Hello Brian, As of the 4.8 release, the outputting of the pepXML results to the directory containing the search engine parameters is a new intentional way to store the files. This allows you to keep one directory with the data (e.g. C:\Inetpub\wwwroot\ISB\data\mydata) and do your searches in separate directories (e.g. C:\Inetpub\wwwroot\ISB\data\mycomet and C:\Inetpub\wwwroot\ISB\data\mytandem). This allows one to run multiple search engines and use iProphet without copying the data to each search directory. Hopefully, this will save you some space and make building more complex processing methods (ones that include multiple search engines) easier to setup and more efficient.
Sorry for the confusion. -David On Thu, Dec 4, 2014 at 11:39 AM, Brian Hampton <[email protected]> wrote: > Hello, > > After doing my first tandem pipeline with v4.8 on a 32bit install of Windows > 7, it is putting the generated files in the parameters directory rather than > in the directory where the spectrum files live. > > I checked the original tandem_params.xml and it specifies the output to be: > full_tandem_output_path which is the same as it is on my Linux installs > where all the output files go to the directory containing the spectrum files > (.mzML). > > Am I missing a setting? > > And I can confirm that ASAPRatio executes much faster than previous > versions. > > > Thanks in advance. > > > Brian Hampton > Protein Analysis Lab > Center for Vascular and Inflammatory Diseases > University of Maryland School of Medicine > 655 West Baltimore Street BRB 7-018 > Baltimore MD 21201 > V: 410-706-8207 > > -- > 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.
