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Xinteract being called with -d"..\..\.." errors out during XPressPeptideParser TPP xinteract ver 4.3.1

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Xinteract being called with -d"..\..\.." errors out during XPressPeptideParser TPP xinteract ver 4.3.1 donw  2011-02-25 10:46
Status: Closed
 
Hi, we are still running a SILAC mzXML of Orbitrap data through Mascot pipeline using TPP toolset Ver 4.3.1 except for Mascot2XML which if Ver 4.4.1

**********************************************************
When trying to run Xpress for quantitation we are seeing the following being passed to xinteract:

25 Feb 2011 11:46:19,781 INFO : running: D:\LabKey Server\bin\xinteract -x20 -Opt -nR -X-nK,6.020129 -nR,10.0083 -m0.01 -d"..\..\.." -No261_08mar17_02_sec9.pep.xml ..\o261_08mar17_02_sec9_raw.pep.xml
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Is there a parameter I am using or failing to use which is causing the -d"..\..\.." to be sent?
It seems this trips of the parser when it is trying to find the mzXML file.

Here are the Pipeline Quantitation parameters I am passing. (Full mascot.xml commands attached)

<note label="pipeline quantitation, residue label mass" type="input">6.020129@K,10.0083@R</note>
<note label="pipeline quantitation, algorithm" type="input">xpress</note>
<note label="pipeline quantitation, mass tolerance" type="input">0.01</note>
<note label="pipeline quantitation, max fractional delta mass" type="input">20</note>
<note label="pipeline quantitation, min peptide prophet" type="input">0.90</note>

