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.
