oops - I just read your last note. Name your Tandem searches with an extension.xtan.xml or just .xml; using .mzXML for those is asking for trouble.
On Wed, May 5, 2010 at 2:43 PM, Jimmy Eng <jke...@gmail.com> wrote: > 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.
