I forgot to mention in my first post that I am using version 4.6.3 Thanks again.
On Wednesday, October 2, 2013 3:44:45 PM UTC-4, [email protected] wrote: > > Hello, I am working my way through the tutorial > <http://tools.proteomecenter.org/wiki/index.php?title=TPP_Tutorial>and I > get a lot of error messages when I run step 5. It looks like the data is > returned properly, but there is a lot of it so I can't be entirely sure. In > addition to the error messages in the output the command is reported as > "FAILED" and returns error code 65280. > > Is this a benign error or is the program really not working? > > I'm using an Optiplex 760 running Windows 7. > > Here is the output: > > c:\Inetpub\tpp-bin\xinteract (TPP v4.6 OCCUPY rev 3, Build 201307241109 > (MinGW)) > > > > running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" > "OR20080317_S_SILAC-LH_1-1_01.tandem.pep.xml" > "OR20080320_S_SILAC-LH_1-1_11.tandem.pep.xml" -L"7"" > > file 1: OR20080317_S_SILAC-LH_1-1_01.tandem.pep.xml > > SUCCESS: CORRECTED data file > c:/Inetpub/wwwroot/ISB/data/demo/tandem/OR20080317_S_SILAC-LH_1-1_01.mzML > in msms_run_summary tag ... > > file 2: OR20080320_S_SILAC-LH_1-1_11.tandem.pep.xml > > SUCCESS: CORRECTED data file > c:/Inetpub/wwwroot/ISB/data/demo/tandem/OR20080320_S_SILAC-LH_1-1_11.mzML > in msms_run_summary tag ... > > processed altogether 19268 results > > INFO: Results written to file: > c:/Inetpub/wwwroot/ISB/data/demo/tandem/interact.pep.xml > > command completed in 7 sec > > > > running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" > > command completed in 0 sec > > > > running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" > "c:/Inetpub/wwwroot/ISB/data/dbase/yeast_orfs_all_REV.20060126.short.fasta"" > > - Searching the tree... > > - Linking duplicate entries... - Printing results... > > > > - Building Commentz-Walter keyword tree...command completed in 5 sec > > > > running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > MINPROB=0.05 ACCMASS" > > using Accurate Mass Bins > > (X! Tandem (k-score)) > > adding Accurate Mass mixture distr > > init with X! Tandem (k-score) trypsin > > MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, > Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive > detector > > > > PeptideProphet (TPP v4.6 OCCUPY rev 3, Build 201307241109 (MinGW)) > AKeller@ISB > > read in 0 1+, 9115 2+, 7794 3+, 1724 4+, 212 5+, 0 6+, and 0 7+ spectra. > > Initialising statistical models ... > > negmean = 0.0533258 > > negmean = -0.20604 > > negmean = -0.967361 > > negmean = 0.313158 > > negmean = 0.95268 > > negmean = -0.2 > > negmean = -0.2 > > Iterations: .........10.........20......... > > model complete after 30 iterations > > command completed in 32 sec > > > > running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml" > > Analyzing 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/demo/tandem/OR20080317_S_SILAC-LH_1-1_01 (X! > Tandem (k-score))"... > > => Found 4059 hits. (0 decoys, 0 excluded) > > => Total so far: 4059 hits. (0 decoys, 0 excluded) > > Parsing search results > "c:/Inetpub/wwwroot/ISB/data/demo/tandem/OR20080320_S_SILAC-LH_1-1_11 (X! > Tandem (k-score))"... > > => Found 3990 hits. (0 decoys, 0 excluded) > > => Total so far: 8049 hits. (0 decoys, 0 excluded) > > The system cannot find the path specified. > > command completed in 2 sec > > > > running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > c:/Inetpub/wwwroot/ISB/data/demo/tandem/interact.pep.xml" > > command completed in 3 sec > > > > running: "C:/Inetpub/tpp-bin/tpp_models.pl "interact.pep.xml"" > > syntax error at C:/Inetpub/tpp-bin/tpp_models.pl line 630, near "$head > qw(min_prob Sensitivity Error_Rate num_correct num_incorrect)" > > Global symbol "$file" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 643. > > syntax error at C:/Inetpub/tpp-bin/tpp_models.pl line 652, near "}" > > Can't use global @_ in "my" at C:/Inetpub/tpp-bin/tpp_models.pl line 655, > near "= @_" > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 657. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 658. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 659. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 660. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 661. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 662. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 663. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 664. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 665. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 666. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 667. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 672. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 682. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 682. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 686. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 686. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 687. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 687. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 688. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 692. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 693. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 695. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 696. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 697. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 701. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 702. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 703. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 705. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 706. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 710. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 711. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 712. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 714. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 716. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 717. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 721. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 722. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 728. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 729. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 731. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 732. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 739. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 740. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 745. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 746. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 747. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 748. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 753. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 754. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 755. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 757. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 758. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 762. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 763. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 764. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 769. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 773. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 774. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 776. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 777. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 780. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 782. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 784. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 785. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 789. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 791. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 791. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 792. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 792. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 796. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 796. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 797. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 799. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 800. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 807. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 808. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 810. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 811. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 815. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 816. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 816. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 818. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 819. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 824. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 825. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 826. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 830. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 831. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 832. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 834. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 834. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 834. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 834. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 836. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 837. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 841. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 842. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 844. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 844. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 846. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 846. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 850. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 851. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 851. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 851. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 851. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 851. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 855. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 855. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 856. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 856. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 859. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 862. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 864. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 864. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 865. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 865. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 866. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 866. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 868. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 868. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 870. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 871. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 874. > > Global symbol "%atts" requires explicit package name at C:/Inetpub/tpp-bin/ > tpp_models.pl line 875. > > Global symbol "$element" requires explicit package name at > C:/Inetpub/tpp-bin/tpp_models.pl line 881. > > syntax error at C:/Inetpub/tpp-bin/tpp_models.pl line 884, near "$head > qw(Error_Rate min_prob num_correct num_incorrect)" > > C:/Inetpub/tpp-bin/tpp_models.pl has too many errors. > > > > command "perl C:/Inetpub/tpp-bin/tpp_models.pl "interact.pep.xml"" > failed: Unknown error > > > > command "C:/Inetpub/tpp-bin/tpp_models.pl "interact.pep.xml"" exited with > non-zero exit code: 255 > > QUIT - the job is incomplete > > command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -OA > OR20080317_S_SILAC-LH_1-1_01.tandem.pep.xml > OR20080320_S_SILAC-LH_1-1_11.tandem.pep.xml" failed: Unknown error > > > Any input is appreciated. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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