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Problem with Sequest search in CPAS 8.1

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Problem with Sequest search in CPAS 8.1 btitz  2009-07-02 11:10
Status: Closed
 
I am trying to run Sequest searches through the LabKey SequestQueue, however, the import of the data into CPAS 8.1 fails.

Initally, I had the same problem as reported in the thread "sequest search retrieval error in v8.1" (https://www.labkey.org/announcements/home/CPAS/Forum/thread.view?rowId=2398). I updated to LabKeySequestQueue8.1-8662, which fixed the pep.xml conversion problem, however, the import of the generated .pep.xml file still fails. This is the log file I get:

--------------------------------LOG FILE------------------------------------------------------------------
02 Jul 2009 08:56:48,759 INFO : Check FASTA validity
02 Jul 2009 08:56:48,759 INFO : =======================================
02 Jul 2009 08:56:48,774 INFO : Checking sequence file validity of E:\people\Bjoern\databases\ipi.HmMs.v3.60.statC.varoxMpYpSpT.fasta.hdr
02 Jul 2009 08:57:00,603 INFO :
02 Jul 2009 08:57:00,634 INFO : MzXML2Search output
02 Jul 2009 08:57:00,634 INFO : =======================================
02 Jul 2009 08:57:00,634 INFO : running: MzXML2Search -dta -B500.0 -O090322BjoernElNGab2r1-3 -C1-4 -P10 E:\people\Bjoern\mzXMLfiles\BJOERN\SBP090305\Elutions\090322BjoernElNGab2r1-3.mzXML
02 Jul 2009 08:57:01,025 INFO :
02 Jul 2009 08:57:01,025 INFO : MzXML2Search - SEQUEST DTA format
02 Jul 2009 08:57:01,025 INFO :
02 Jul 2009 08:57:01,040 INFO : Reading E:\people\Bjoern\mzXMLfiles\BJOERN\SBP090305\Elutions\090322BjoernElNGab2r1-3.mzXML
02 Jul 2009 08:57:01,040 INFO : Getting the index offset
02 Jul 2009 08:57:01,040 INFO : Reading the index

{...}

02 Jul 2009 09:58:59,550 DEBUG: Submitting URL 'http://10.47.221.213:8080/SequestQueue/SequestQueue?taskId=1246550262589&cmd=status'.
02 Jul 2009 09:59:29,551 DEBUG: Submitting URL 'http://10.47.221.213:8080/SequestQueue/SequestQueue?taskId=1246550262589&cmd=status'.
02 Jul 2009 09:59:29,551 INFO : Sequest search status: COMPLETE

