How can I download 4.7. version? There are still links to the 4.6.3 as the latest at wiki webpage. Thanks!
W dniu piątek, 28 lutego 2014 08:18:47 UTC+2 użytkownik user1 napisał: > > 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]> 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]. >>> To post to this group, send email to [email protected]. >>> 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. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
