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
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