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 <[email protected]> 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" <[email protected]> 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 [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.
