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

[Raaisa, R. <fnu...@ya...>]

Hello Matt,

Thanks a lot! I tried this command:

docker run -it -v /Users/raaisa:/raaisa chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /raaisa/BP_INS1E\ drug\ screen_6-21-17_17aug17.wiff -o /raaisa

and it worked like a charm!!

You were right, it has to be the bind-mounted one.

Thanks and Regards,
Raaisa

On Thu, Mar 21, 2019 at 1:30 PM Chambers, Matthew <mat...@gm...<mailto:mat...@gm...>> wrote:
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<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhub.docker.com%2Fr%2Fchambm%2Fpwiz-skyline-i-agree-to-the-vendor-licenses&data=02%7C01%7Cfnu.raaisa%40yale.edu%7Ca1d0db75d9a54c3c0ed708d6ae22eb13%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C1%7C636887862341810216&sdata=ow3sfEIq0jloN%2FCQsuZuikqficYx%2FjV5qyXRTKV%2BNaQ%3D&reserved=0>

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


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Raaisa
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