Actually it failed because it wasn't run in Semiparametric mode. Check the box next to use nonparametric models and try again. On Mar 27, 2014 7:27 AM, "Jimmy Eng" <[email protected]> wrote:
> 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. > -- 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.
