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. 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