Re: [proteowizard-support] msconvert: Not able to find the output files

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

Hi Raaisa,

I forgot to add the -o parameter to change the output directory to the bind-mounted one (also the image has been moved to the proteowizard 
organization rather than my personal account):
|docker run -it --rm -e WINEDEBUG=-all -v /your/data:/data proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert 
/data/file.raw *-o /data*|

Hope this helps,
-Matt


On 3/20/2019 6:10 PM, Raaisa, Raaisa wrote:
> Hello Proteowizard team,
>
> First of all thanks for creating such a great tool. msconvert is really helpful for converting .wiff files to .mzML and I have using it 
> without issues for a long time. I have been using MSConvertGUI for file conversions and recently ran into an issue of "illegal character" 
> in filename. Turns out one of the sample names had quotation marks which created issues. I then decided to try out the msconvert 
> commandline version on my MacOS and I was successfully able to convert the files as shown by my terminal.
>
> The only thing is I am not able to see these files in my directory. I am wondering if this is some docker issue and I am not passing the 
> command correctly. I wrote the command in this format:
>
> # |docker run -it --rm -e WINEDEBUG=-all -v /your/data:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/file.raw|
>
> as explained on the link:
> https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses
>
> Have you seen this issue before and if yes, could you suggest anything to resolve? Please let me know if any more information is required.
>
> Thanks in advance,
> Raaisa
>
>
> -- 
> Raaisa
> <https://www.linkedin.com/in/raaisa-raaisa-50bb0862>
>
>
>
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