Hi Simon, This error indicates that the PepXMLViewer failed when it tried to index your pepxml file. .pepprophet.xml is not a normal extension produced by the TPP for a pepXML file. Can you describe exactly how you arrived at this pepXML file?
Thanks, -David On Wed, Jun 9, 2010 at 1:46 AM, Simon Michnowicz <[email protected]> wrote: > Dear Group, > I ran xinteract on a pepXML file that was generated from a Mascot > search, and it exited with an error message. > > command "/mnt/sanfs/APCF-PROD/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi - > I /mnt/sanfs/APCF-PROD/results/tpp/2010-06-08/simon- > J2468.pepprophet.xml" exited with non-zero exit code: 11 > > I am afraid I do not know what this error means. I found the input > pepXML only had a few number of entries, so am I right to think that > this is cause of the error?(The Mascot search was done using > incorrect parameters, resulting in a poor output) > I have two questions: > (1) How much data do you need to provide a satisfactory run for > peptideProphet? Is it possible to check this before calling xinteract? > (2) I looked at the .dat=>pepXML conversion via Mascot2XML. I expected > a 1:1 mapping for proteins, however I found only a subset of proteins > being placed in the file. Is there some internal filtering that occurs > here? The scores were all low, which might have taxed any algorithm to > do this. > > Much thanks for any assistance. > Simon Michnowicz > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
