Hello Nikhil, It seems that you are running an old version of the TPP (4.3.1); I would suggest installing the newest available version (4.4.1) to see if this problem still shows up for you. You seem to be running the command from Petunia on a Windows install, is that correct? Did you simply download the TPP, or did you build it from the source code?
I am at this point not sure that the quotes are to blame, since this seems to work for many other instances of the TPP out there. Hope this helps, --Luis On Tue, Nov 23, 2010 at 9:04 AM, Nikhil Garge <[email protected]> wrote: > Hi, > > I am not able to run ProteinProphet. I get following error: > > c:\Inetpub\tpp-bin\ProteinProphet > c:/Inetpub/wwwroot/ISB/data/PeptideProphetOutput.pep.xml > c:/Inetpub/wwwroot/ISB/data/interact.prot.xml > > ________________________________ > > ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the > original Perl by A. Keller (TPP v4.3 JETSTREAM rev 1, Build 200909091257 > (MinGW)) > (xml input) (report Protein Length) (using degen pep info) > > pipe "C:/Inetpub/tpp-bin/DatabaseParser > "c:/Inetpub/wwwroot/ISB/data/PeptideProphetOutput.pep.xml"" failed: Invalid > argument > > Command FAILED > ************* > Looks like the "DatabaseParser" command is not able to execute. It might > have added some unwanted quotes (in command). Becuase when I remove quotes > and run the same command on DOS prompt, it runs OK (showing me the FASTA > file path). > >> C:/Inetpub/tpp-bin/DatabaseParser >> c:/Inetpub/wwwroot/ISB/data/PeptideProphetOutput.pep.xml ----- >> this command runs fine > > Please help me to make a smooth proteinProphet run. > > Thanks, > ~Nikhil > > -- > 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.
