MSGF+ data can be processed using the semi-parametric model as written in the WARNING messages. To enable you must use -OP when running xinteract. I suggest you try the following xinteract command:
xinteract -OPd -p0 -dXXX_ *.xml On Thu, Mar 24, 2016 at 1:07 AM, Honglan Li <[email protected]> wrote: > > Hi, everyone. > > I want to run PeptideProphet using MS-GF+ results. > > But it's not works well. > > In order to run PeptideProphet, we converted *.mzid to pepXML using > idconvert (tpp 4.8 , ubuntu 14.04) > > Each psm have five types of scores: > -raw > -denovo > -SepcEValue > -IsotopeError > > > *Then we executed the PeptideProphet with coverted file (cmd: xinteract > -dXXX_ *.xml) and received such errors as follows:* > > Would you please give me some advises for solving this problem? > > Thanks a lot. > > > > ---- > running: "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml' > DECOY=XXX_" > Using Decoy Label "XXX_". > (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 > Segmentation fault (core dumped) > > > > > > > -- > 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 https://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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
