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Question about X! tendem parameters

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Question about X! tendem parameters wonjong.moon  2006-11-13 12:49
Status: Closed
 
1. I would like know all the default parameters for X! tendem search in CPAS
e.g. tryptic cleavage, 2.0 parent mass error range, etc.

2. I would like to search for all peptides cleavage not restricted to tryptic cleavage, which parameter should I override?

Thank you.

Wonjong
 
 
wongch responded:  2006-11-14 03:24
  1. You can find the information at Wiki Configure X! Tandem Parameters. To get the defaults used, you can check out default_input.xml as per Wiki Set Up the Data Pipeline.
  2. Not too sure if this is what you are looking for… you might want to try "protein, cleavage semi" and/or "protein, cleavage site". See also http://www.thegpm.org/TANDEM/api/index.html as mentioned in Wiki Configure X! Tandem Parameters.
 
brendanx responded:  2006-11-14 04:23
To view the defaults:
- Click the "Setup" button in the "Data Pipeline" section.
- Click the "Set Defaults" link in the "X! Tandem specific settings section".
- You will find yourself on a page that contains the default parameters used for the search.
 
If you are using the "cluster pipeline" the "Set Defaults" setting will not be present, and you must instead look into the <pipeline bin>/tandem/default_input.xml file.
 
To specify "nonspecific cleavage" you can use the following:
 
<!-- Nonsecific cleavage search -->
<note type="input" label="protein, cleavage site">[X]|[X]</note>

If you specify only this parameter, then the Tandem2XML converter will calculate number of missed cleavages (NMC) assuming a Trypsin digest of the sample. If that is not really the digestion used on the sample you can use the following to specify something else:

<!-- Used Trypsin and GluC on sample -->
<note type="input" label="pipeline prophet, sample cleavage site">[DEKR]|{P}</note>
<!-- Nonsecific cleavage search -->
<note type="input" label="protein, cleavage site">[X]|[X]</note>

Finally, I would like to note that this unspecified searches are about 10-20 times slower than "semi-cleavage" searches (i.e. only a single end is forced to have the correct cleavage), and in my investigation the extra time seems of little benefit. If you have a ton of processor time to spare, then go for it. Otherwise, I suggest using:

<note type="input" label="protein, cleavage semi">yes</note>

instead.

Good luck.

--Brendan
 
wonjong.moon responded:  2006-11-17 14:29
I tried the following parameters, but I failed to upload mzXML files.
<!-- Nonsecific cleavage search -->
<note type="input" label="protein, cleavage site">[X]|[X]</note>