02 Jul 2009 09:59:29,551 INFO : Retrieving Sequest search result...
02 Jul 2009 09:59:30,785 INFO : Sequest search result retrieved.
02 Jul 2009 09:59:30,785 INFO : Retreiving remote log file.
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 07:58:30,309 INFO ServletJob : Seting status to 'SEARCHING'.
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 07:58:30,434 INFO ServletJob : running: C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\SequestQueue\bin\MzXML2Search.exe -dta -M2 -C1-4 -P10 090322BjoernElNGab2r1-3.mzXML from the 'C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\SequestQueue\input\1246550262589' directory.
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:03:11,232 INFO ServletJob : running: c:\Xcalibur\system\programs\BioworksBrowser\sequest27.exe *.dta from the 'C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\SequestQueue\input\1246550262589\090322BjoernElNGab2r1-3' directory.
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:03:34,923 INFO ServletJob :
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:03:34,923 INFO ServletJob : TurboSEQUEST v.27 (rev. 12), (c) 1998-2005
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:03:34,923 INFO ServletJob : Molecular Biotechnology, Univ. of Washington, J.Eng/S.Morgan/J.Yates
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:03:34,923 INFO ServletJob : Licensed to Thermo Electron Corp.
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:03:34,923 INFO ServletJob :
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:03:34,923 INFO ServletJob : Reading parameter file sequest.params ...
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:03:34,923 INFO ServletJob : Chosen enzyme: Trypsin(KR/P) 1 KR P
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:03:34,923 INFO ServletJob :
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:03:34,923 INFO ServletJob : Reading input file 090322BjoernElNGab2r1-3.00055.00055.2.dta ...
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:03:34,923 INFO ServletJob : >> (M+H)+ mass = 905.68376 ~ 0.0226 (+2), fragment tol = 1.0000, MONO/MONO
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:03:34,923 INFO ServletJob : >> protein database, C:\database\ipi.HmMs.v3.60.statC.varoxMpYpSpT.fasta.hdr, index C:\database\ipi.HmMs.v3.60.statC.varoxMpYpSpT.fasta.hdr
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:58:55,696 INFO ServletJob : running: C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\SequestQueue\bin\Out2XML.exe 090322BjoernElNGab2r1-3 1 from the 'C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\SequestQueue\input\1246550262589' directory.
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:58:55,821 INFO ServletJob : params file here: 090322BjoernElNGab2r1-3\sequest.params
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:58:55,853 INFO ServletJob : WARNING: Peptide XXXXXXXSAHAGARSWHLGTHLATHLCR contains an X, skipping (use -all option to override) ...
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:58:55,853 INFO ServletJob : WARNING: Peptide XXXXXXXSAHAGARSWHLGTHLATHLCR contains an X, skipping (use -all option to override) ...
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:58:55,853 INFO ServletJob : WARNING: Peptide VXPVRLR contains an X, skipping (use -all option to override) ...
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:58:55,868 INFO ServletJob : WARNING: Peptide XPVPVWVIILAVLAGLLLLAVLVFVMYRMGFFK contains an X, skipping (use -all option to override) ...
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:58:55,868 INFO ServletJob : WARNING: Peptide XPVPVWVIILAVLAGLLLLAVLVFVMYRMGFFK contains an X, skipping (use -all option to override) ...
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:58:55,900 INFO ServletJob : WARNING: Peptide XXXXKHGPI contains an X, skipping (use -all option to override) ...
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:58:55,915 INFO ServletJob : WARNING: Peptide LXSLIVXK contains an X, skipping (use -all option to override) ...
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:58:55,915 INFO ServletJob : WARNING: Peptide XPPSGPRGTLLLLPLLLLLLLR contains an X, skipping (use -all option to override) ...
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:58:55,915 INFO ServletJob : WARNING: Peptide XPPSGPRGTLLLLPLLLLLLLR contains an X, skipping (use -all option to override) ...
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:58:55,931 INFO ServletJob : WARNING: Peptide LSWLSIXELRLAK contains an X, skipping (use -all option to override) ...
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:59:11,056 INFO ServletJob : Moved 'C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\SequestQueue\input\1246550262589\090322BjoernElNGab2r1-3.xml' to 'C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\SequestQueue\output' dir.
02 Jul 2009 09:59:30,785 INFO : 02 Jul 2009 08:59:11,056 INFO ServletJob : Seting status to 'COMPLETE'.
02 Jul 2009 09:59:30,785 INFO : End of Sequest server log.
02 Jul 2009 09:59:30,785 INFO : Finished retreiving remote log file.
02 Jul 2009 09:59:30,801 INFO : Cleaning search file from remote sequest server.
02 Jul 2009 09:59:30,801 DEBUG: Submitting URL 'http://10.47.221.213:8080/SequestQueue/SequestQueue?taskId=1246550262589&cmd=clean'.
02 Jul 2009 10:01:57,493 ERROR: Exception class java.io.IOException connect(http://10.47.221.213:8080/SequestQueue,)=http://10.47.221.213:8080/SequestQueue/SequestQueue?taskId=1246550262589&cmd=clean
02 Jul 2009 10:01:57,509 INFO : Sequest session ended.
02 Jul 2009 10:01:57,509 INFO : bsdtar.exe output
02 Jul 2009 10:01:57,509 INFO : =======================================
02 Jul 2009 10:01:57,509 INFO : running: bsdtar.exe czf E:\people\Bjoern\mzXMLfiles\BJOERN\SBP090305\Elutions\sequest\ipiHmMs360_pYST_V2\090322BjoernElNGab2r1-3.work\090322BjoernElNGab2r1-3.pep.tgz *
--------------------------------END OF LOG FILE------------------------------------------------------------------

CPAS shows an error for this run in the pipeline and the search results are not imported. Is there an easy way, how to fix this problem?

