Matt, The version we are seeing the problem with is:
MyriMatch 1.6.74 (2010-7-2) FreiCore 1.6.107 (2010-6-21) ProteoWizard MSData 2.1.2068 (2010-6-21) ProteoWizard Proteome 2.1.2071 (2010-6-21) Vanderbilt University Mass Spectrometry Research Center, D.Tabb/M.Chambers/S.Dasari Licensed under the Mozilla Public License. On Thu, Aug 12, 2010 at 6:22 AM, Ben Collins <[email protected]> wrote: > Great, thanks David - your suggestion worked. > > Matt, FYI when I open the Myrimatch pepXML output in notepad and search for > '<sample_enzyme' I get no result so it seems like this tag is missing for me > also. I'm using MyriMatch 1.6.75 (2010-7-14). > > Thanks, > Ben > > > On Wed, Aug 11, 2010 at 5:35 PM, David Shteynberg < > [email protected]> wrote: > >> Apologies for any rushed conclusions, but we came across this bug at >> the isb just yesterday. I will have to verify the exact version of MM >> that failed to generate this tag at isb. BTW RefreshParser was fixed >> to generate a reasonable error in this scenario instead of a seg >> fault. >> >> David >> >> >> >> On 8/11/10, Matthew Chambers <[email protected]> wrote: >> > Er, in what version of MM have you seen this bug? I don't remember >> that >> > bug, and that code hasn't been changed since at least March 2009. >> > Latest version gives: >> > <sample_enzyme name="trypsin"> >> > <specificity cut="KRM" no_cut="" sense="C" /> >> > </sample_enzyme> >> > This search was configured to allow cleavage after protein N-terminal >> > methionines, which unfortunately pepXML cannot represent properly. >> > >> > -Matt >> > >> > >> > On 8/11/2010 10:35 AM, David Shteynberg wrote: >> >> 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]<spctools-discuss%[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. >> > To post to this group, send email to [email protected]. >> > To unsubscribe from this group, send email to >> > [email protected]<spctools-discuss%[email protected]> >> . >> > For more options, visit this group at >> > http://groups.google.com/group/spctools-discuss?hl=en. >> > >> > >> >> -- >> Sent from my mobile device >> >> -- >> 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]<spctools-discuss%[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. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]<spctools-discuss%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- Joe Slagel Institute for Systems Biology [email protected] (206) 732-1362 -- 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.
