Ruby,
The problem likely has nothing to do with the -Etrypsin option in the
Out2XML command. Do you have a bunch of *.out files in the directory
c:\Inetpub\wwwroot\ISB\data\RG_81_2\
Are those files named something like RG_81_2.00001.00001.1.out?
- Jimmy
On Tue, Mar 1, 2011 at 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
>>
>> > --
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>>
>> --
>> Joe Slagel
>> Institute for Systems Biology
>> jsla...@systemsbiology.org
>> (206) 732-1362
>
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