msconvert Instrument index not available for requested device

[bernt-matthias]

hey @chambm another user just reported another one for tool version 3.0.20287.2 I already asked for the data set.

had an exit code 1 with stderr:

Could not load wine-gecko. HTML rendering will be disabled.
Could not load wine-gecko. HTML rendering will be disabled.
wine: configuration in '/tmp/7580446.1.usvc/tmp.Y4mfRXkUZ3' has been updated.

and stdout

format: mzML 
    m/z: Compression-Zlib, 64-bit
    intensity: Compression-Zlib, 32-bit
    rt: Compression-Zlib, 64-bit
ByteOrder_LittleEndian
 indexed="true"
outputPath: outputs
extension: .mzML
contactFilename: 
runIndexSet: [0,0] 

spectrum list filters:
  
chromatogram list filters:
  
filenames:
  50_50_100a0a.raw
  
processing file: 50_50_100a0a.raw
[RawFileImpl::ctor()] Instrument index not available for requested device
Parameter name: instrumentIndex

[bernt-matthias]

Command line for this job is msconvert '50_50_100a0a.raw' --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --filter "peakPicking vendor msLevel=1-" --mz64 --inten32 --zlib --outfile '50_50_100a0a'

I increased the available memory for the tool (from 8 to 37GB) and now get:

[SpectrumList_Thermo::spectrum()] Error retrieving spectrum "controllerType=0 controllerNumber=1 scan=34161": [RawFileThreadImpl::getMassList()] Exception of type 'System.OutOfMemoryException' was thrown.

So it seems to be a memory problem. I have also increased the memory to 57GB without success. Do you have any experience how much memory is needed?

Its also odd that msconvert is quite idle most of the time. When looking it the output of the job stats it looks like its mostly doing memory operations:

wallclock    415.448      
cpu          132.228      
mem          1262.465          
io           14.832            
iow          0.680             
ioops        1040100