Thanks
Don


Part of Log file where error first occurs below. Parameters used to kick off run in file attached mascot.xml. Log file is attached.
25 Feb 2011 11:46:19,781 INFO : =======================================
25 Feb 2011 11:46:19,781 INFO : Working directory is D:\LabKey Server\files\Kolla MS2\@files\.\mascot\MascotSearchTest2SilacQuantTry2\o261_08mar17_02_sec9.work
25 Feb 2011 11:46:19,781 INFO : running: D:\LabKey Server\bin\xinteract -x20 -Opt -nR -X-nK,6.020129 -nR,10.0083 -m0.01 -d"..\..\.." -No261_08mar17_02_sec9.pep.xml ..\o261_08mar17_02_sec9_raw.pep.xml
25 Feb 2011 11:46:19,781 INFO :
25 Feb 2011 11:46:19,781 INFO : D:\LabKey Server\bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909211148 (MSVC))
25 Feb 2011 11:46:19,781 INFO :
25 Feb 2011 11:46:19,781 INFO : running: "InteractParser "o261_08mar17_02_sec9.pep.xml" "..\o261_08mar17_02_sec9_raw.pep.xml" -L"7""
25 Feb 2011 11:46:20,046 INFO : file 1: ..\o261_08mar17_02_sec9_raw.pep.xml
25 Feb 2011 11:46:21,203 INFO : processed altogether 4417 results
25 Feb 2011 11:46:22,109 INFO : command completed in 3 sec
25 Feb 2011 11:46:22,109 INFO :
25 Feb 2011 11:46:22,109 INFO : running: "PeptideProphetParser "o261_08mar17_02_sec9.pep.xml" EXTRAITRS=20"
25 Feb 2011 11:46:22,125 INFO : (MASCOT)
25 Feb 2011 11:46:22,250 INFO : results for charge 1: 0 id tot and 0 adj scores
25 Feb 2011 11:46:22,468 INFO : results for charge 2: 3167 id tot and 1086 adj scores
25 Feb 2011 11:46:22,468 INFO : results for charge 2: 12.384 adj_ion_mean and 18.6871 adj_ion_hom mean 35.0093id mean0.941093 correlation (r)
25 Feb 2011 11:46:22,468 INFO : 2+ ion - id = 1.06625*(ion - hom) + -7.54113 with error = 5.81113
25 Feb 2011 11:46:22,468 INFO : mean ion - id: 12.384, mean ion - hom: 18.6871
25 Feb 2011 11:46:22,625 INFO : results for charge 3: 1250 id tot and 149 adj scores
25 Feb 2011 11:46:22,625 INFO : results for charge 3: 4.80601 adj_ion_mean and 11.5607 adj_ion_hom mean 33.7552id mean0.951477 correlation (r)
25 Feb 2011 11:46:22,625 INFO : 3+ ion - id = 1.10366*(ion - hom) + -7.953 with error = 4.20348
25 Feb 2011 11:46:22,625 INFO : mean ion - id: 4.80601, mean ion - hom: 11.5607
25 Feb 2011 11:46:22,750 INFO : results for charge 4: 0 id tot and 0 adj scores
25 Feb 2011 11:46:22,875 INFO : results for charge 5: 0 id tot and 0 adj scores
25 Feb 2011 11:46:22,984 INFO : results for charge 6: 0 id tot and 0 adj scores
25 Feb 2011 11:46:22,984 INFO : results for charge 6: -0 adj_ion_mean and -0 adj_ion_hom mean 0id mean-1.#IND correlation (r)
25 Feb 2011 11:46:23,109 INFO : results for charge 7: 0 id tot and 0 adj scores
25 Feb 2011 11:46:23,109 INFO : init with MASCOT trypsin
25 Feb 2011 11:46:23,406 INFO : MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ Orbitrap, Ionization: NSI, Analyzer: FTMS, Detector: unknown
25 Feb 2011 11:46:23,406 INFO :
25 Feb 2011 11:46:23,406 INFO : PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909211148 (MSVC)) AKeller@ISB
25 Feb 2011 11:46:23,406 INFO : read in 0 1+, 3082 2+, 1227 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
25 Feb 2011 11:46:23,406 INFO : Initialising statistical models ...
25 Feb 2011 11:46:23,531 INFO : Iterations: .........10.........20...
25 Feb 2011 11:46:23,546 INFO : model complete after 24 iterations
25 Feb 2011 11:46:24,125 INFO : command completed in 2 sec
25 Feb 2011 11:46:24,125 INFO :
25 Feb 2011 11:46:24,125 INFO : running: "XPressPeptideParser "o261_08mar17_02_sec9.pep.xml" -nK,6.020129 -nR,10.0083 -m0.01 -d..\..\.."
25 Feb 2011 11:46:24,343 INFO : XPRESS error - cannot open file from basename d:/LabKey Server/files/Kolla MS2/@files/mascot/MascotSearchTest2SilacQuantTry2/o261_08mar17_02_sec9.work/o261_08mar17_02_sec9, will try to derive from scan names
25 Feb 2011 11:46:24,343 INFO : scan-derived scan file d:/LabKey Server/files/Kolla MS2/@files/mascot/MascotSearchTest2SilacQuantTry2/o261_08mar17_02_sec9.mzXML (from ) not found, cannot proceed...
25 Feb 2011 11:46:24,343 INFO :
25 Feb 2011 11:46:24,343 INFO : command "XPressPeptideParser "o261_08mar17_02_sec9.pep.xml" -nK,6.020129 -nR,10.0083 -m0.01 -d..\..\.." failed: Operation not permitted
25 Feb 2011 11:46:24,343 INFO :
25 Feb 2011 11:46:24,343 INFO : command "XPressPeptideParser "o261_08mar17_02_sec9.pep.xml" -nK,6.020129 -nR,10.0083 -m0.01 -d..\..\.." exited with non-zero exit code: 1
25 Feb 2011 11:46:24,343 INFO : QUIT - the job is incomplete
25 Feb 2011 11:46:24,343 INFO : Failed to complete task 'org.labkey.ms2.pipeline.TPPTask'
25 Feb 2011 11:46:24,343 ERROR: Failed to remove work directory D:\LabKey Server\files\Kolla MS2\@files\.\mascot\MascotSearchTest2SilacQuantTry2\o261_08mar17_02_sec9.work unexpected files found:
o261_08mar17_02_sec9.pep.xml
o261_08mar17_02_sec9.pep.xml.tmp.a01468
25 Feb 2011 11:46:25,296 ERROR: Failed running D:\LabKey Server\bin\xinteract, exit code 1
org.labkey.api.pipeline.PipelineJobException: Failed running D:\LabKey Server\bin\xinteract, exit code 1
    at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:1075)
    at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:935)
    at org.labkey.ms2.pipeline.TPPTask.run(TPPTask.java:410)
    at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:585)
    at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:813)
    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)
 
 
adam responded:  2011-02-26 07:41
Don,

I'm not super familiar with the MS2 pipeline code, but it looks like -d specifies the path to the mzXML file, relative to the work directory, and it's always included with xpress searches. Has this parameter been added in any of your previous (successful) searches? What was the value there? Can you confirm where the mzXML file is relative to the work directory (mentioned at the top of the log fragment you included)?

Adam
 
brendanx responded:  2011-02-26 08:05
Hi Don,
I might try rerunning this in a directory without @ in the name. As you can see from the output:

XPRESS error - cannot open file from basename d:/LabKey Server/files/Kolla MS2/@files/mascot/MascotSearchTest2SilacQuantTry2/o261_08mar17_02_sec9.work/o261_08mar17_02_sec9

Means that ../../.. is the d:/LabKey Server/files/Kolla MS2/@files directory (three levels up from the .work directory), where hopefully your .mzXML files are actually located. It doesn't seem like this should be a problem, but it is the only thing that looks remotely unusual.

Otherwise, Adam's suggestion of comparing what is different between this run and others that have succeeded for you is a good one. Hopefully this is not the first time you have attempted to run Xpress.

Good luck!

--Brendan