Hi David! You are absolutelly right! The file exist (pep.xml), but I cannot open it, even via 'browse files'. I have the AccMass images in the proper directory. The protein file is not created at all. Below you wiil find the further comunicat after the peptide and protein prophet had finshed work (overnight, failed with code 256). Usually, I am using the option run the protein prophet directly after peptide prophet. But I have checked even the peptide prophet and again run takes too long (until it is finished by the server, due to time limit).
Thanks a lot! Best regards, Agnieszka running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml" command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml" failed: Operation not permitted command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml" exited with non-zero exit code: 1 QUIT - the job is incomplete command "c:\Inetpub\tpp-bin\xinteract -N100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml -p0.05 -l6 -PREC -OApu -dDECOY_ 100214-Agn-Er-Golgi-E10-100ul-01.tandem.pep.xml" failed: Operation not permitted W dniu czwartek, 27 lutego 2014 19:38:12 UTC+2 użytkownik David Shteynberg napisał: > > I think the results are probably there as PeptideProphet finished ok and > the failing step is the step that plots the models and some performance > metrics. It might be complaining about not being able to find gnuplot on > your system for generating the images. I would suggest trying to reinstall > the TPP and perhaps try the latest 4.7.0 version. You should be able to > view the results by going to Utilites->BrowseFiles and finding the > file 100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml in your directory. > Are there corresponding png files that have AccMass in their names present > in that directory? > > > -David > > > On Thu, Feb 27, 2014 at 7:35 AM, user1 <[email protected]<javascript:> > > wrote: > >> Hi, >> >> I am trying to run the mzXML files with TPP. The X! Tandem search is correct >> and as an output we get the pep.xml file. The problems starts, when I want >> to run the peptide prophet. I start the run and it cannont be compleated. I >> have run several samples so far and I have not faced this problem. I was >> trying even run the samples which I had run previosly, but again with the >> same results. Please find attached below the dialog window. Any ideas what >> can be wrong? Thank you in advance! >> >> >> c:\Inetpub\tpp-bin\xinteract (TPP v4.6 OCCUPY rev 3, Build 201307241109 >> (MinGW)) >> >> running: "C:/Inetpub/tpp-bin/InteractParser >> "100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml" >> "100214-Agn-Er-Golgi-E10-100ul-01.tandem.pep.xml" -I -L"6"" >> file 1: 100214-Agn-Er-Golgi-E10-100ul-01.tandem.pep.xml >> SUCCESS: CORRECTED data file >> c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01.mzXML >> in msms_run_summary tag ... >> Unknown file type. No file loaded. >> Failed to open input file >> 'c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01.mzML'. >> processed altogether 51735 results >> INFO: Results written to file: >> c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml >> command completed in 98 sec >> >> running: "C:/Inetpub/tpp-bin/DatabaseParser >> "100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml"" >> command completed in 0 sec >> >> running: "C:/Inetpub/tpp-bin/RefreshParser >> "100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml" >> "c:/Inetpub/wwwroot/ISB/data/dbase/BCaRun_301013/CONCAT_Uniprot_reviewed_human_301013.fasta"" >> - Searching the tree... >> - Linking duplicate entries... - Printing results... >> >> - Building Commentz-Walter keyword tree...command completed in 25 sec >> >> running: "C:/Inetpub/tpp-bin/PeptideProphetParser >> "100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml" MINPROB=0.05 ACCMASS >> DECOY=DECOY_" >> using Accurate Mass Bins >> Using Decoy Label "DECOY_". >> (X! Tandem (k-score)) >> adding Accurate Mass mixture distr >> init with X! Tandem (k-score) trypsin >> MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ Orbitrap >> Velos, Ionization: nanoelectrospray, Analyzer: radial ejection linear ion >> trap, Detector: electron multiplier >> >> PeptideProphet (TPP v4.6 OCCUPY rev 3, Build 201307241109 (MinGW)) >> AKeller@ISB >> read in 0 1+, 27515 2+, 20201 3+, 3650 4+, 364 5+, 0 6+, and 0 7+ spectra. >> Initialising statistical models ... >> Found 10795 Decoys, and 40935 Non-Decoys >> Iterations: .........10.........20........ >> model complete after 29 iterations >> command completed in 127 sec >> >> running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i >> 100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml -d "DECOY_"" >> Analyzing 100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml ... >> Reading Accurate Mass Model model +1 ... >> Reading Accurate Mass Model model +2 ... >> Reading Accurate Mass Model model +3 ... >> Reading Accurate Mass Model model +4 ... >> Reading Accurate Mass Model model +5 ... >> Reading Accurate Mass Model model +6 ... >> Reading Accurate Mass Model model +7 ... >> Parsing search results >> "c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01 >> (X! Tandem (k-score))"... >> => Found 33382 hits. (0 decoys, 0 excluded) >> => Total so far: 33382 hits. (0 decoys, 0 excluded) >> The system cannot find the path specified. >> command completed in 13 sec >> >> running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I >> c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml" >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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