TPP 4.8 msconvert error

[Brian Hampton]

I just started using 4.8 on a 32 bit install of Win 7.  Using Petunia I began by converting Sciex .wiff files to mzML and got the following error and output from this command:

NOTE: I can run the same command in a CMD window and it succeeds.

c:\Inetpub\tpp-bin\msconvert c:/Inetpub/wwwroot/ISB/data/projects/carotid/sds/141202-3t/02Dec14-BH-RABA-Fxn1.wiff -v --mzML -o c:/Inetpub/wwwroot/ISB/data/projects/carotid/sds/141202-3t -z --filter "peakPicking true [1,2]"

format: mzML 
    m/z: Compression-Zlib, 64-bit
    intensity: Compression-Zlib, 32-bit
    rt: Compression-Zlib, 64-bit
ByteOrder_LittleEndian
 indexed="true"
outputPath: c:/Inetpub/wwwroot/ISB/data/projects/carotid/sds/141202-3t
extension: .mzML
contactFilename: 

filters:
  peakPicking true [1,2]
  
filenames:
  c:/Inetpub/wwwroot/ISB/data/projects/carotid/sds/141202-3t\02Dec14-BH-RABA-Fxn1.wiff
  
processing file: c:/Inetpub/wwwroot/ISB/data/projects/carotid/sds/141202-3t\02Dec14-BH-RABA-Fxn1.wiff
[WiffFileImpl::getSampleNames] The type initializer for 'Clearcore2.Data.WiffReader.WiffSampleRun' threw an exception.

[Luis Mendoza]

Hi Brian,

I have not seen that msconvert error; can you still reproduce it?  (we once encountered a similar error that went away after running msconvert once via the command-line.)   Otherwise I can only suggest looking at the file permissions in that directory.

Does the previous version of TPP/msconvert work with that same file?  What about other raw file formats?

Thanks for trying out the new release,

--Luis

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[Steffen Neumann]

Hi,

the same exception has been reported before when running msconvert under linux with wine:
http://tools.proteomecenter.org/wiki/index.php?title=Msconvert_Wine#AB_Sciex_wiff_files_throw_an_exception
And I still see the same error on a much more recent wine version in our converter Virtual Machine
at https://github.com/phnmnl/pwiz-appliance

Although you work on Windows 7, you get the same error when not running under cmd.exe,
so it might be some environment setting that's missing from within your TPP ?
Maybe we have the same issue, and some simple setting (language ?!) could help.

Yours,
Steffen