I've been able to reproduce the issue. It's due to the fairly recent improvements to the CleavageRules variable which now supports of cleavage agent names
(from the PSI-MS CV), Perl zero-width regular expressions (like those in the PSI-MS CV) while still supporting the old proprietary syntax. This bug only
manifests for the new syntaxes, but since I changed the default value to be "trypsin/p" instead of the old syntax equivalent, the default produces the bugged
behavior. :) I am working on a fix.
Thanks,
-Matt
On 8/12/2010 12:03 PM, Joe Slagel wrote:
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]
<mailto:[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]
<mailto:[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]
<mailto:[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]
<mailto:[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
>>>
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