Hi Ben, The latest version of myrimatch leaves out the sample enzyme flag that RefreshParser relies on. Simply add these two lines to the top of your myrimatch pep.xml files to get them to process:
<sample_enzyme name="trypsin"> </sample_enzyme> This a temporary solution that will allow RefreshParser to process Myrimatch results for now, until Myrimatch fixes its pepXML output. Cheers, -David On Wed, Aug 11, 2010 at 6:30 AM, Ben Collins <[email protected]> wrote: > 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. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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