labkey.ms2.pipeline.SequestPipelineJob.search(SequestPipelineJob.java:329)
    at org.labkey.ms2.pipeline.AbstractMS2SearchPipelineJob.run(AbstractMS2SearchPipelineJob.java:276)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
22 Oct 2007 23:36:53,546 FATAL: Upload FAILED