Hi, I'm trying to get TPP to work with Myrimatch pepXML output. Everything seems to be going okay but I get an error at the RefreshParser stage (see output below). The only slightly unusual thing I did was to change '.pepXML' extensions that Myrimatch produces to the TPP convention '.pep.xml'. I'm using the windows release version (4.3.1) on Windows Vista Business 64 bit (this configuration normally works fine with TPP).
Many thanks for any suggestions, Ben # Commands for session DUQCFMUJJ on Wed Aug 11 13:41:25 2010 # BEGIN COMMAND BLOCK ###### BEGIN Command Execution ###### [Wed Aug 11 13:41:25 2010] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/ data/ben_data/100721_MCF7_SCX; c:\Inetpub\tpp-bin\xinteract - Nmyri_test_interact.pep.xml -p0.05 -l7 -OA -ddecoy_ c:/Inetpub/wwwroot/ ISB/data/ben_data/100721_MCF7_SCX/100721_MCF7_SCX-r002.myri.pep.xml c:/ Inetpub/wwwroot/ISB/data/ben_data/100721_MCF7_SCX/100721_MCF7_SCX- r003.myri.pep.xml c:/Inetpub/wwwroot/ISB/data/ben_data/100721_MCF7_SCX/ 100721_MCF7_SCX-r004.myri.pep.xml OUTPUT: c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909091257 (MinGW)) running: "C:/Inetpub/tpp-bin/InteractParser "myri_test_interact.pep.xml" "c:/Inetpub/wwwroot/ISB/data/ben_data/ 100721_MCF7_SCX/100721_MCF7_SCX-r002.myri.pep.xml" "c:/Inetpub/wwwroot/ ISB/data/ben_data/100721_MCF7_SCX/100721_MCF7_SCX-r003.myri.pep.xml" "c:/Inetpub/wwwroot/ISB/data/ben_data/100721_MCF7_SCX/100721_MCF7_SCX- r004.myri.pep.xml" -L"7"" file 1: c:/Inetpub/wwwroot/ISB/data/ben_data/100721_MCF7_SCX/ 100721_MCF7_SCX-r002.myri.pep.xml file 2: c:/Inetpub/wwwroot/ISB/data/ben_data/100721_MCF7_SCX/ 100721_MCF7_SCX-r003.myri.pep.xml file 3: c:/Inetpub/wwwroot/ISB/data/ben_data/100721_MCF7_SCX/ 100721_MCF7_SCX-r004.myri.pep.xml processed altogether 41870 results results written to file c:/Inetpub/wwwroot/ISB/data/ben_data/ 100721_MCF7_SCX/myri_test_interact.pep.xml direct your browser to http://localhost/ISB/data/ben_data/100721_MCF7_SCX/myri_test_interact.pep.shtml command completed in 231 sec running: "C:/Inetpub/tpp-bin/PeptideProphetParser "myri_test_interact.pep.xml" MINPROB=0.05 ACCMASS DECOY=decoy_" using Accurate Mass Bins Using Decoy Label "decoy_". (MyriMatch) WARNING!! The discriminant function for Myrimatch is not yet complete. It is presented here to help facilitate trial and discussion. Reliance on this code for publishable scientific results is not recommended. WARNING: Myrimatch only support semi-parametric PeptideProphet modelling, which relies on a DECOY search. adding Accurate Mass mixture distr WARNING: Myrimatch only support semi-parametric PeptideProphet modelling, which relies on a DECOY search. WARNING: Myrimatch only support semi-parametric PeptideProphet modelling, which relies on a DECOY search. WARNING: Myrimatch only support semi-parametric PeptideProphet modelling, which relies on a DECOY search. WARNING: Myrimatch only support semi-parametric PeptideProphet modelling, which relies on a DECOY search. WARNING: Myrimatch only support semi-parametric PeptideProphet modelling, which relies on a DECOY search. WARNING: Myrimatch only support semi-parametric PeptideProphet modelling, which relies on a DECOY search. init with MyriMatch MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909091257 (MinGW)) akel...@isb read in 399 1+, 19065 2+, 17201 3+, 758 4+, 56 5+, 5 6+, and 4 7+ spectra. Initialising statistical models ... Iterations: .........10.........20.........30 WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 31 iterations command completed in 315 sec running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i myri_test_interact.pep.xml" Analyzing myri_test_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 "100721_MCF7_SCX-r002 (MyriMatch)"... => Total of 313 hits. Parsing search results "100721_MCF7_SCX-r003 (MyriMatch)"... => Total of 4614 hits. Parsing search results "100721_MCF7_SCX-r004 (MyriMatch)"... => Total of 4303 hits. command completed in 11 sec running: "C:/Inetpub/tpp-bin/DatabaseParser "myri_test_interact.pep.xml"" command completed in 3 sec running: "C:/Inetpub/tpp-bin/RefreshParser "myri_test_interact.pep.xml" "C:\Inetpub\wwwroot\ISB\data\dbase \uniprot_human_CP_canonical_isoform_cRAP_decoy_2010_08.fasta"" command "C:/Inetpub/tpp-bin/RefreshParser "myri_test_interact.pep.xml" "C:\Inetpub\wwwroot\ISB\data\dbase \uniprot_human_CP_canonical_isoform_cRAP_decoy_2010_08.fasta"" failed: Unknown error command "C:/Inetpub/tpp-bin/RefreshParser "myri_test_interact.pep.xml" "C:\Inetpub\wwwroot\ISB\data\dbase \uniprot_human_CP_canonical_isoform_cRAP_decoy_2010_08.fasta"" exited with non-zero exit code: 255 QUIT - the job is incomplete command "c:\Inetpub\tpp-bin\xinteract -Nmyri_test_interact.pep.xml - p0.05 -l7 -OA -ddecoy_ c:/Inetpub/wwwroot/ISB/data/ben_data/ 100721_MCF7_SCX/100721_MCF7_SCX-r002.myri.pep.xml c:/Inetpub/wwwroot/ ISB/data/ben_data/100721_MCF7_SCX/100721_MCF7_SCX-r003.myri.pep.xml c:/ Inetpub/wwwroot/ISB/data/ben_data/100721_MCF7_SCX/100721_MCF7_SCX- r004.myri.pep.xml" failed: Unknown error END OUTPUT RETURN CODE:65280 ###### End Command Execution ###### # All finished at Wed Aug 11 13:51:14 2010 # END COMMAND BLOCK -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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