Re: [proteowizard-support] Error running MSConvert

[Chambers, M. <mat...@gm...>]

Hi Manuel,

Does this error repeat at the same scan every time? If so, does it also happen on native Windows? If not, does it always error, or only 
sometimes?

Thanks for the report,
-Matt


On 3/15/2019 1:12 PM, Manuel Belmadani wrote:
> 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... <mailto: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
>
>
>
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