Msconvert error

[bernt-matthias]

Could not load wine-gecko. HTML rendering will be disabled. 
 Could not load wine-gecko. HTML rendering will be disabled. 
 wine: configuration in '/tmp/7578869.1.usva28/tmp.jmcwfuLVTe' has been updated. 
 Error writing run 1 in "180714_NJ_Bastida_AZ4.raw": 
 [SpectrumList_Thermo::spectrum()] Error retrieving spectrum "controllerType=0 controllerNumber=1 scan=30140": [RawFileThreadImpl::getMassList()] Object reference not set to an instance of an object. 
 

Tool Version | 3.0.20287.2

Ping @chambm

[chambm]

Can you test on Windows (or send me the file) to see if the error happens there as well?

[bernt-matthias]

Thanks for the reply I have asked the user.

[bernt-matthias]

Sent you links to the data (also for #548) on gitter

[chambm]

Problem doesn't seem to occur on Windows. Does it happen on the same scan every time for this user? What conversion settings were they using?

[bernt-matthias]

Problem doesn't seem to occur on Windows. Does it happen on the same scan every time for this user?

Seems so - I tested a couple of times.

Does it happen on the same scan every time for this user?

Not exactly. I have seen a few similar values: scan=26253, scan=26160, scan=26231

What conversion settings were they using?

The generated command line is $WINE msconvert '180714_NJ_Bastida_ALP195.raw' --outdir outputs --mzML --runIndexSet 0 --stripLocationFromSourceFiles --mz64 --inten32 --zlib --outfile '180714_NJ_Bastida_ALP195'

Maybe as a side note: We are running the tool with singularity.

[bernt-matthias]

One more thing: msconvert returns exit code 0 despite the error. Would be really nice to have a non-0 exit code in case of error.