I attached a log file and screen capture for parameter setting. Would you see if I did it correctly, please?
----------------------------------------------------------------------------------------------------
17 Nov 2006 13:43:08,110 INFO : X! Tandem search for DSL01-081506-TZ-0199-GEL-FT-13.mzXML
17 Nov 2006 13:43:08,114 INFO : =======================================
17 Nov 2006 13:43:08,179 INFO : tandem.exe output
17 Nov 2006 13:43:08,184 INFO : =======================================
17 Nov 2006 13:43:08,185 INFO : running: tandem.exe input.xml
17 Nov 2006 13:43:08,371 INFO :
17 Nov 2006 13:43:08,376 INFO : X! TANDEM 2 (2006.09.15.1)
17 Nov 2006 13:43:08,380 INFO :
17 Nov 2006 13:43:13,690 INFO : Loading spectra ...... loaded.
17 Nov 2006 13:43:13,693 INFO : Spectra matching criteria = 11957
17 Nov 2006 13:43:13,696 INFO : Pluggable scoring enabled.
17 Nov 2006 13:43:13,699 INFO : Starting threads . started.
17 Nov 2006 13:43:13,702 INFO : Computing models:
17 Nov 2006 13:43:13,705 INFO :
17 Nov 2006 13:49:19,695 INFO : Spectrum-to-sequence matching process in progress | 50 ks
17 Nov 2006 13:54:59,739 INFO : Spectrum-to-sequence matching process in progress | 100 ks
17 Nov 2006 13:56:59,603 INFO : Spectrum-to-
17 Nov 2006 13:56:59,618 INFO :
17 Nov 2006 13:56:59,622 INFO : kilosequences modelled = 111
17 Nov 2006 13:56:59,697 INFO : Model refinement:
17 Nov 2006 13:56:59,700 INFO : Creating report:
17 Nov 2006 13:56:59,783 INFO :     initial calculations ..... done.
17 Nov 2006 13:56:59,788 INFO :     sorting ..... done.
17 Nov 2006 13:57:13,071 INFO :     finding repeats ..... done.
17 Nov 2006 13:57:13,078 INFO :     evaluating results ..... done.
17 Nov 2006 13:57:13,685 INFO :     calculating expectations ..... done.
17 Nov 2006 13:57:22,078 INFO :     writing results ..... done.
17 Nov 2006 13:57:22,156 INFO :
17 Nov 2006 13:57:22,158 INFO : Valid models = 238
17 Nov 2006 13:57:22,161 INFO :
17 Nov 2006 13:57:22,164 INFO :
17 Nov 2006 13:57:22,561 INFO : Tandem2XML output
17 Nov 2006 13:57:22,567 INFO : =======================================
17 Nov 2006 13:57:22,570 INFO : running: Tandem2XML /proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13.xtan.xml /proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13-raw.pep.xml
17 Nov 2006 13:57:27,783 INFO : xinteract output
17 Nov 2006 13:57:27,786 INFO : =======================================
17 Nov 2006 13:57:27,788 INFO : running: xinteract -p0 -Opt -nR -NDSL01-081506-TZ-0199-GEL-FT-13.pep.xml /proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13-raw.pep.xml
17 Nov 2006 13:57:27,857 INFO :
17 Nov 2006 13:57:27,859 INFO : /usr/local/tpp/bin/xinteract (TPP v2.9 GALE rev.3, Build 200610171545)
17 Nov 2006 13:57:27,862 INFO :
17 Nov 2006 13:57:27,865 INFO : running: "InteractParser DSL01-081506-TZ-0199-GEL-FT-13.pep.xml '/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13-raw.pep.xml'"
17 Nov 2006 13:57:27,886 INFO : file 1: /proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13-raw.pep.xml
17 Nov 2006 13:57:36,620 INFO : processed altogether 10506 results
17 Nov 2006 13:57:40,995 INFO : command completed in 13 sec
17 Nov 2006 13:57:41,017 INFO :
17 Nov 2006 13:57:41,031 INFO : running: "PeptideProphetParser DSL01-081506-TZ-0199-GEL-FT-13.pep.xml MINPROB=0"
17 Nov 2006 13:57:41,034 INFO : (X! Tandem) (minprob 0)
17 Nov 2006 13:57:41,038 INFO : init with X! Tandem trypsin
17 Nov 2006 13:57:46,272 INFO : MS Instrument info: Manufacturer: ThermoFinnigan, Model: LTQ, Ionization: ESI, Analyzer: Ion Trap, Detector: EMT
17 Nov 2006 13:57:46,277 INFO :
17 Nov 2006 13:57:46,283 INFO : PeptideProphet v3.0 April 1, 2004 (TPP v2.9 GALE rev.3, Build 200610171545) AKeller@ISB
17 Nov 2006 13:57:46,287 INFO : read in 1371 1+, 4546 2+, and 4589 3+ spectra
17 Nov 2006 13:57:46,519 INFO : iteration 1 2 3 4 5 6 7 8 9 10 11 12 13 model complete after 14 iterations
17 Nov 2006 13:57:56,373 INFO : command completed in 16 sec
17 Nov 2006 13:57:56,379 INFO :
17 Nov 2006 13:57:56,380 INFO : running: ""ProteinProphet.pl" DSL01-081506-TZ-0199-GEL-FT-13.pep.xml DSL01-081506-TZ-0199-GEL-FT-13.pep-prot.shtml XML_INPUT NOPLOT"
