Here is the error msgs we are getting:

04 Jan 2011 15:09:57,171 INFO : mascot client output
04 Jan 2011 15:09:57,171 INFO : =======================================
04 Jan 2011 15:09:57,671 INFO : ../bin/ms-searchcontrol.exe - Version 2.2.03 - Server: Microsoft-IIS/6.0
04 Jan 2011 15:09:58,015 INFO : Creating Mascot session...
04 Jan 2011 15:09:58,453 INFO : Mascot session#CPAS_155198483757390 started.
04 Jan 2011 15:09:58,453 INFO : Creating Mascot search task...
04 Jan 2011 15:09:58,953 INFO : Mascot search task#129417539801 created with 'nph-mascot.exe'.
04 Jan 2011 15:09:58,953 INFO : Submitting search to Mascot server...
04 Jan 2011 15:09:58,953 INFO : Submitting query file, size=0
04 Jan 2011 15:09:58,953 ERROR: Failed to find Mascot query file 'D:\LabKey Server\Data\Don\Ding_K562\mascot\Mascot_search\K562_dwband8_Test.work\input.xml'.

04 Jan 2011 15:09:59,171 INFO : Fail to submit search to Mascot server.
04 Jan 2011 15:09:59,578 INFO : Mascot session ended.
04 Jan 2011 15:09:59,578 ERROR: Failed to remove work directory D:\LabKey Server\Data\Don\Ding_K562\mascot\Mascot_search\K562_dwband8_Test.work unexpected files found:
input.xml
04 Jan 2011 15:09:59,578 ERROR: Error code 3

Ding,

Have you successfully run other Mascot searches on your server?

LabKey server 9.1 is a fairly old release (released in early 2009). There have been 5 releases since 9.1(the current version is 10.3). If possible, I strongly recommend upgrading your server to the latest release and attempting the search again.

- A feature list and download information for the latest version of LabKey Server is located at https://www.labkey.org/wiki/home/Documentation/page.view?name=whatsnew103
- Upgrade documentation is available at https://www.labkey.org/wiki/home/Documentation/page.view?name=upgrade

If you need any assistance with the upgrade we would be glad to help.

Thank you,

Brian Connolly

Hi Ding,

I agree with Brian's suggestion that you upgrade to the newest LabKey Server release. That said, it's possible that it won't fix this particular problem.

The log output:

Submitting query file, size=0

indicates that the MGF file that's been submitting to Mascot is 0 bytes in size. Can you verify this? It should be in in:

D:\LabKey Server\Data\Don\Ding_K562\mascot\Mascot_search\K562_dwband8_Test.work

A little earlier in the log file, you should see the command line that the server is using to invoke MzXML2Search, a TPP tool that converts mzXML files to MGF. You could try running it manually to see if you get the same resulting file, or if there's an error message that's produced during the conversion.

Thanks,
Josh

Hi, I am a colleague of Dings.

We do intend to upgrade CPAS, we were holding off due to the SQL upgrade needed as well as a Mascot upgrade on the same server box.

Yeah, I did think that the file size = 0 was odd.

When looking on the server to where the files were created/located I noticed that it generated the mgf file in the same directory as the mzXML file (D:\LabKey Server\Data\Don\Ding_K562\) and not in the folder where it was trying to submit from (D:\LabKey Server\Data\Don\Ding_K562\mascot\Mascot_search\K562_dwband8_Test.work)

The only file in the K562_dwband8_Test.work dir was the index.xml file with the initial search parameters.

Tested the mgf file which was created, and it is valid and can be manually searched on our mascot server.