Re: [Open-ms-general] error with handling temp files

[Achim T. <ach...@ne...>]

Hi Chris,

many thanks for the reply. Do I need to install a different version of OpenMS? The one I have does not have a --debug option:
C:\>OpenMSInfo
OpenMS Version:
==================
Version      : 1.11.1
Build time   : Nov 13 2013, 16:36:04
SVN revision : 11976

Installation information:
==================
Data path    : C:/Program Files/OpenMS-1.11/share/OpenMS
Temp path    : C:/Users/achim/AppData/Local/Temp
Userdata path: C:/Users/achim/

Build information:
==================
Source path  : C:/dev/AUTO_PACKAGE/release/OpenMS
Binary path  : C:/dev/AUTO_PACKAGE/release/OpenMS_build

OS Information:
==================
Name: Windows
Version: 6.1
Architecture: 64bit


C:\>TOPPAS --debug "W:\Tools\TOPPAS workflows\MascotSearchOnly.toppas"
Unknown option(s) '[--debug]' given. Aborting!

TOPPAS -- An assistant for GUI-driven TOPP workflow design.

Usage:
 TOPPAS [options] [files]

Options are:
  --help           Shows this help
  -ini <File>      Sets the INI file (default: ~/.TOPPAS.ini)
Many thanks for your help,
Achim

Achim Treumann
Director, NUPPA
Newcastle University Protein and Proteome Analysis
Devonshire Building
Devonshire Terrace
Newcastle upon Tyne NE1 7RU

http://www.ncl.ac.uk/business/facilities/research/nuppa.htm
email: ach...@ne...
phone: 0191 2084804
________________________________
From: Chris Bielow [chr...@fu...]
Sent: 28 May 2014 1:48 PM
To: 'General OpenMS discussion'
Subject: Re: [Open-ms-general] error with handling temp files

Hi Achim,

since its hard to reprocuce your environment, could you please run the following test:

Start TOPPAS in debug mode via command line:
$ TOPPAS --debug MascotSearchOnly.toppas

Upon running the pipeline there will be debug messages like
Enqueue: "c:/dev/oms_build12/bin/debug/MascotAdapterOnline" "-no_progress" "-in …

Run the command for MascotAdapterOnline on another command line, right after the pipeline fails (such that the temp files are still present).
Let us know what the sole command does (exit without error, create all the files its supposed to?!).

This way we can figure out if its TOPPAS or the Adapter.

Thx
Cheers
Chris




From: Achim Treumann [mailto:ach...@ne...]
Sent: Tuesday, May 27, 2014 6:24 PM
To: General OpenMS discussion ‎[ope...@li...]‎
Subject: [Open-ms-general] error with handling temp files

Dear OpenMS team / users,

I am trying to run a very straightforward pipeline (attached) that performs a Mascot search on a small file (using MascotOnlineAdaptor and this is successful), followed by IDPosteriorErrorProbability and an export of the results to a txt file. TOPPAS is crashing on me (Windows7, X64) with the following error message:

Caught exception: 'FileNotFound' with message 'the file
D:\LocalData_D\temp\2014-05-27_170208_NUPPA-W01_3688_1\TOPPAS_tmp\MascotSearchOnly\003_IDPosteriorErrorProbability\output_name\Achim-P10-4.idXML_tmp3' could not be found'
[OK]

The directory is there (written by TOPPAS, so I presume it is not a problem with read/write privileges), but the files is indeed missing. I have set both, the home_dir and the temp_dir variable in /home/.Openms/openms.ini to 'D:\LocalData_D\temp'

Following this, TOPPAS exits.

Any suggestions of what I might be doing wrong?

Best wishes and many thanks in advance,
Achim

Achim Treumann
Director, NUPPA
Newcastle University Protein and Proteome Analysis
Devonshire Building
Devonshire Terrace
Newcastle upon Tyne NE1 7RU

http://www.ncl.ac.uk/business/facilities/research/nuppa.htm
email: ach...@ne...<mailto:ach...@ne...>
phone: 0191 2084804