Hello Peter, There could be several things causing this.
1. incomplete or corrupted iProphet pepXML. Can you check the file sizes and the closing tags to make sure that you files are complete? 2. system limitation on the length of the command. You can use InteractParser with -W flag to combine your iProphet pepXMLs into one huge pepXML file. 3. unknown bug Can you check each of your iProphet pepXMLs to make sure that they are complete first and check for any upstream error messages from your iProphet runs? Also iProphet works well when combining PeptideProphet results, can you perhaps combine your PeptideProphet runs into a smaller number of iProphet pepXMLs by grouping more of your PeptideProphet pepXMLs together in iProphet before you run ProteinProphet? Thanks, -David On Wed, Sep 9, 2015 at 10:41 PM, ha...@uow.edu.au <snoor...@gmail.com> wrote: > Hi, > > > I'm trying to generate a prot.xml file from 120 interact.ipro.pep.xml > files. There seems to be some numerical limit on ProteinProphet as when I > try to add all the ipro files the system immediately returns an error 256 > code. If I choose a smaller number, say 10 ipro files, it goes to > completion. Is there some max number of files that can be combined with > ProteinProphet? Is there some way around this? It's an absolute requirement > for me to make a prot.xml file from this data. > > > I'm using TPP v 4.8.0 on aWin7 system, 64-bit, 64 GB RAM. > > > If this is a known problem, I guess I could just pool more pep.xml files > into each ipro file to reduce my overall number of files input into > ProteinProphet. I've got some very large interact.ipro.pep.xml that are > taking time to process into the prot.xml but that's to be expected. > > > Thanks, > > > Peter > > -- > 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. > -- 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.
