IPP protein prophet
geert
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
Brian Pratt
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
geert
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:
> 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
>
>
>
> -----Original Message-----
> From: Insili...@googlegroups.com [mailto:Insili...@googlegroups.com]
>
> On Behalf Of geert
> Sent: Monday, July 09, 2007 2:53 AM
> To: Insilicos IPP
> Subject: [IPP list] IPP protein prophet
>
> 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- Tekst uit oorspronkelijk bericht niet weergeven -
>
> - Tekst uit oorspronkelijk bericht weergeven -
Brian Pratt
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.
hey Brian,
regards,
Geert
> -------