I believe that PeptideProphet failed because you told it to use a decoy tag that it could not find in any of the search results. Apparently the decoy tag in MSGF+ is always "XXX_" and can't be changed. So you must set that as the decoy tag and make sure that same decoy tag is used in MyriMatch.
Another option is to use a self generated target-decoy database and turn off the auto-decoy option in the search engines. On Thu, Mar 27, 2014 at 2:29 AM, <[email protected]> wrote: > Hi, > I try to combine two different search engine results using iProphet. > One is myrimatch, the other is MSGF+. > The decoy database search is auto conducted by each search engine. > But iProphet failed, exactly PeptideProphetParser failed, when I > select "Analysis Pipeline (Tandem)" -> "Analyze Peptides" in TPP 4.6.3 to > combine them. > The parameters for PeptideProphet and InterProphet are showed below. > > > <https://lh6.googleusercontent.com/-aIAyfalUSIo/UzPtqmRkHoI/AAAAAAAAAAM/RcNaJf-gpcU/s1600/QQ%E5%9B%BE%E7%89%8720140327172121.jpg> > > > <https://lh5.googleusercontent.com/-rfMJq_uvl4c/UzPt7QykkQI/AAAAAAAAAAU/DGzmgdsYqhQ/s1600/QQ%E5%9B%BE%E7%89%8720140327172230.jpg> > > Here is the log. > > running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > MINPROB=0.01 DECOY=###REV###" > > Using Decoy Label "###REV###". > (MS-GF+) > WARNING!! The discriminant function for MSGFPL 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: MSGFPL only support semi-parametric PeptideProphet modelling, which > relies on a DECOY search. > WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which > relies on a DECOY search. > WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which > relies on a DECOY search. > WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which > relies on a DECOY search. > WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which > relies on a DECOY search. > WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which > relies on a DECOY search. > WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which > relies on a DECOY search. > init with MS-GF+ trypsin > two different search engines specified: MS-GF+ and MyriMatch > > command "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > MINPROB=0.01 DECOY=###REV###" failed: Operation not permitted > > command "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > MINPROB=0.01 DECOY=###REV###" exited with non-zero exit code: 1 > QUIT - the job is incomplete > > > Can any body tell me why this happen? Why the PeptideProphetParser > failed? > > By the way, it didn't print error information when I try the command > manually. > Thanks very much! > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
