Re: Problem of installing TPP V4.02

[Luis Mendoza]

Hello Bin,
Glad you got it to work.  Regarding the sequest error, please make sure that
your parameters file has the appropriate access permissions (i.e. that it can
be read by other users).  You can find info on how to do this by searching the
posts on this forum.
--Luis

On Tue, Sep 9, 2008 at 9:03 AM, Hong Yang <denk...@yahoo.com> wrote:

Hi Luis,   Thank you, I got it. Another question here. What's wrong as below when I run database search. Thnaks. Bin # Commands for session CAM9KPP0U on Tue Sep 9 11:58:12 2008 # BEGIN COMMAND BLOCK ###### BEGIN Command Execution ###### [Tue Sep 9 11:58:12 2008] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; runsearch -pc:/Inetpub/wwwroot/ISB/data/human_IPI_3.33_Ammon.params -P15 OT00034.mzML OUTPUT: RUNSEARCH Written by J.Eng (c) 2000 Cannot read c:/Inetpub/wwwroot/ISB/data/human_IPI_3.33_Ammon.params. END OUTPUT RETURN CODE:256 ###### End Command Execution ###### ###### BEGIN Command Execution ###### [Tue Sep 9 11:58:12 2008] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; runsearch -pc:/Inetpub/wwwroot/ISB/data/human_IPI_3.33_Ammon.params -P15 OT00038.mzXML OUTPUT: RUNSEARCH Written by J.Eng (c) 2000 Cannot read c:/Inetpub/wwwroot/ISB/data/human_IPI_3.33_Ammon.params. END OUTPUT RETURN CODE:256 ###### End Command Execution ###### # All finished at Tue Sep 9 11:58:12 2008 # END COMMAND BLOCK --- On Mon, 9/8/08, Luis Mendoza <lmen...@systemsbiology.org> wrote: From: Luis Mendoza <lmen...@systemsbiology.org> Subject: Re: Problem of installing TPP V4.02 To: denk...@yahoo.com Date: Monday, September 8, 2008, 4:29 PM Hello Bin, I think you have installed the Cygwin version of the TPP.  Which page/link are you trying to install it from? I strongly suggest you uninstall the version you have, and instead go to this page to install the native Windows version (follow the first link at the top) : http://tools.proteomecenter.org/wiki/index.php?title=Main_Page We have a few versions still floating around, so sorry for the confusion. --Luis On Mon, Sep 8, 2008 at 1:09 PM, Hong Yang <denk...@yahoo.com> wrote: Hi Luis,   Thank you so much. I tried to install it using "direct connection" and "port 80". The problem is still there. I can't open TPP through "TPP Web tools". I am wondering if it needed to uninstall the software and reinstall it again? or something else? Thank you! Bin   --- On Mon, 9/8/08, Luis Mendoza <lmen...@systemsbiology.org> wrote: From: Luis Mendoza <lmen...@systemsbiology.org> Subject: Re: Problem of installing TPP V4.02 To: "Denky" <denk...@yahoo.com> Date: Monday, September 8, 2008, 12:37 PM Hello Denky, I suggest you install the native Windows distribution of the TPP, which uses Windows Apache on port 80.  Or just try port 80, in case that's the version you already installed! : http://localhost/tpp-bin/tpp_gui.pl Let us know if this does not solve your problem. --Luis On Mon, Sep 8, 2008 at 12:34 PM, Denky <denk...@yahoo.com> wrote: Dear All, I installed TPP v 4.02 in the computer (Windows XP). Everything looked good. I saw "TPP Web Tools" and "Cygwin" in the desktop. However, when I clicked it, it popped up to http://localhost:1441/tpp-bin/tpp_gui.pl, and shown "Internet Explorer cannot display the webpage". I tried to start cygapache2_start and cygapache2_stop in administrative Tools/services. It said "the cygapache2_start service on local computer started and then stopped. Some services stop automatically if they have no work to do, for example, the performance logs and alerts service". I asked university IT people, they said it maybe because of this software that needed special Server Port, and the computers on campus don't be allowed to use this function. I am wondering if someone can help me to figure out what's wrong with it? Great thanks, Denky

[Luis Mendoza]

Hello Bin,
It looks like an error on our distribution of these support files.
Using a text editor (e.g. WordPad), please open the file
C:\Inetpub\tpp-bin\tandem_params.xml

Look for the 2 lines that contain _DEFAULT_INPUT_LOCATION_/
and replace this string with: C:\Inetpub\tpp-bin\

For example, this line:
<note type="input" label="list path, taxonomy information">_DEFAULT_INPUT_LOCATION_/taxonomy.xml</note>

would become:
<note type="input" label="list path, taxonomy information">C:\Inetpub\tpp-bin\taxonomy.xml</note>

Hope this helps!  We will fix this issue for the next release of the TPP.
--Luis

On Tue, Sep 9, 2008 at 9:27 AM, Hong Yang <denk...@yahoo.com> wrote:

