Menu
▾
▴
Re: [Open-ms-general] error with handling temp files
|
From: Achim T. <ach...@ne...> - 2014-05-30 19:12:00
|
Hi Stephan, many thanks - the link worked and I have downloaded the new version. When I run my workflow with this version, I do not get a crash (without changing any of the parameters). Thanks again for helping me out, 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: Aiche, Stephan [Ste...@fu...] Sent: 30 May 2014 09:59 To: General OpenMS discussion Cc: Bielow, Chris Subject: Re: [Open-ms-general] error with handling temp files He Achim, please try the following link to download the Installer for the Windows 64bit Version. CDash itself does not provide any binaries. http://ftp.mi.fu-berlin.de/OpenMS/nightly_binaries/OpenMS-head_Win64_setup.exe Cheers Stephan On 29 May 2014, at 11:12, Achim Treumann <ach...@ne...<mailto:ach...@ne...>> wrote: Hi Chris, this link does not appear to work for me. When I try to find a binary on http://cdash.openms.de/index.php?project=OpenMS there appear to be none for Win7_64. Do you know if it is worth trying one of the Win8 binaries? 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 ________________________________ From: Chris Bielow [chr...@fu...<mailto:chr...@fu...>] Sent: 28 May 2014 21:00 To: Achim Treumann; General OpenMS discussion Subject: RE: [Open-ms-general] error with handling temp files 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<http://ftp.mi.fu-berlin.de/pub/OpenMS/nightly_binaries>/ Cheers Chris On 28. Mai 2014 19:57:32 MESZ, Achim Treumann <ach...@ne...<mailto: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...<mailto:ach...@ne...> phone: 0191 2084804 ________________________________ From: Chris Bielow [chr...@fu...<mailto: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...<mailto: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 -- Diese Nachricht wurde von meinem Android-Mobiltelefon mit K-9 Mail gesendet. ------------------------------------------------------------------------------ Time is money. Stop wasting it! Get your web API in 5 minutes. www.restlet.com/download<http://www.restlet.com/download> http://p.sf.net/sfu/restlet_______________________________________________ Open-ms-general mailing list Ope...@li... https://lists.sourceforge.net/lists/listinfo/open-ms-general |
