It's not an error but rather a warning. The warning by itself doesn't indicate a critical problem (although I suspect you might have other problems). Take a look at your pep.xml file and see if it looks like it has reasonable content in it.
Some things to note: - your tandem input file should be the Tandem search results xml and not be an .mzXML file (which is the raw mass spec data) - use .pep.xml as the extension to the created pepXML file to stick with the conventions that the TPP tools expect - ideally your Tandem search used the mzXML file as input otherwise you might have compatibility issues with tools in the TPP which expect inputs to follow certain conventions - ignore last two bullet points if you're not using rest of TPP tools On Wed, May 5, 2010 at 1:20 PM, Jesse J <firstblackphan...@gmail.com> wrote: > I'm trying to run Tandem2XML to convert an X!Tandem output file to > pepXML, but I get an error every time I try to run it. > > When I run: Tandem2XML /full/path/name/to/tandem_output.mzXML /full/ > path/name/to/test.pepXML > I get the errors: > WARNING: Failed to open mzXML file. > Output will not contain retention times. > > I tried searching for any sort of documentation on Tandem2XML but I > can't find any, so I can't figure out what the problem even is. > > Notes: If it's of any importance, I'm using Ubuntu and running the > program under wine. Also, I'm unsure of what the file extension for > the X!Tandem output is, so I simply gave it the mzXML extension. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > 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 spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