Hi Luis,   Sorry for another question when I use X!Tanem. How to deal with these two issues: Loading spectra Failed to open: "_DEFAULT_INPUT_LOCATION_/isb_default_input_kscore.xml" The taxonomy parameter file "_DEFAULT_INPUT_LOCATION_/taxonomy.xml" could not be found. Many thanks, Bin   ************************************   # Commands for session CAM9KPP0U on Tue Sep 9 12:20:22 2008 # BEGIN COMMAND BLOCK ###### BEGIN Command Execution ###### [Tue Sep 9 12:20:23 2008] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; tandem c:/Inetpub/wwwroot/ISB/data/OT00034.mzML.params OUTPUT: X! TANDEM 2 (2007.07.01.2) Loading spectra . Failed to open: "_DEFAULT_INPUT_LOCATION_/isb_default_input_kscore.xml" The taxonomy parameter file "_DEFAULT_INPUT_LOCATION_/taxonomy.xml" could not be found. Check your settings and try again. An error was detected while loading the input parameters. Please follow the advice above or contact a GPM administrator to help you.END OUTPUT RETURN CODE:64512 ###### End Command Execution ###### ###### BEGIN Command Execution ###### [Tue Sep 9 12:20:23 2008] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; tandem c:/Inetpub/wwwroot/ISB/data/OT00038.tandem.params OUTPUT: X! TANDEM 2 (2007.07.01.2) Loading spectra . Failed to open: "_DEFAULT_INPUT_LOCATION_/isb_default_input_kscore.xml" The taxonomy parameter file "_DEFAULT_INPUT_LOCATION_/taxonomy.xml" could not be found. Check your settings and try again. An error was detected while loading the input parameters. Please follow the advice above or contact a GPM administrator to help you.END OUTPUT RETURN CODE:64512 ###### End Command Execution ###### # All finished at Tue Sep 9 12:20:23 2008 # END COMMAND BLOCK

[Hong Yang]

Hi Luis,   Thanks. I changed that. Here is another question. It seemed the program fail to recognize mzXML file shown as below. I converted mzXML to .mgf format. However, the system can't find the file in Database search. I am sorry for many basic questions, but I believe your answers will help me to save a lot of time. Many thanks, Bin     # Commands for session CAM9KPP0U on Tue Sep  9 16:26:33 2008

# BEGIN COMMAND BLOCK ###### BEGIN Command Execution ######

[Tue Sep  9 16:26:33 2008] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; tandem c:/Inetpub/wwwroot/ISB/data/OT00038.tandem.params

OUTPUT: X! TANDEM 2 (2007.07.01.2) Loading spectra .

Failed to read spectrum file: full_mzXML_filepath Most likely: an unsupported data file type: Use dta, pkl, mgf, mzdata (v.1.05) or mxzml (v.2.0) files ONLY! (4)

An error was detected while loading the input parameters. Please follow the advice above or contact a GPM administrator to help you.END OUTPUT RETURN CODE:64512 ###### End Command Execution ######

# All finished at Tue Sep  9 16:26:33 2008 # END COMMAND BLOCK

[Luis Mendoza]

Hello Bin,
This error is also related to some inconsistencies in the default tandem_params.xml
that we distribute, when running the search from within Petunia (the GUI).

Please go to the tandem_params.xml file and delete the following lines:
 
<note type="input" label="spectrum, path">full_mzXML_filepath</note>
<note type="input" label="output, path">full_tandem_output_path</note>

as well as:

<note type="input" label="list path, taxonomy information">_DEFAULT_INPUT_LOCATION_/taxonomy.xml</note>

The values for these are dynamically inserted by Petunia when running the Tandem search.

Hope this helps, and let us know if you run into other errors!
--Luis

[Hong Yang]

Hi Luis,   Thank you so much! It looked running. I run a datebase searching last Thursday, but today it said 'my commands are still running". When I update  "view output so far", the page shown as below came out. I can't do next step. Is there a method to stop running database searching? I guess there is still something need to be modified in Parameter file. Bin   # Commands for session 4TSQWEDY9 on Thu Sep 11 12:22:47 2008

# BEGIN COMMAND BLOCK ###### BEGIN Command Execution ######

[Thu Sep 11 12:22:47 2008] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data; tandem c:/Inetpub/wwwroot/ISB/data/Bob33_1.tandem.params

OUTPUT: X! TANDEM 2 (2007.07.01.2)

Loading spectra ... loaded. Spectra matching criteria = 5680 Pluggable scoring enabled. Starting threads . started. Computing models: 1234567890123456789012345678901234567890123456789 | 50 ks 01234567 sequences modelled = 58 ks Model refinement: Creating report: initial calculations  ..... done. sorting  ..... done. finding repeats ..... done. evaluating results ..... done. calculating expectations ..... done. writing results ..... done. Valid models = 109