I think I have resolved the problem. The spectrum title in pepXML must contains no space while running PeptideProphet. Thank you very much!
在 2014年10月17日星期五UTC+8下午11时09分41秒，David Shteynberg写道： > > In this case you will need to delve into the details of the pepXML > format output by your method and correct the problems therein. If you > post an example pepXML file you have generated I can see if it is an > easy fix. > -David > > > > On Fri, Oct 17, 2014 at 12:06 AM, 李桂林 <ligui...@gmail.com <javascript:>> > wrote: > > But what if I only have the mzid files? Because I have successfully run > the > > peptideprophet for mzid-transformed pepXML in TPP 4.6.3. Now both 4.6.3 > and > > 4.7.1 fail. > > > > 在 2014年10月17日星期五UTC+8上午12时26分56秒，David Shteynberg写道： > >> > >> The problem is the idconvert generated pepxml is not compatible. I > >> believe MyriMatch includes pepxml output directly. That's more likely > to > >> work. > >> > >> David > >> > >> On Oct 15, 2014 10:06 PM, "李桂林" <ligui...@gmail.com> wrote: > >>> > >>> But now I get a new problem when I tried to run PeptideProphet (TPP > >>> 4.7.1) for Myrimatch search result. > >>> Here is how I do this > >>> 1. search against a target-decoy database with Myrimatch > >>> 2. transform the mzid file to pepXML using ProteoWizard idconvert > >>> 3. run PeptideProphet with command 'path\to\xinteract -Nout.pep.xml > -p0 > >>> -l6 -OAP -Od -d###REV### input.pepXML' > >>> The InteractParser terminated in an unusual way reporting error > >>> Assertion failed: px != 0, file > >>> > c:\release_4-7-1\trans_proteomic_pipeline\extern\boost_1_54_0\boost\smart_ptr\shared_ptr.hpp, > > > >>> line 653 > >>> How this happen? Anyone know about this? > >>> > >>> 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 spctools-discu...@googlegroups.com. > >>> To post to this group, send email to spctools...@googlegroups.com. > >>> 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 spctools-discu...@googlegroups.com <javascript:>. > > To post to this group, send email to spctools...@googlegroups.com > <javascript:>. > > 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