Thanks a lot in advance!

Björn
 
 
jeckels responded:  2009-07-02 17:57
Hi Björn,

I encourage you to upgrade to CPAS 9.1 and the corresponding release of SequestQueue. They contain a handful of fixes for Sequest that will likely be helpful. It may not affect this particular issue though.

Can you send a list of files that are in your E:\people\Bjoern\mzXMLfiles\BJOERN\SBP090305\Elutions\sequest\ipiHmMs360_pYST_V2\090322BjoernElNGab2r1-3.work directory? That would help give more information about how far the job got before failing.

Thanks,
Josh
 
btitz responded:  2009-07-02 18:46
Assigned To: jeckels
Hi Josh,

Thanks for your quick answer. We thought about the CPAS 9.1 upgrade, but are unsure, whether we want to go through the (potential) trouble at the moment :-)

Since my last post, my problem evolved a little bit. I just rerun the search without any (intended) changes to the programs or parameters and now I get an error at a later step of the pipeline (the MS2 import fails):

----------------LOG FILE----------------------------
02 Jul 2009 16:58:14,831 INFO : 02 Jul 2009 15:57:59,575 INFO ServletJob : Seting status to 'COMPLETE'.
02 Jul 2009 16:58:14,831 INFO : End of Sequest server log.
02 Jul 2009 16:58:14,831 INFO : Finished retreiving remote log file.
02 Jul 2009 16:58:14,831 INFO : Cleaning search file from remote sequest server.
02 Jul 2009 16:58:14,831 DEBUG: Submitting URL 'http://10.47.221.213:8080/SequestQueue/SequestQueue?taskId=1246576161159&cmd=clean'.
02 Jul 2009 17:00:47,711 INFO : Sequest session ended.
02 Jul 2009 17:00:47,711 INFO : bsdtar.exe output
02 Jul 2009 17:00:47,711 INFO : =======================================
02 Jul 2009 17:00:47,711 INFO : running: bsdtar.exe czf E:\people\Bjoern\mzXMLfiles\BJOERN\SBP090305\Elutions\sequest\ipiHmMsV360_fixC_varM_pYST_3\090322BjoernElNGab2r1-3.work\090322BjoernElNGab2r1-3.pep.tgz *
02 Jul 2009 17:02:04,401 INFO : xinteract output
02 Jul 2009 17:02:04,401 INFO : =======================================
02 Jul 2009 17:02:04,401 INFO : running: xinteract -Opt -x20 -N090322BjoernElNGab2r1-3.pep.xml ..\090322BjoernElNGab2r1-3_raw.pep.xml
02 Jul 2009 17:02:04,401 INFO :
02 Jul 2009 17:02:04,401 INFO : xinteract (TPP v3.4 SQUALL rev.1, Build 200803020850(Win32))
02 Jul 2009 17:02:04,401 INFO :
02 Jul 2009 17:02:04,401 INFO : running: "InteractParser "090322BjoernElNGab2r1-3.pep.xml" "..\090322BjoernElNGab2r1-3_raw.pep.xml""
02 Jul 2009 17:02:04,994 INFO : file 1: ..\090322BjoernElNGab2r1-3_raw.pep.xml
02 Jul 2009 17:02:06,557 INFO : processed altogether 16139 results
02 Jul 2009 17:02:07,697 INFO : command completed in 3 sec
02 Jul 2009 17:02:07,697 INFO :
02 Jul 2009 17:02:07,697 INFO : running: "PeptideProphetParser "090322BjoernElNGab2r1-3.pep.xml" EXTRAITRS=20"
02 Jul 2009 17:02:07,713 INFO : (SEQUEST)
02 Jul 2009 17:02:07,713 INFO : init with SEQUEST trypsin
02 Jul 2009 17:02:08,448 INFO : MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ Orbitrap, Ionization: NSI, Analyzer: FTMS, Detector: unknown
02 Jul 2009 17:02:08,448 INFO :
02 Jul 2009 17:02:08,448 INFO : PeptideProphet v3.0 April 1, 2004 (TPP v3.4 SQUALL rev.1, Build 200803020850(Win32)) AKeller@ISB
02 Jul 2009 17:02:08,448 INFO : read in 989 1+, 3053 2+, 3457 3+, 3907 4+, and 0 5+ spectra
02 Jul 2009 17:02:08,448 INFO : Initialising statistical models ...
02 Jul 2009 17:02:08,541 INFO : iteration 1 2 Too much overlap detected at high f-vals: negSlice = 4.75519 > posSlice = 4.20261
02 Jul 2009 17:02:09,604 INFO : 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Too much overlap detected at high f-vals: negSlice = 4.66423 > posSlice = 2.73969
