Re: [proteowizard-support] Error running MSConvert

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

Hi,

It doesn't do it consistently actually, I reran it after I noticed and it
terminated pretty quickly.

This was run on a Google Cloud Compute VM  running Ubuntu 18.04 using data
stored on a local disk (local to the VM). I don't think it's revelant in
this case but I was running 7 concurrent calls (suing `xargs -P7`) with the
same command this over 24 files and this is the only one that failed.

I noticed a similar issue when using gscfuse (a network mounted filesystem
using the google cloud buckets) on multiple concurrent processes (using
different files in each process). gscfuse is known to have issues when
multiple process try to read from a mount at the same time, so the
performance got quite bad (as expected) but it also seemed to leave the
processes in a zombie state (Ssl state Interruptible sleep, multithreaded).

Sorry I don't have more information on how to reproduce this consistently.
It would be nice if the docker image would exit/terminate (or have an
option to specify that) when that failure occurs.

Hope this is useful! And thank you for your development/support of this
software.

On Fri, Mar 15, 2019 at 10:58 AM Chambers, Matthew <
mat...@gm...> wrote:

> 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....
> 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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