From the error message in the log, CPAS is failing to parse the pep.xml file. There's a problem on line 339. If you take a look, it might give you a pointer as to the cause of the problem. Also, can you attach the file, or at least the first 500 lines if it's very large?

Yes, line 339 is:

<parameter name="pipeline, protocol description" value="<note type=" input" label="protein, cleavage semi">

which is not valid XML. You can fix this file by changing it to:

<parameter name="pipeline, protocol description" value="protein, cleavage semi"/>

You should also edit /protocols/xtandem/Partial.xml to change:

  <note label="pipeline, protocol description" type="input">&lt;note type="input" label="protein, cleavage semi"&gt;yes&lt;/note&gt;</note>

to:

  <note label="pipeline, protocol description" type="input">protein, cleavage semi</note>

Or this will happen every time you use that protocol. Apparently the pipeline doesn't like it when you put XML tags in your protocol description.

I will post a bug here, but try to stay away from <> in your protocol description until you get our next release.

Thank you very much.

Here's the link to the whole files xtan.xml. pep.xml. prot.xml

http://binf.gmu.edu/wmoon/MF-pl1011-Dec05.zip

I will fix that line, try to load again. Thank you.

I fixed the line 339 and partial.xml as you said, but another error message I got.
I checked the line 59262 in pep.xml and prot.xml. I don't see something wrong. You can find the lines if you download the files from the link in my previous post. Thank you.

26 Jan 2007 16:36:19,107 INFO : Finished trying to load data file file:/proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.pep.xml into the system
26 Jan 2007 16:36:19,109 INFO : Trying to load data file file:/proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.pep.xml into the system
26 Jan 2007 16:36:19,139 INFO : Finished trying to load data file file:/proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.pep.xml into the system
26 Jan 2007 16:36:19,142 INFO : Trying to load data file file:/proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.prot.xml into the system
26 Jan 2007 16:36:19,151 INFO : Starting to load ProteinProphet file /proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.prot.xml
26 Jan 2007 16:36:19,157 INFO : Resolved referenced PepXML file to /proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.pep.xml
26 Jan 2007 16:36:19,166 INFO : MFL25-101906-pl1011.pep.xml has already been loaded so it does not need to be reloaded
26 Jan 2007 16:36:55,919 INFO : Loaded 50 protein groups...
26 Jan 2007 16:37:11,204 INFO : Loaded 100 protein groups...
26 Jan 2007 16:37:21,184 INFO : Loaded 150 protein groups...
26 Jan 2007 16:37:30,941 INFO : Loaded 200 protein groups...
26 Jan 2007 16:37:34,015 FATAL: Exception during load
org.fhcrc.cpas.exp.XarFormatException: org.fhcrc.cpas.exp.ExperimentException: com.ctc.wstx.exc.WstxParsingException: Unexpected '<' in attribute value
 at [row,col {unknown-source}]: [59262,10]
    at org.fhcrc.cpas.exp.XarReader.loadDataFile(XarReader.java:925)
    at org.fhcrc.cpas.exp.XarReader.loadDoc(XarReader.java:340)
    at org.fhcrc.cpas.exp.XarReader.parseAndLoad(XarReader.java:164)
    at org.fhcrc.cpas.exp.XarReader.uploadRun(XarReader.java:116)
    at org.fhcrc.cpas.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:124)
    at org.fhcrc.cpas.exp.ExperimentPipelineJob.run(ExperimentPipelineJob.java:133)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
    at java.util.concurrent.FutureTask.run(FutureTask.java:123)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:168)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
    at java.lang.Thread.run(Thread.java:595)
Caused by: org.fhcrc.cpas.exp.ExperimentException: com.ctc.wstx.exc.WstxParsingException: Unexpected '<' in attribute value
 at [row,col {unknown-source}]: [59262,10]
    at org.fhcrc.cpas.ms2.ProteinProphetExperimentDataHandler.importFile(ProteinProphetExperimentDataHandler.java:36)
    at org.fhcrc.cpas.exp.XarReader.loadDataFile(XarReader.java:921)
    ... 13 more
Caused by: com.ctc.wstx.exc.WstxParsingException: Unexpected '<' in attribute value
 at [row,col {unknown-source}]: [59262,10]
    at com.ctc.wstx.sr.StreamScanner.throwParseError(StreamScanner.java:396)
    at com.ctc.wstx.sr.WstxStreamReader.parseNormalizedAttrValue(WstxStreamReader.java:1834)
    at com.ctc.wstx.sr.WstxStreamReader.handleNsAttrs(WstxStreamReader.java:2862)
    at com.ctc.wstx.sr.WstxStreamReader.handleStartElem(WstxStreamReader.java:2767)
    at com.ctc.wstx.sr.WstxStreamReader.nextFromTree(WstxStreamReader.java:2691)
    at com.ctc.wstx.sr.WstxStreamReader.next(WstxStreamReader.java:971)
    at org.fhcrc.cpas.tools.XMLStreamReaderWrapper.next(XMLStreamReaderWrapper.java:246)
    at org.fhcrc.cpas.tools.ProtXmlReader$Protein.loadChildren(ProtXmlReader.java:162)
    at org.fhcrc.cpas.tools.ProtXmlReader$Protein.<init>(ProtXmlReader.java:155)
    at org.fhcrc.cpas.tools.ProteinGroup.getProteins(ProteinGroup.java:109)
    at org.fhcrc.cpas.ms2.ProteinProphetImporter.importFile(ProteinProphetImporter.java:115)
    at org.fhcrc.cpas.ms2.ProteinProphetExperimentDataHandler.importFile(ProteinProphetExperimentDataHandler.java:28)
    ... 14 more
26 Jan 2007 16:37:34,019 FATAL: Upload FAILED

Well, at line 59261 (the line about where the error is reported) I see:

         <annotation protein_description="2" num_tot_proteins="/>

I have no idea why ProteinProphet would write this line. It sure looks corrupted. You might want to see if this happens every time you run this. If so, then report to the Sashimi project.

You should be able to fix this quickly by changing the line to:

         <annotation protein_description="2" num_tot_proteins="1"/>