02 Jul 2009 17:02:09,635 INFO : model complete after 32 iterations
02 Jul 2009 17:02:10,432 INFO : command completed in 3 sec
02 Jul 2009 17:02:10,432 INFO :
02 Jul 2009 17:02:10,432 INFO : running: "DatabaseParser "090322BjoernElNGab2r1-3.pep.xml""
02 Jul 2009 17:02:10,463 INFO : command completed in 0 sec
02 Jul 2009 17:02:10,463 INFO :
02 Jul 2009 17:02:10,463 INFO : running: "RefreshParser "090322BjoernElNGab2r1-3.pep.xml" "C:\database\ipi.HmMs.v3.60.statC.varoxMpYpSpT.fasta.hdr""
02 Jul 2009 17:02:20,870 INFO : - Building Commentz-Walter keyword tree... - Searching the tree...
02 Jul 2009 17:02:20,870 INFO : - Linking duplicate entries... - Printing results...
02 Jul 2009 17:02:20,870 INFO :
02 Jul 2009 17:02:20,870 INFO : command completed in 10 sec
02 Jul 2009 17:02:20,870 INFO :
02 Jul 2009 17:02:20,870 INFO : running: "ProteinProphet "090322BjoernElNGab2r1-3.pep.xml" "090322BjoernElNGab2r1-3.pep-prot.xml" XML NOPLOT"
02 Jul 2009 17:02:20,885 INFO : ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v3.4 SQUALL rev.1, Build 200803020850(Win32))
02 Jul 2009 17:02:20,932 INFO : . . . reading in E:/people/Bjoern/mzXMLfiles/BJOERN/SBP090305/Elutions/sequest/ipiHmMsV360_fixC_varM_pYST_3/090322BjoernElNGab2r1-3.work/090322BjoernElNGab2r1-3.pep.xml. . .
02 Jul 2009 17:02:21,026 INFO : . . . read in 0 1+, 228 2+, 182 3+, 492 4+ spectra with min prob 0.05
02 Jul 2009 17:02:24,292 INFO : (xml input) (using degen pep info)
02 Jul 2009 17:02:25,432 INFO : command completed in 5 sec
02 Jul 2009 17:02:25,432 INFO : InteractParser "090322BjoernElNGab2r1-3.pep.xml" "..\090322BjoernElNGab2r1-3_raw.pep.xml" 3 sec
02 Jul 2009 17:02:25,432 INFO : PeptideProphetParser "090322BjoernElNGab2r1-3.pep.xml" EXTRAITRS=20 3 sec
02 Jul 2009 17:02:25,432 INFO : RefreshParser "090322BjoernElNGab2r1-3.pep.xml" "C:\database\ipi.HmMs.v3.60.statC.varoxMpYpSpT.fasta.hdr" 10 sec
02 Jul 2009 17:02:25,432 INFO : ProteinProphet "090322BjoernElNGab2r1-3.pep.xml" "090322BjoernElNGab2r1-3.pep-prot.xml" XML NOPLOT 5 sec
02 Jul 2009 17:02:25,432 INFO : job completed in 21 sec
02 Jul 2009 17:02:25,448 INFO : Starting to import XAR
02 Jul 2009 17:02:25,464 INFO : Existing protocol with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MS2.SequestSearch:2' is referenced by other experiment runs, so it cannot be updated
02 Jul 2009 17:02:25,464 INFO : Existing protocol with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MS2.XInteract.PeptideProphet:2' is referenced by other experiment runs, so it cannot be updated
02 Jul 2009 17:02:25,479 INFO : Existing protocol with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MS2.XInteract.ProteinProphet:2' is referenced by other experiment runs, so it cannot be updated
02 Jul 2009 17:02:25,479 INFO : Existing protocol with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MS2.SequestAnalysis:3' is referenced by other experiment runs, so it cannot be updated
02 Jul 2009 17:02:25,479 INFO : Existing protocol with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MarkRunOutput:2' is referenced by other experiment runs, so it cannot be updated
02 Jul 2009 17:02:25,479 INFO : Protocol with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MS2.SequestSearch:2' matches a protocol with the same LSID that has already been loaded.
02 Jul 2009 17:02:25,479 INFO : Protocol with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MS2.XInteract.PeptideProphet:2' matches a protocol with the same LSID that has already been loaded.
02 Jul 2009 17:02:25,479 INFO : Protocol with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MS2.XInteract.ProteinProphet:2' matches a protocol with the same LSID that has already been loaded.