17 Nov 2006 13:57:56,783 INFO :
17 Nov 2006 13:57:56,787 INFO : ProteinProphet.pl v2.0 (TPP v2.9 GALE rev.3, Build 200610171545) AKeller August 15, 2003 (xml input) (using degen pep info)
17 Nov 2006 13:57:56,789 INFO : Calling /usr/local/tpp/bin/DatabaseParser "/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13.pep.xml"
17 Nov 2006 13:57:59,129 INFO : processing /proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13.pep.xml ... read in 39 1+, 297 2+, and 0 3+ spectra with min prob 0.05
17 Nov 2006 13:58:02,544 INFO : Reading results.
17 Nov 2006 13:58:02,564 INFO : sh: batchcoverage: command not found
17 Nov 2006 13:58:03,082 INFO : command completed in 7 sec
17 Nov 2006 13:58:03,086 INFO : InteractParser DSL01-081506-TZ-0199-GEL-FT-13.pep.xml '/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/DSL01-081506-TZ-0199-GEL-FT-13.work/DSL01-081506-TZ-0199-GEL-FT-13-raw.pep.xml' 13 sec
17 Nov 2006 13:58:03,088 INFO : PeptideProphetParser DSL01-081506-TZ-0199-GEL-FT-13.pep.xml MINPROB=0 16 sec
17 Nov 2006 13:58:03,089 INFO : "ProteinProphet.pl" DSL01-081506-TZ-0199-GEL-FT-13.pep.xml DSL01-081506-TZ-0199-GEL-FT-13.pep-prot.shtml XML_INPUT NOPLOT 7 sec
17 Nov 2006 13:58:03,091 INFO : job completed in 36 sec
17 Nov 2006 13:58:03,184 INFO : Existing protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MarkRunOutput:2' is referenced by other experiment runs, so it cannot be updated
17 Nov 2006 13:58:03,207 INFO : Finished loading Experiment with LSID 'urn:lsid:sbri.org:Experiment.Folder-52:DefaultExperiment'
17 Nov 2006 13:58:03,243 INFO : Finished loading Protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XTandemSearch:2'
17 Nov 2006 13:58:03,261 INFO : Finished loading Protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.ConvertToPepXml:2'
17 Nov 2006 13:58:03,281 INFO : Finished loading Protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XInteract.PeptideProphet:2'
17 Nov 2006 13:58:03,303 INFO : Finished loading Protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XInteract.ProteinProphet:2'
17 Nov 2006 13:58:03,325 INFO : Finished loading Protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XTandemAnalysis:3'
17 Nov 2006 13:58:03,334 INFO : Finished loading Protocol with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MarkRunOutput:2'
17 Nov 2006 13:58:03,426 INFO : Found an existing entry for Data LSID urn:lsid:sbri.org:Data.Folder-52-Xar-58947dac-4c10-1029-b4e8-f528764dc076:..%2FDSL01-081506-TZ-0199-GEL-FT-13.mzXML, not reloading its values from scratch
17 Nov 2006 13:58:03,428 INFO : Finished loading Data with LSID 'urn:lsid:sbri.org:Data.Folder-52-Xar-58947dac-4c10-1029-b4e8-f528764dc076:..%2FDSL01-081506-TZ-0199-GEL-FT-13.mzXML'
17 Nov 2006 13:58:03,450 INFO : Finished loading Data with LSID 'urn:lsid:sbri.org:Data.Folder-52-Xar-58947db4-4c10-1029-b4e8-f528764dc076:tandem.xml'
17 Nov 2006 13:58:03,467 INFO : Finished loading Data with LSID 'urn:lsid:sbri.org:Data.Folder-52-Xar-58947db4-4c10-1029-b4e8-f528764dc076:..%2F..%2F..%2Fdatabases%2Fsequences_HuPf_052506.fasta'
17 Nov 2006 13:58:03,603 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XTandemAnalysis:3'
17 Nov 2006 13:58:03,681 INFO : Finished loading Data with LSID 'urn:lsid:sbri.org:Data.Run-157:XTanFile'
17 Nov 2006 13:58:03,683 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XTandemSearch:2'
17 Nov 2006 13:58:03,716 INFO : Finished loading Data with LSID 'urn:lsid:sbri.org:Data.Run-157:PepXmlFile'
17 Nov 2006 13:58:03,718 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.ConvertToPepXml:2'
17 Nov 2006 13:58:03,748 INFO : Finished loading Data with LSID 'urn:lsid:sbri.org:Data.Run-157:ScoredPepXmlFile'
17 Nov 2006 13:58:03,750 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XInteract.PeptideProphet:2'
17 Nov 2006 13:58:03,783 INFO : Finished loading Data with LSID 'urn:lsid:sbri.org:Data.Run-157:ProteinScoresFile'
17 Nov 2006 13:58:03,784 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MS2.XInteract.ProteinProphet:2'
