Hey SunSun, I've had a number of problems running through mascot data. The most usual error for me is that the <msms_run_summary base_name= in the pep.xml is set erroneously. This is especially true if you are running Mascot2XML on a merged Mascot search where results from multiple MGF files are in one .dat output file. Libra reads the msms_run summary_base_name= and raw_data= to get the location and extension of input data. I've recently wrote a bit of Java to split the results from Mascot output files into their own pep.xmls after Mascot2XML and I'm not really aware of another way to do it, though I've missed something. If this is your problem I'd need to adapt it a bit (right now it only runs as part of our pipeline, not stand-alone) but I'd be happy to send it over if you need it.
Your first check should be if this: c:/Inetpub/wwwroot/ISB/data/2ndhospital/1/F003158.mzXML is an actual data file. It looks like a mascot-search ID to me. Den söndagen den 14:e oktober 2012 kl. 02:45:19 UTC+2 skrev sunsun: > > Dear TPP team, > I'm running a 8plex iTRAQ data analysis using the Mascot-TPP-Libra > pipeline. It went through peptideProphet and proteinProphet smoothly > without Libra. However, when I add Libra option into the picture, it > generate an error. It seems the Libra quantitation require the spectrum > data in mzXML format, however, all I have is mg files. Do I really need to > convert everything to mzXML? or is there something else going wrong that I > really unaware off. Please help me out! > thank you so much! > SunSun > > > here is the error message I got: > > *EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data/2ndhospital/1; > c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.95 -l7 -O > -Lcondition_zeyuiTRAQtest1.xml-1 F003158.pep.xml F003159.pep.xml > F003160.pep.xml * > > c:\Inetpub\tpp-bin\xinteract (TPP v4.6 OCCUPY rev 0, Build 201208170820 > (MinGW)) > > running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" > "F003158.pep.xml" "F003159.pep.xml" "F003160.pep.xml" -L"7"" > file 1: F003158.pep.xml > file 2: F003159.pep.xml > file 3: F003160.pep.xml > processed altogether 2737 results > > > results written to file > c:/Inetpub/wwwroot/ISB/data/2ndhospital/1/interact.pep.xml > > direct your browser to > http://localhost/ISB/data/2ndhospital/1/interact.pep.shtml > > > > command completed in 5 sec > > running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" > command completed in 1 sec > > running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" > "c:/Inetpub/wwwroot/ISB/data/dbase/zeyu_human.1.fasta"" > - Searching the tree... > - Linking duplicate entries... - Printing results... > > - Building Commentz-Walter keyword tree...command completed in 18 sec > > running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > MINPROB=0.95" > (MASCOT) > results for charge 1: 9 id tot and 1 adj scores > results for charge 2: 512 id tot and 16 adj scores > results for charge 3: 903 id tot and 46 adj scores > results for charge 3: 7.65044 adj_ion_mean and 23.2164 adj_ion_hom mean > 37.4548id mean0.928281 correlation (r) > 3+ ion - id = 1.02138*(ion - hom) + -16.0625 with error = 6.00641 > mean ion - id: 7.65044, mean ion - hom: 23.2164 > results for charge 4: 347 id tot and 1 adj scores > results for charge 5: 966 id tot and 1 adj scores > results for charge 6: 0 id tot and 0 adj scores > results for charge 7: 0 id tot and 0 adj scores > init with MASCOT trypsin > MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: > UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN > > PeptideProphet (TPP v4.6 OCCUPY rev 0, Build 201208170820 (MinGW)) > AKeller@ISB > read in 5 1+, 382 2+, 813 3+, 324 4+, 886 5+, 0 6+, and 0 7+ spectra. > Initialising statistical models ... > Iterations: .........10.........20.. > WARNING: Mixture model quality test failed for charge (1+). > WARNING: Mixture model quality test failed for charge (4+). > WARNING: Mixture model quality test failed for charge (5+). > model complete after 23 iterations > command completed in 5 sec > > running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml" > Analyzing interact.pep.xml ... > Parsing search results "c:/Inetpub/wwwroot/ISB/data/2ndhospital/1/F003158 > (MASCOT)"... > => Total of 12 hits. > => Total of 0 decoy hits. > => Total of 0 excluded hits. > Parsing search results "c:/Inetpub/wwwroot/ISB/data/2ndhospital/1/F003159 > (MASCOT)"... > => Total of 14 hits. > => Total of 0 decoy hits. > => Total of 0 excluded hits. > Parsing search results "c:/Inetpub/wwwroot/ISB/data/2ndhospital/1/F003160 > (MASCOT)"... > => Total of 45 hits. > => Total of 0 decoy hits. > => Total of 0 excluded hits. > command completed in 5 sec > > running: "C:/Inetpub/tpp-bin/LibraPeptideParser "interact.pep.xml" > -ccondition_zeyuiTRAQtest1.xml" > Failed to open input file > 'c:/Inetpub/wwwroot/ISB/data/2ndhospital/1/F003158.mzXML'. > could not open input file > c:/Inetpub/wwwroot/ISB/data/2ndhospital/1/F003158.mzXML > > command "C:/Inetpub/tpp-bin/LibraPeptideParser "interact.pep.xml" > -ccondition_zeyuiTRAQtest1.xml" failed: Operation not permitted > > command "C:/Inetpub/tpp-bin/LibraPeptideParser "interact.pep.xml" > -ccondition_zeyuiTRAQtest1.xml" exited with non-zero exit code: 1 > QUIT - the job is incomplete > > command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.95 -l7 -O > -Lcondition_zeyuiTRAQtest1.xml-1 F003158.pep.xml F003159.pep.xml > F003160.pep.xml" failed: Operation not permitted > > *Command FAILED* > RETURN CODE:256 > > > The Libra condition.xml was generated within TPP using the default 8plex > setting. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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