Error combining multiple pepXML files with ProteinProphet command v4.7.0

[GATTACA]

Hello Everyone,

I'm trying to generate a single ProteinProphet protXML file from two pepXML files.
The pepXML files are replicates runs of an experiment searched with the same parameters and database using MASCOT.

When I run this command at the terminal:

ProteinProphet interact-ISO25.pep.xml interact-ISO26.pep.xml interact-merged.prot.xml


I get the following output and error (in red):
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v0.0 Development (DEV) rev 0, Build 201404071016 (linux))
 (xml input) (no FPKM) (report Protein Length) (using degen pep info)
. . . reading in /home/dfermin/projects/hwchoi/interact-ISO25.pep.xml. . .
. . . read in 0 1+, 51475 2+, 21321 3+, 850 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05
. . . reading in /home/dfermin/projects/hwchoi/interact-ISO26.pep.xml. . .
. . . read in 0 1+, 33367 2+, 9900 3+, 172 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::ios_base::failure> >'
  what():  failed opening file: No such file or directory


This is a new one on me.
The error occurs with the stable release of TPP 4.7.0 and with the development release (SVN revision 6468).
I'm running TPP on CentOS 6.5 64bit (fully patched).

Any suggestions for a work around?

Thanks in advance,
Damian

[David Shteynberg]

This error means it couldn't read some file.  Could be the database path? Check to make sure all the files are in place.  Any older version you have laying around to try might be next best call.

David

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[Damian]

Thanks for the quick reply.
You were right about the database path.
I have the pep.xml files and the database file in the same folder but the <database_refresh_timestamp> in the pepXML files was set to absolute path to the FASTA file. I used sed to fix the database path and it works now.

Thanks,
Damian

David Shteynberg wrote:

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[Ruby]

Hi David-
I get the same error as stated above using 4.6.3 when trying to combine multiple tandem.pep.xml together via peptide prophet. I have checked and my FASTA database is in the folder with all my tandem.pep.xml files and the path designated in the xml file does point to the same directory where they are all stored. Thus, is there another explanation for this error?

Many thanks!
Rebekah