17 Nov 2006 13:58:03,802 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:sbri.org:Protocol.Folder-52:MarkRunOutput:2'
17 Nov 2006 13:58:03,804 INFO : Finished loading ExperimentRun with LSID 'urn:lsid:sbri.org:ExperimentRun.Folder-52:MS2-xtandem%2FNonSpecificSearch%2FDSL01-081506-TZ-0199-GEL-FT-13'
17 Nov 2006 13:58:03,808 INFO : Trying to load data file file:/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/tandem.xml into the system
17 Nov 2006 13:58:03,813 INFO : No experiment data handler registered for mime type text/xml on file file:/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/tandem.xml, no special loading will be done on this file.
17 Nov 2006 13:58:03,815 INFO : Finished trying to load data file file:/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/tandem.xml into the system
17 Nov 2006 13:58:03,817 INFO : Trying to load data file file:/proteomics/Duffy/CPASPiplineRoot/databases/sequences_HuPf_052506.fasta into the system
17 Nov 2006 13:58:03,821 ERROR: The data file /proteomics/Duffy/CPASPiplineRoot/databases/sequences_HuPf_052506.fasta is not under the folder's pipeline root, file:/proteomics/Duffy/CPASPiplineRoot/wj/. It will not be loaded.
17 Nov 2006 13:58:03,823 INFO : Trying to load data file file:/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/DSL01-081506-TZ-0199-GEL-FT-13.xtan.xml into the system
17 Nov 2006 13:58:03,827 INFO : No experiment data handler registered for mime type text/xml on file file:/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/DSL01-081506-TZ-0199-GEL-FT-13.xtan.xml, no special loading will be done on this file.
17 Nov 2006 13:58:03,829 INFO : Finished trying to load data file file:/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/DSL01-081506-TZ-0199-GEL-FT-13.xtan.xml into the system
17 Nov 2006 13:58:03,830 INFO : Trying to load data file file:/proteomics/Duffy/CPASPiplineRoot/wj/xtandem/NonSpecificSearch/DSL01-081506-TZ-0199-GEL-FT-13.pep.xml into the system
17 Nov 2006 13:58:03,882 INFO : prepareRun: Starting upload from "DSL01-081506-TZ-0199-GEL-FT-13.pep.xml"
17 Nov 2006 13:58:03,899 INFO : Clearing out existing MS2 data for DSL01-081506-TZ-0199-GEL-FT-13.pep.xml
17 Nov 2006 13:58:03,942 INFO : Finished clearing out existing MS2 data for DSL01-081506-TZ-0199-GEL-FT-13.pep.xml
17 Nov 2006 13:58:03,967 ERROR: XMLStreamException in next()
com.ctc.wstx.exc.WstxParsingException: Unexpected close tag </search_summary>; expected </parameter>.
 at [row,col {unknown-source}]: [367,16]
    at com.ctc.wstx.sr.StreamScanner.throwParseError(StreamScanner.java:396)
    at com.ctc.wstx.sr.WstxStreamReader.reportWrongEndElem(WstxStreamReader.java:3078)
    at com.ctc.wstx.sr.WstxStreamReader.readEndElem(WstxStreamReader.java:3020)
    at com.ctc.wstx.sr.WstxStreamReader.nextFromTree(WstxStreamReader.java:2682)
    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.PepXmlLoader$PepXmlFraction.handleSearchSummary(PepXmlLoader.java:201)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.assembleRunInfo(PepXmlLoader.java:178)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.getNextFraction(PepXmlLoader.java:152)
    at org.fhcrc.cpas.tools.PepXmlLoader$FractionIterator.next(PepXmlLoader.java:119)
    at org.fhcrc.cpas.ms2.PepXmlImporter.uploadRun(PepXmlImporter.java:90)
    at org.fhcrc.cpas.ms2.MS2Importer.upload(MS2Importer.java:181)
    at org.fhcrc.cpas.ms2.MS2Manager.addRun(MS2Manager.java:367)
    at org.fhcrc.cpas.ms2.MS2Manager.addRun(MS2Manager.java:356)
    at org.fhcrc.cpas.ms2.PepXmlExperimentDataHandler.importFile(PepXmlExperimentDataHandler.java:93)
    at org.fhcrc.cpas.exp.XarReader.loadDataFile(XarReader.java:921)
    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.ms2.pipeline.XTandemPipelineJob.search(XTandemPipelineJob.java:584)
    at org.fhcrc.cpas.ms2.pipeline.XTandemPipelineJob.run(XTandemPipelineJob.java:189)
    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)
17 Nov 2006 13:58:03,970 ERROR: MS2 data upload failed
java.lang.RuntimeException: XMLStreamException in next()
