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geert  
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 More options Jul 9 2007, 5:52 am
From: geert <geert.zeg...@gmail.com>
Date: Mon, 09 Jul 2007 02:52:31 -0700
Local: Mon, Jul 9 2007 5:52 am
Subject: IPP protein prophet
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Hi,

I seem to have a problem with running protein prophet after analyzing
search results with peptide prophet (which does work).
When I try to view protein prophet results I always get the message
"c:/Inetpub/wwwroot/ISB/data/interact-prot.xml (file not found: not
created or deleted?) " and the command box says:

"c:\Inetpub\ipp-bin\runprophet -Om c:/Inetpub/wwwroot/ISB/data/
test.xml c:/Inetpub/wwwroot/ISB/data/interact-prot.xml
--------------------------------------------------------------------------- -----

ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the
original Perl by A. Keller (IPP v1.0  rev.9, Build 200704251131)
. . . reading in c:/Inetpub/wwwroot/ISB/data/test.xml. . .
. . . read in 0 1+, 0 2+, and 0 3+ spectra with min prob 0.05
 (xml input) (using degen pep info)
* * * cannot find database: /disk3/mascot/sequence/Sprot/current/
Sprot_53.1.fasta, no coverage information possible * * *

command 'C:\Inetpub\ipp-bin\ProteinProphet.exe c:\Inetpub\wwwroot\ISB
\data\test.xml c:\Inetpub\wwwroot\ISB\data\interact-prot.xml
XML_INPUT' failed with code 1: Operation not permitted
Command Finished "

Can anyone help me fixing this problem?

kind regards

Geert zegels


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Brian Pratt  
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 More options Jul 9 2007, 2:15 pm
From: "Brian Pratt" <brian.pr...@insilicos.com>
Date: Mon, 9 Jul 2007 11:15:41 -0700
Local: Mon, Jul 9 2007 2:15 pm
Subject: RE: [IPP list] IPP protein prophet
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Hi Geert,

One slightly ugly way to solve the problem would be to create a directory
        C:/disk3/mascot/sequence/Sprot/current/
then copy the database file into it.

I'm a bit surprised to see the error, though, since the Mascot2XML converter
normally would have sorted this out in the pepXML.

Cheers,

Brian Pratt


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geert  
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 More options Jul 10 2007, 3:03 am
From: geert <geert.zeg...@gmail.com>
Date: Tue, 10 Jul 2007 00:03:49 -0700
Local: Tues, Jul 10 2007 3:03 am
Subject: Re: IPP protein prophet
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hey Brian,

thanks for the quick reply!
I'm just started this year with my PhD, so I'm quite new to the field
of bioinformatics, therefore I may have a stupid question. Which
database file do you mean?

regards,

Geert

On 9 jul, 20:15, "Brian Pratt" <brian.pr...@insilicos.com> wrote:


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Brian Pratt  
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 More options Jul 10 2007, 12:52 pm
From: "Brian Pratt" <brian.pr...@insilicos.com>
Date: Tue, 10 Jul 2007 09:52:20 -0700
Local: Tues, Jul 10 2007 12:52 pm
Subject: RE: [IPP list] Re: IPP protein prophet
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No worries.  The error message indicates that it's unable to locate the
FASTA database file named "Sprot_53.1.fasta".  The term "database" is used
pretty loosely, it's not a database in the Oracle or mySQL sense but rather
a text file of protein descriptions.


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