It works now. Thanks. Both files took almost 500 iterations, but atleast
that is fast and not infinite. :)
Greg
On Wed, Sep 24, 2008 at 6:11 PM, David Shteynberg <
[EMAIL PROTECTED]> wrote:
> Hi Greg,
>
> Thanks for submitting this bug report. I have addressed the issue and
> committed my code
Hi Greg,
Thanks for submitting this bug report. I have addressed the issue and
committed my code to SVN. Please try it out and let me know of any other
problems you encounter.
Thanks,
-David
On Wed, Sep 24, 2008 at 2:18 PM, Greg Bowersock <[EMAIL PROTECTED]> wrote:
> I already posted the pep.
I already posted the pep.xml file after InteractParser. Do you want the
sequest directory and database, or just the file that was uploaded over the
weekend?
Greg
On Wed, Sep 24, 2008 at 3:16 PM, David Shteynberg <
[EMAIL PROTECTED]> wrote:
> Thanks for the clarification. Can you post the proble
Thanks to Luis and Ulrich. Here are some answers. All my spectra
numbers do look like spectrum2...2. How do I fix that?
My itraq signals are fine, although I am only using 3 tags (no 117). I
am able to seen them show up on Mascot, and on different spectra
viewers. For some reason, when I
Thanks for the clarification. Can you post the problem datasets to our FTP
site and send me the filename?
-David
On Wed, Sep 24, 2008 at 1:00 PM, Greg Bowersock <[EMAIL PROTECTED]> wrote:
> Sorry it was PeptideProphetParser that had the loop. InteractParser was the
> last step that worked befor
Sorry it was PeptideProphetParser that had the loop. InteractParser was the
last step that worked before the failure, so it got stuck in my head. Sorry
about the confusion.
Greg
On Wed, Sep 24, 2008 at 2:29 PM, David Shteynberg <
[EMAIL PROTECTED]> wrote:
> Hi Greg,
>
> InteractParser is not an it
Hi Greg,
InteractParser is not an iterative tool. Are you sure you got the name of
the tool that's failing correct? Please double check.
Thanks,
-David
On Sun, Sep 21, 2008 at 7:35 PM, [EMAIL PROTECTED] <[EMAIL PROTECTED]>wrote:
>
> I have 2 sequest searches (out of 21) that I ran this weeken
Hello Carla,
First thing I would look at is the spectrum of identified peptides - can you
tell if they have good iTraq reporter ion signals? (Click on the "ions"
link
in the PepXMLViewer to launch the Spectrum Viewer, then click on the
"zoom 112 - 122" checkbox and press "Go".)
Next I would make
Hi Carla,
this usually happens to me if Mascot2XML doesn't find the right scan
number for identified peptides in mzXML. Are all your spectra numbers
like 0.0.2 (or whatever charge state)?
Cheers,
Ulrich
On Sep 24, 2008, at 12:15 PM, Luis Mendoza wrote:
> Hello Carla,
> First thing
My tpp install does not look at all like the example on
http://tools.proteomecenter.org/wiki/index.php?title=TPP:Using_Petunia.
Here is an image of what mine looks like:
http://groups.google.com/group/spctools-discuss/web/tpp.nocss.png. It
seems like it might not be seeing the .css.
Is this a co
Hi,
I am running Libra with Mascot data (on TPP 4.0.2), and it runs, but
all peptides contain the messages in PeptideProphet:
[libra1: unavailable] [libra2: unavailable] [libra3: unavailable]
[libra4: unavailable]
I looked up previous posts, however, cannot find the reason why this
happens,
Gah disregard this. This happened on an earlier install, so I
tried again on a development server. I needed to mount a couple of
network folders, and accidentaly mounted /usr/local from the old
server so when I tried to run the programs, it was using the messed up
binaries. Thanks for th
I haven't seen that behavior either. I'd suggest removing all of the
binaries that you created, wiping out your install directory and trying to
compile again. It almost seems like the path was wrong for an initial
attempt and the files aren't being overwritten (or recreated) with the new
compile. Y
Hi Jason,
Sorry to hear that you've having troubles. I'm routinely building on
linux and haven't noticed this problem. Are you using the official
4.0.2 release, or the development SVN trunk?
Natalie
On Wed, Sep 24, 2008 at 8:20 AM, Jason <[EMAIL PROTECTED]> wrote:
>
> I am trying to get tpp w
I am trying to get tpp working. I have created a file called
Makefile.config.incl with the following
-
TPP_ROOT=/usr/local/www/tpp/
TPP_WEB=/tpp/
XSLT_PROC=/usr/bin/xsltproc
--
All of the binary executables in /usr/local/www/tpp/bin complain when
they run with errors like this:
"error
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