    at org.fhcrc.cpas.tools.PepXmlLoader$FractionIterator.next(PepXmlLoader.java:124)
    at org.fhcrc.cpas.ms2.PepXmlImporter.uploadRun(PepXmlImporter.java:90)
    at org.fhcrc.cpas.ms2.MS2Importer.upload(MS2Importer.java:181)
    at org.fhcrc.cpas.ms2.MS2Manager.addRun(MS2Manager.java:367)
    at org.fhcrc.cpas.ms2.MS2Manager.addRun(MS2Manager.java:356)
    at org.fhcrc.cpas.ms2.PepXmlExperimentDataHandler.importFile(PepXmlExperimentDataHandler.java:93)
    at org.fhcrc.cpas.exp.XarReader.loadDataFile(XarReader.java:921)
    at org.fhcrc.cpas.exp.XarReader.loadDoc(XarReader.java:340)
    at org.fhcrc.cpas.exp.XarReader.parseAndLoad(XarReader.java:164)
    at org.fhcrc.cpas.exp.XarReader.uploadRun(XarReader.java:116)
    at org.fhcrc.cpas.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:124)
    at org.fhcrc.cpas.ms2.pipeline.XTandemPipelineJob.search(XTandemPipelineJob.java:584)
    at org.fhcrc.cpas.ms2.pipeline.XTandemPipelineJob.run(XTandemPipelineJob.java:189)
    at java.util.concurrent.Executors$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: com.ctc.wstx.exc.WstxParsingException: Unexpected close tag </search_summary>; expected </parameter>.
 at [row,col {unknown-source}]: [367,16]
    at com.ctc.wstx.sr.StreamScanner.throwParseError(StreamScanner.java:396)
    at com.ctc.wstx.sr.WstxStreamReader.reportWrongEndElem(WstxStreamReader.java:3078)
    at com.ctc.wstx.sr.WstxStreamReader.readEndElem(WstxStreamReader.java:3020)
    at com.ctc.wstx.sr.WstxStreamReader.nextFromTree(WstxStreamReader.java:2682)
    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.PepXmlLoader$PepXmlFraction.handleSearchSummary(PepXmlLoader.java:201)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.assembleRunInfo(PepXmlLoader.java:178)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.getNextFraction(PepXmlLoader.java:152)
    at org.fhcrc.cpas.tools.PepXmlLoader$FractionIterator.next(PepXmlLoader.java:119)
    ... 20 more
17 Nov 2006 13:58:03,976 FATAL: Exception during load
java.lang.RuntimeException: XMLStreamException in next()
    at org.fhcrc.cpas.tools.PepXmlLoader$FractionIterator.next(PepXmlLoader.java:124)
    at org.fhcrc.cpas.ms2.PepXmlImporter.uploadRun(PepXmlImporter.java:90)
    at org.fhcrc.cpas.ms2.MS2Importer.upload(MS2Importer.java:181)
    at org.fhcrc.cpas.ms2.MS2Manager.addRun(MS2Manager.java:367)
    at org.fhcrc.cpas.ms2.MS2Manager.addRun(MS2Manager.java:356)
    at org.fhcrc.cpas.ms2.PepXmlExperimentDataHandler.importFile(PepXmlExperimentDataHandler.java:93)
    at org.fhcrc.cpas.exp.XarReader.loadDataFile(XarReader.java:921)
    at org.fhcrc.cpas.exp.XarReader.loadDoc(XarReader.java:340)
    at org.fhcrc.cpas.exp.XarReader.parseAndLoad(XarReader.java:164)
    at org.fhcrc.cpas.exp.XarReader.uploadRun(XarReader.java:116)
    at org.fhcrc.cpas.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:124)
    at org.fhcrc.cpas.ms2.pipeline.XTandemPipelineJob.search(XTandemPipelineJob.java:584)
    at org.fhcrc.cpas.ms2.pipeline.XTandemPipelineJob.run(XTandemPipelineJob.java:189)
    at java.util.concurrent.Executors$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: com.ctc.wstx.exc.WstxParsingException: Unexpected close tag </search_summary>; expected </parameter>.
 at [row,col {unknown-source}]: [367,16]
    at com.ctc.wstx.sr.StreamScanner.throwParseError(StreamScanner.java:396)
    at com.ctc.wstx.sr.WstxStreamReader.reportWrongEndElem(WstxStreamReader.java:3078)
    at com.ctc.wstx.sr.WstxStreamReader.readEndElem(WstxStreamReader.java:3020)
    at com.ctc.wstx.sr.WstxStreamReader.nextFromTree(WstxStreamReader.java:2682)
    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.PepXmlLoader$PepXmlFraction.handleSearchSummary(PepXmlLoader.java:201)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.assembleRunInfo(PepXmlLoader.java:178)
    at org.fhcrc.cpas.tools.PepXmlLoader$PepXmlFraction.getNextFraction(PepXmlLoader.java:152)
    at org.fhcrc.cpas.tools.PepXmlLoader$FractionIterator.next(PepXmlLoader.java:119)
    ... 20 more
17 Nov 2006 13:58:03,977 FATAL: Upload FAILED
 
