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use one database file for different MS2 runs

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use one database file for different MS2 runs wonjong.moon  2007-02-19 13:22
Status: Closed
Assigned To: adam
 
I am using CPAS 1.6. I want to use one fasta file for all MS2 runs. I do not like to create a subfolder 'databases' for each MS2 run.

I set /proteomics/Duffy/CPAS/3550_3 for a pipeline root directory
      /proteomics/Duffy/CPAS/databases for a database root directory

Actual locations of mzXML files
       proteomics\Duffy\CPAS\3550_3\MF-pl1011\MFL25-101906-pl1011.mzXML
       proteomics\Duffy\CPAS\3550_3\MF-pl840\MFL45-101906-pl840.mzXML

Even though I had an error message, it looks like x!tandem, peptideProphet, and proteinProphet worked OK.
Is it correct? Is there other way to use one fasta file as a database for many MS2 rusn?
Thank you.


19 Feb 2007 12:31:10,335 ERROR: The data file /proteomics/Duffy/CPAS/databases/HuPlas01Dec05.fasta is not under the folder's pipeline root, file:/proteomics/Duffy/CPAS/3550_3/. It will not be loaded.
 
 
jeckels responded:  2007-02-20 09:35
That error message is misleading, your FASTA file did end up successfully loading. There are a couple of different phases in which CPAS attempts to load data, and the error message is the output of the first phase. I'll tone down the severity of the message in 2.0, but for now please just ignore that output. Your approach for sharing the same database directory is fine.

Thanks,
Josh