02 Jul 2009 17:02:25,479 INFO : Protocol with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MS2.SequestAnalysis:3' matches a protocol with the same LSID that has already been loaded.
02 Jul 2009 17:02:25,495 INFO : Protocol with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MarkRunOutput:2' matches a protocol with the same LSID that has already been loaded.
02 Jul 2009 17:02:25,495 INFO : Protocol import complete
02 Jul 2009 17:02:25,495 INFO :
02 Jul 2009 17:02:25,495 INFO : Protocol action set import complete
02 Jul 2009 17:02:25,495 INFO :
02 Jul 2009 17:02:25,495 INFO : Found an existing entry for Data LSID urn:lsid:mednet.ucla.edu:Data.Folder-34-Xar-b66da9f7-f078-102b-a248-dd86a882004f:..%2F..%2F090322BjoernElNGab2r1-3.mzXML, not reloading its values from scratch
02 Jul 2009 17:02:25,495 INFO : Finished loading Data with LSID 'urn:lsid:mednet.ucla.edu:Data.Folder-34-Xar-b66da9f7-f078-102b-a248-dd86a882004f:..%2F..%2F090322BjoernElNGab2r1-3.mzXML'
02 Jul 2009 17:02:25,495 INFO : Found an existing entry for Data LSID urn:lsid:mednet.ucla.edu:Data.Folder-34-Xar-d7376f81-494e-102c-b142-dd86a882f4d2:sequest.xml, not reloading its values from scratch
02 Jul 2009 17:02:25,495 INFO : Finished loading Data with LSID 'urn:lsid:mednet.ucla.edu:Data.Folder-34-Xar-d7376f81-494e-102c-b142-dd86a882f4d2:sequest.xml'
02 Jul 2009 17:02:25,511 INFO : Found an existing entry for Data LSID urn:lsid:mednet.ucla.edu:Data.Folder-34-Xar-d7376f81-494e-102c-b142-dd86a882f4d2:..%2F..%2F..%2F..%2F..%2F..%2Fdatabases%2Fipi.HmMs.v3.60.statC.varoxMpYpSpT.fasta.hdr, not reloading its values from scratch
02 Jul 2009 17:02:25,511 INFO : Finished loading Data with LSID 'urn:lsid:mednet.ucla.edu:Data.Folder-34-Xar-d7376f81-494e-102c-b142-dd86a882f4d2:..%2F..%2F..%2F..%2F..%2F..%2Fdatabases%2Fipi.HmMs.v3.60.statC.varoxMpYpSpT.fasta.hdr'
02 Jul 2009 17:02:25,511 INFO : Starting input import complete
02 Jul 2009 17:02:25,511 INFO :
02 Jul 2009 17:02:25,542 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MS2.SequestAnalysis:3'
02 Jul 2009 17:02:25,557 INFO : Finished loading Data with LSID 'urn:lsid:mednet.ucla.edu:Data.Run-504:SequestFile'
02 Jul 2009 17:02:25,557 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MS2.SequestSearch:2'
02 Jul 2009 17:02:25,573 INFO : Finished loading Data with LSID 'urn:lsid:mednet.ucla.edu:Data.Run-504:ScoredPepXmlFile'
02 Jul 2009 17:02:25,573 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MS2.XInteract.PeptideProphet:2'
02 Jul 2009 17:02:25,604 INFO : Finished loading Data with LSID 'urn:lsid:mednet.ucla.edu:Data.Run-504:ProteinScoresFile'
02 Jul 2009 17:02:25,604 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MS2.XInteract.ProteinProphet:2'
02 Jul 2009 17:02:25,604 INFO : Finished loading ProtocolApplication with LSID 'urn:lsid:mednet.ucla.edu:Protocol.Folder-34:MarkRunOutput:2'
02 Jul 2009 17:02:25,604 INFO : Finished loading ExperimentRun with LSID 'urn:lsid:mednet.ucla.edu:ExperimentRun.Folder-34:MS2-mzXMLfiles%2FBJOERN%2FSBP090305%2FElutions%2Fsequest%2FipiHmMsV360_fixC_varM_pYST_3%2F090322BjoernElNGab2r1-3'
02 Jul 2009 17:02:25,604 INFO :
02 Jul 2009 17:02:25,604 INFO : Trying to load data file file:/E:/PEOPLE/BJOERN/mzXMLfiles/BJOERN/SBP090305/Elutions/sequest/ipiHmMsV360_fixC_varM_pYST_3/090322BjoernElNGab2r1-3.pep.xml into the system
02 Jul 2009 17:02:25,620 INFO : Starting import from 090322BjoernElNGab2r1-3.pep.xml
02 Jul 2009 17:02:25,620 INFO : Starting to clear out any previously imported data for 090322BjoernElNGab2r1-3.pep.xml