brendanx responded:  2006-11-17 17:24
Well, if I were you I'd now be looking at that .pep.xml file to see if I could understand why CPAS thinks it is corrupted. Does it look corrupted to you?

Also, I think your lack of 'batchcoverage' looks slightly interesting:

17 Nov 2006 13:58:02,564 INFO : sh: batchcoverage: command not found

batchcoverage.exe is part of the Windows distribution, and for Linux, it should get built in the Trans Proteomic Pipeline with the XML_ONLY build.

Any ideas what happened to your batchcoverage executable? Are you running Windows or Linux?
 
wonjong.moon responded:  2006-11-20 11:17
CPAS at SBRI is running on a single LINUX machine. I am testing CPAS to see whether it fits for your data pipeline and analysis. Our LINUX administrator installed CPAS, I don't have permissions to modify files. I am using the web interface only. I can copy data files to CPAS pipeline root (I guess which was mounted on LINUX).

I saw terms 'fraction pipleline', 'cluster pipeline', 'minipipeline'.
Does 'minipipeline' mean a single machine running CPAS web interface like our case?

If we want to use 'cluster pipeline', is it freely available?
I guess it's freely available, but we should pay for the setup and supports.

Were all the necessary files for 'cluster pipeline' already installed when CPAS was installed?
Thank you in advance.
 
wongch responded:  2006-11-20 18:28
'mini-pipeline' refers to the single machine CPAS installation, which is sufficient for small to medium thru'put. Your current installation is a 'mini-pipeline' as reflected in your log above.

The 'cluster pipeline', I believe, (like and as part of CPAS,) is distributed freely under the Apache Software License Version 2.0.
You can locate it at https://hedgehog.fhcrc.org/tor/stedi/branches/release1.6/tools/pipeline/bin/
It is not distributed with the standard CPAS installation currently as the mini-pipeline can serve most general scenarios well. But it is available in the SVN. (If you browse a little, you will find many other useful tools.)

Setting cluster pipeline up does require more informatics skill and I will suggest that you get an actual support contract if you wish to spend your time on something else. Please note that the cluster-pipeline still needs the standard CPAS installation to submit the searches.

You can perform a search on "cluster pipeline" at the search webpart at top right section of https://cpas.fhcrc.org/Project/home/support/begin.view? You will have all the necessary information to start off. Try other keywords for the search and you should be able to find more information.
 
adam responded:  2007-01-04 08:54