[proteowizard-support] Error running MSConvert

[Manuel B. <man...@gm...>]

Hi,

Encountered a crash using the msconvert docker image on Linux.

Process was hanging a few days after it stopped working. Noticed the STDERR
had this info. It seems like the output mzML file is not empty either. It's
about 1.5Gb (gzipped) while the other
.RAW files are 2.5Gb and completed correctly and have nothing in the STDERR
logs.

*COMMAND:*
docker run --rm -e WINEDEBUG=-all -v /home/z/local/RAW:/data -v
/home/z/development/TMT/RawData:/RawData
chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert
/data/tmt_b04_07.raw --gzip -o /RawData

*STDERR:*
$ cat RawData/rushtmt_b04_07.raw.err
[SpectrumWorkerThreads::work] error in thread:
[SpectrumList_Thermo::spectrum()] Unknown exception retrieving spectrum
"controllerType=0 controllerNumber=1 scan=43319"
[C:\pwiz\msconvert.exe] Caught unknown exception.
Please report this error to su...@pr....
Attach the command output and this version information in your report:

ProteoWizard release: 3.0.19056 (6b6b0a2b4)
Build date: Feb 25 2019 17:17:16

*STDOUT:*
RawData/rushtmt_b04_07.raw.log
format: mzML
    m/z: Compression-None, 64-bit
    intensity: Compression-None, 32-bit
    rt: Compression-None, 64-bit
ByteOrder_LittleEndian
 indexed="true"
outputPath: /RawData
extension: .mzML.gz
contactFilename:
runIndexSet:

spectrum list filters:

chromatogram list filters:

filenames:
  /data\rushtmt_b04_07.raw

processing file: /data\rushtmt_b04_07.raw
calculating source file checksums
writing output file: /RawData\rushtmt_b04_07.mzML.gz