So perhaps it is something wrong with my system? I just placed the
pep.xml file that Jimmy created for me into my c:/Inetpub/wwwroot/ISB/
data folder.
Via petunia I tried to run PeptideProphet with that file, I get the
following error:
Output Files
* c:/Inetpub/wwwroot/ISB/data/interact.pep.shtml [ Unreadable! ]
Command 1 [Thu Mar 3 16:23:28 2011] [ Show / Hide ]
run_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\xinteract -
Ninteract.pep.xml -p0.05 -l7 -OAg c:/Inetpub/wwwroot/ISB/data/
RG_83_top10_mips_off_2.pep.xml
command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -
OAg c:/Inetpub/wwwroot/ISB/data/RG_83_top10_mips_off_2.pep.xml"
failed: Unknown error
Command FAILED
Any suggestions would be greatly appreciated!
Thanks!
Ruby
On Mar 3, 3:43 pm, Jimmy Eng <jke...@gmail.com> wrote:
> I'm stumped as I can't replicate the error. Ruby sent me her data and
> I had no problems running Out2XML to generate the pep.xml file. Both
> on a Windows box and under Linux.
>
> - Jimmy
>
> On Mar 1, 1:58 pm, Ruby <rgund...@jhmi.edu> wrote:
>
> > Hi-
> > I just downloaded the latest version of TPP this week, so version:
> > TPP v4.4 VUVUZELA rev 1, Build 201010121551 (MinGW)
>
> > I'm still really hoping for an answer for the -Etrypsin error.....I'm
> > stuck until I get that figured out.
>
> > Thanks!!
> > Ruby
>
> > On Feb 28, 12:04 pm, Joe Slagel <jsla...@systemsbiology.org> wrote:
>
> > > Hi Rudy,
>
> > > For both questions you have, what version of TPP are you using? and I'm
> > > assuming you are trying to convert the .RAW to mzXML using the petunia
> > > interface? (And I'll defer to others on your first question...unless you
> > > don't get an answer).
>
> > > -Joe
>
> > > On Sat, Feb 26, 2011 at 6:02 PM, Ruby <rubycell7...@gmail.com> wrote:
> > > > Hi-
> > > > 1) I'm trying to use the TPP to process my Sequest search results.
> > > > (since I have access to sequest only on a cluster, I'm not able to use
> > > > the TPP to setup the search, which is what I'd like to do). Rather,
> > > > I'm trying to use the .out files for peptide & proteinprophet
> > > > processing.
>
> > > > However, I get this error when I try to process my directory that has
> > > > the .out files from the Sequest search.
>
> > > > command "c:\Inetpub\tpp-bin\Out2XML c:/Inetpub/wwwroot/ISB/data/
> > > > RG_81_2 1 -Etrypsin" failed: Unknown error
>
> > > > Is this due to the fact that I did a semi-enzyme search? How can I
> > > > work around this? I didn't see a semi-enzyme choice in the 'options'
> > > > section of the convert to pepXML page.
>
> > > > 2) I'd like to do an XTandem search via the TPP. When I try to
> > > > convert .RAW to mzXML, I get this error:
> > > > 'c:\Inetpub\tpp-bin\ReAdW' is not recognized as an internal or
> > > > external command, operable program or batch file.
>
> > > > I thought that TPP wasn't using ReAdW anymore, but rather the
> > > > MSConverter. I have downloaded the MSFileReader, but what parts of
> > > > that go in the tpp-bin directory?? Basically, how do I get it
> > > > configured so that it uses MSConvert for processing the .RAW files?
>
> > > > Thanks!
> > > > Ruby
>
> > > > --
> > > > You received this message because you are subscribed to the Google
> > > > Groups
> > > > "spctools-discuss" group.
> > > > To post to this group, send email to spctools-discuss@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.
>
> > > --
> > > Joe Slagel
> > > Institute for Systems Biology
> > > jsla...@systemsbiology.org
> > > (206) 732-1362
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To post to this group, send email to spctools-discuss@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.
