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

[Chris B. <chr...@fu...>]

Sorry, the feature was added post release. You'll need the current dev (=head) version from
ftp://ftp.mi.fu-berlin.de/pub/OpenMS/nightly_binaries/

Cheers Chris


On 28. Mai 2014 19:57:32 MESZ, Achim Treumann <ach...@ne...> wrote:
>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

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