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]. >>> 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]. > 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. 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