02 Jul 2009 17:02:25,651 INFO : 0.03 seconds to clear out any previously imported data for 090322BjoernElNGab2r1-3.pep.xml
02 Jul 2009 17:02:25,651 INFO : Starting to import FASTA file C:\database\ipi.HmMs.v3.60.statC.varoxMpYpSpT.fasta.hdr
02 Jul 2009 17:02:27,729 INFO : FASTA file "c:/database/ipi.HmMs.v3.60.statC.varoxMpYpSpT.fasta.hdr" not imported, but another file, 'e:/PEOPLE/BJOERN/databases/ipi.HmMs.v3.60.fasta', has the same checksum
02 Jul 2009 17:02:27,745 INFO : 2.09 seconds to import FASTA file C:\database\ipi.HmMs.v3.60.statC.varoxMpYpSpT.fasta.hdr
02 Jul 2009 17:02:27,745 INFO : Starting to import peptide search results for fraction 1, analysis of file null
02 Jul 2009 17:02:27,745 INFO : Importing MS/MS results is 0% complete
02 Jul 2009 17:02:27,745 INFO : Importing MS/MS results is 1% complete
02 Jul 2009 17:02:27,745 ERROR: MS2 import failed
java.lang.NullPointerException
    at org.labkey.common.tools.PepXmlLoader$PeptideIterator.hasNext(PepXmlLoader.java:416)
    at org.labkey.ms2.PepXmlImporter.importRun(PepXmlImporter.java:114)
    at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:181)
    at org.labkey.ms2.MS2Manager.importRun(MS2Manager.java:424)
    at org.labkey.ms2.MS2Manager.addRun(MS2Manager.java:415)
    at org.labkey.ms2.PepXmlExperimentDataHandler.importFile(PepXmlExperimentDataHandler.java:103)
    at org.labkey.experiment.XarReader.loadDataFile(XarReader.java:1083)
    at org.labkey.experiment.XarReader.loadDoc(XarReader.java:314)
    at org.labkey.experiment.XarReader.parseAndLoad(XarReader.java:106)
    at org.labkey.experiment.api.ExperimentServiceImpl.loadXar(ExperimentServiceImpl.java:549)
    at org.labkey.api.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:110)
    at org.labkey.experiment.pipeline.XarImportTask.run(XarImportTask.java:105)
    at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:429)
    at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:534)
    at org.labkey.ms2.pipeline.AbstractMS2SearchPipelineJob.run(AbstractMS2SearchPipelineJob.java:151)
    at java.util.concurrent.Executors$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)
02 Jul 2009 17:02:27,761 INFO :
02 Jul 2009 17:02:27,761 FATAL: Exception during import
java.lang.NullPointerException
    at org.labkey.common.tools.PepXmlLoader$PeptideIterator.hasNext(PepXmlLoader.java:416)
    at org.labkey.ms2.PepXmlImporter.importRun(PepXmlImporter.java:114)
    at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:181)
    at org.labkey.ms2.MS2Manager.importRun(MS2Manager.java:424)
    at org.labkey.ms2.MS2Manager.addRun(MS2Manager.java:415)
    at org.labkey.ms2.PepXmlExperimentDataHandler.importFile(PepXmlExperimentDataHandler.java:103)
    at org.labkey.experiment.XarReader.loadDataFile(XarReader.java:1083)
    at org.labkey.experiment.XarReader.loadDoc(XarReader.java:314)
    at org.labkey.experiment.XarReader.parseAndLoad(XarReader.java:106)
    at org.labkey.experiment.api.ExperimentServiceImpl.loadXar(ExperimentServiceImpl.java:549)
    at org.labkey.api.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:110)
    at org.labkey.experiment.pipeline.XarImportTask.run(XarImportTask.java:105)
    at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:429)
    at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:534)
    at org.labkey.ms2.pipeline.AbstractMS2SearchPipelineJob.run(AbstractMS2SearchPipelineJob.java:151)
    at java.util.concurrent.Executors$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)
02 Jul 2009 17:02:27,761 FATAL: XAR import FAILED
-------------END OF LOG FILE-----------------------------------------

