I fetched the labkey 2.0 source code yesterday from https://hedgehog.fhcrc.org/tor/stedi/branches/release2.0.
and used it for mascot search. Here is the problem i came across:

The error in the log for the run:

24 Apr 2007 19:09:29,930 INFO : Mascot search for 060508_Yeast_ITRAQ_F14.mzXML
24 Apr 2007 19:09:29,932 INFO : =======================================
24 Apr 2007 19:09:30,374 INFO : MzXML2Search output
24 Apr 2007 19:09:30,383 INFO : =======================================
24 Apr 2007 19:11:24,077 INFO : running: MzXML2Search -mgf 060508_Yeast_ITRAQ_F14.mzXML
24 Apr 2007 19:11:24,306 INFO :
24 Apr 2007 19:11:24,308 INFO : MzXML2Search - Mascot Generic Format
24 Apr 2007 19:11:24,309 INFO :
24 Apr 2007 19:11:24,317 INFO : Reading 060508_Yeast_ITRAQ_F14.mzXML
24 Apr 2007 19:11:24,319 INFO : Getting the index offset
24 Apr 2007 19:11:24,320 INFO : Reading the index
24 Apr 2007 19:12:15,127 INFO : scan: 1 000% 2 000%
   3 000% 4 000% 5 000% 6

...............................................
099% 5107 099% 5108 099% 5109 100%
24 Apr 2007 19:12:15,161 INFO : Done.
24 Apr 2007 19:12:15,163 INFO :
24 Apr 2007 19:12:15,167 INFO : mascot client output
24 Apr 2007 19:12:15,173 INFO : =======================================
24 Apr 2007 19:12:15,769 INFO : ../bin/ms-searchcontrol.exe - Version 2.1.0 - Server: Apache/2.0.52 (CentOS)
24 Apr 2007 19:12:15,803 INFO : Creating Mascot session...
24 Apr 2007 19:12:15,850 INFO : Mascot session# started.
24 Apr 2007 19:12:15,852 INFO : Creating Mascot search task...
24 Apr 2007 19:12:15,951 INFO : Mascot search task#117743473501 created with 'nph-mascot.exe'.
24 Apr 2007 19:12:15,955 INFO : Submitting search to Mascot server...
24 Apr 2007 19:12:15,996 INFO : Submitting query file, size=227796521
24 Apr 2007 19:12:45,962 INFO : Mascot search task status: query upload completed
24 Apr 2007 19:19:02,812 INFO : Search submitted.
24 Apr 2007 19:19:02,829 INFO : Mascot search status verbose reporting on
24 Apr 2007 19:19:33,060 INFO : Mascot search status: complete

24 Apr 2007 19:19:43,064 INFO : Retrieving Mascot search result...
24 Apr 2007 19:19:43,184 INFO : Downloaded 47 bytes of result file.
24 Apr 2007 19:19:43,187 INFO : First line of Mascot result file does not start with 'MIME-Version:'... will remove file
24 Apr 2007 19:19:43,189 INFO : First 1 line(s)
problem=Error return from ms-searchcontrol.exe
24 Apr 2007 19:19:43,192 INFO : Mascot session ended.
24 Apr 2007 19:19:43,194 ERROR: Failed running Mascot.

In cpas-errors. log:

ERROR PipelineJob 2007-04-24 16:22:30,245 JobThread-2.1 : Failed running Mascot.


However, i have checked the .dat file from Mascot, it is starting with "MIME-Version: 1.0 (Generated by Mascot version 1.0)".




Does anyone have any idea what might be the problem?

Thank you!

Runxuan