Hi Andreas,
This software is still in early testing, thanks for trying it out. When I run the software it is done after PeptideProphet or iProphet processing. You can either specify the exact mod to use or if nothing is given PTMProphet uses a default of STY,79.9799 . The latest version of this software is in SVN trunk. If you need me to troubleshoot your specific datafile please let me know. -David On Thu, Jan 12, 2012 at 10:39 AM, Andreas Quandt <[email protected]> wrote: > dear list, > > i ran some tests with ptmprophetparser (tpp v4.5.1) on the output of > xtandem, omssa and myrimatch after xinteract has been run on the original > search engine output. > unfortunately, each test produced a different error: > > >> PTMProphetParser interact_myrimatch.pep.xml > Unknown file type. No file loaded. > Segmentation fault > >> PTMProphetParser interact_tandem.pep.xml > .................................... > .................................... > .................................... > (continues like that and does not stop even after 1h) > > $ /cluster/apps/tpp/4.5.1/bin/PTMProphetParser interact_omssa.pep.xml > Failed to open input file > '/cluster/work/scr3/quandtan/workflow/614/0/0/omssa/vagas_B1110_086.pep.xml.mzXML'. > Segmentation fault > > it would be greatly appreciated if one of you, especially david ;-), could > give me some advice on how to solve the problem. > furthermore, i would like to kindly ask for help regading two other > questions: > - is ptmprophet is better applied after running xinteract or iprophet? > - what is the difference of specifying e.g. STY,80 as parameter or not > specific modification at all? > > many thanks in advance for any help from your side! > > cheers, > andreas > > > > > -- > 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.