At this state, the "090322BjoernElNGab2r1-3.work" directory already got deleted? In the parent directory (...\sequest\ipiHmMs360_pYST_V2\) I got:
090322BjoernElNGab2r1-3.search.xar.xml
090322BjoernElNGab2r1-3.prot.xml
090322BjoernElNGab2r1-3.pep.xml
090322BjoernElNGab2r1-3.pep.tgz
090322BjoernElNGab2r1-3.log
all.log
sequest.params
sequest.xml

Thanks a lot!

Best,

Björn
 
jeckels responded:  2009-07-03 09:19
Hi Björn,

This is a bug that was fixed in version 8.2:

https://www.labkey.org/issues/home/Developer/issues/details.view?issueId=5904

The problem is that some Sequest searches end up producing a pepXML that's a little different than we used to expect. Unfortunately, I don't know of an easy way to add the <search_hit> elements that 8.1 expects, but as of 8.2 we should import the file correctly.

Thanks,
Josh
 
wnels2 responded:  2009-07-06 06:59
Hi Björn,
I would encourage you to upgrade to the current version for better support but here's something to try.
It looks like you are using a Sequest indexed database (the fasta.hdr file). The SequestQueue is now set up to use the Sequest auto index feature.
If I remmember correctly, if you create a shortcut from c:/database/ipi.HmMs.v3.60.statC.varoxMpYpSpT.fasta.hdr to c:/database/ipi.HmMs.v3.60.statC.varoxMpYpSpT.fasta it will be able to load the database.

Sequest and CPAS will not be able to share the same database root.

Bill