failling on Thermo.raw

[jorgeboucas]

laptop:~/MSConvertGUI-docker$ docker run --rm -v /tmp/.X11-unix:/tmp/.X11-unix:rw -v $PWD:/data:rw msconvertgui /bin/bash -c "cd /data; wine msconvert small.RAW"
format: mzML 
    m/z: Compression-None, 64-bit
    intensity: Compression-None, 32-bit
    rt: Compression-None, 64-bit
ByteOrder_LittleEndian
 indexed="true"
outputPath: .
extension: .mzML
contactFilename: 

spectrum list filters:
  
chromatogram list filters:
  
filenames:
  small.RAW
  
processing file: small.RAW
0034:err:ole:marshal_object Failed to create an IRpcStubBuffer from IPSFactory for {00000126-0000-0000-c000-000000000046} with error 0x80004002
0009:err:ole:ClientIdentity_QueryMultipleInterfaces IRemUnknown_RemQueryInterface failed with error 0x80004002
writing output file: .\small.mzML
0037:err:ole:ClientRpcChannelBuffer_SendReceive called from wrong apartment, should have been 0x80000cafe
0037:err:ole:xCall RpcChannelBuffer SendReceive failed, 8001010e
0036:err:ole:ClientRpcChannelBuffer_SendReceive called from wrong apartment, should have been 0x80000cafe
0036:err:ole:xCall RpcChannelBuffer SendReceive failed, 8001010e
[SpectrumWorkerThreads::work] error in thread: [SpectrumList_Thermo::spectrum()] Error setting controller to: 0,1 ([ThermoRawFile] [RawFileImpl::setCurrentController()] Failed call to XRawfile: Unknown error 0x8001010E)
[SpectrumWorkerThreads::work] error in thread: [SpectrumList_Thermo::spectrum()] Error setting controller to: 0,1 ([ThermoRawFile] [RawFileImpl::setCurrentController()] Failed call to XRawfile: Unknown error 0x8001010E)
0039:err:ole:ClientRpcChannelBuffer_SendReceive called from wrong apartment, should have been 0x80000cafe
0039:err:ole:xCall RpcChannelBuffer SendReceive failed, 8001010e
[SpectrumWorkerThreads::work] error in thread: [SpectrumList_Thermo::spectrum()] Error setting controller to: 0,1 ([ThermoRawFile] [RawFileImpl::setCurrentController()] Failed call to XRawfile: Unknown error 0x8001010E)
0038:err:ole:ClientRpcChannelBuffer_SendReceive called from wrong apartment, should have been 0x80000cafe
0038:err:ole:xCall RpcChannelBuffer SendReceive failed, 8001010e
[SpectrumWorkerThreads::work] error in thread: [SpectrumList_Thermo::spectrum()] Error setting controller to: 0,1 ([ThermoRawFile] [RawFileImpl::setCurrentController()] Failed call to XRawfile: Unknown error 0x8001010E)

It would be great if you could provide me some help or this or let me know of an alternative solution for doing this conversion on a linux machine.

[sneumann]

Hi, I am afraid in the above you are calling the msconvert.exe command line tool.
Even in Rene's container this is known to not work. Only the GUI works,
since that was writte in C#, while the command line was written in C++.
There are differences in how they can (not) properly access Thermo DLLs under wine.
If you are a dedicated windows hacker, you could contact the pwiz team
and offer help to migrate the command line tool to C# !
Yours, Steffen