Erik, I tried this before, but the libraproteinratioparser keep crashing all the time: here is the error message I got when I try to use it to process the prot.xml:
*This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. * any quick remedy to this problem? thanks! SunSun On Wed, Oct 31, 2012 at 1:13 AM, ChargedPeptide <[email protected]> wrote: > Oh, that's much easier :) > In this case you would need to do the following: > Run your mascot->pep.xml with libra quantities and also X!tandem -> > pep.xml (If this is the same data ran with different search engines, if it > is different data as well you need to process each batch separatley and set > an experiment ID for each set, let me know if this applies and I'll give > you som detail) > > Run iprophet on both your output pep.xmls to get a pep.xml with combined > spectral matches and iProbabilities. > Run protein-prophet on the iProphet output pep.xml. > Now you will have a prot.xml with no quantities displayed. > Manually run libraproteinratioparser (or similiar name, can't check now , > on train) as this: > libraproteinratioparser <your prot.xml> -c<your libra condition file> > > Voila. Enjoy your final prot.xml. > > Let me know if this works out for you. > > Den måndagen den 29:e oktober 2012 kl. 19:35:06 UTC+1 skrev sunsun: >> >> Erik, >> Thanks for the reply. However, the problem you described is not what I >> have encountered. I did the search separately without merging them, so I >> have individual dat. files that corresponding to each mzXML.In my case, the >> Libra have no problem to read the data at all. I can do the >> Mascot-TPP-Libra successfully, and I can also do the Tandem-TPP-Libra >> successfully, >> but I just haven't find a way to combine both data into a prot.xml. >> >> Despite of that, I think your Java script is very interesting and may >> help others if they want to try it out. >> Thanks for the help. >> >> SunSun >> >> >> On Sun, Oct 28, 2012 at 11:41 PM, ChargedPeptide <[email protected]>wrote: >> >>> 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/**InteractPa**rser "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/**2n**dhospital/1/interact.pep.xml >>>> >>>> direct your browser to >>>> http://localhost/ISB/data/**2ndh**ospital/1/interact.pep.**shtml >>>> <http://localhost/ISB/data/2ndhospital/1/interact.pep.shtml> >>>> >>>> >>>> >>>> command completed in 5 sec >>>> >>>> running: "C:/Inetpub/tpp-bin/**DatabasePa**rser "interact.pep.xml"" >>>> command completed in 1 sec >>>> >>>> running: "C:/Inetpub/tpp-bin/**RefreshPar**ser "interact.pep.xml" >>>> "c:/Inetpub/wwwroot/ISB/data/**d**base/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/**PeptidePro**phetParser "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/**ProphetMod**els.pl -i interact.pep.xml" >>>> Analyzing interact.pep.xml ... >>>> Parsing search results >>>> "c:/Inetpub/wwwroot/ISB/data/**2**ndhospital/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/**2**ndhospital/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/**2**ndhospital/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/**LibraPepti**deParser "interact.pep.xml" >>>> -ccondition_zeyuiTRAQtest1.**xml**" >>>> Failed to open input file >>>> 'c:/Inetpub/wwwroot/ISB/data/**2**ndhospital/1/F003158.mzXML'. >>>> could not open input file >>>> c:/Inetpub/wwwroot/ISB/data/**2n**dhospital/1/F003158.mzXML >>>> >>>> command "C:/Inetpub/tpp-bin/**LibraPepti**deParser "interact.pep.xml" >>>> -ccondition_zeyuiTRAQtest1.**xml**" failed: Operation not permitted >>>> >>>> command "C:/Inetpub/tpp-bin/**LibraPepti**deParser "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. >>> To view this discussion on the web visit https://groups.google.com/d/** >>> msg/spctools-discuss/-/**YVdRAe93h40J<https://groups.google.com/d/msg/spctools-discuss/-/YVdRAe93h40J> >>> . >>> To post to this group, send email to spctools...@googlegroups.**com. >>> To unsubscribe from this group, send email to spctools-discu...@** >>> googlegroups.com. >>> >>> For more options, visit this group at http://groups.google.com/** >>> group/spctools-discuss?hl=en<http://groups.google.com/group/spctools-discuss?hl=en> >>> . >>> >> >> >> >> -- >> *Sun* >> >> -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/HefPZZmaIk4J. > > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- *Sun* -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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