Re: [proteowizard-support] Question about peakpicking filter

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

Hi Vidya,

Your Docker run wrapper seems to be mangling the quotes. It works using the official 'docker run' command.

-Matt


On 3/5/2019 7:22 PM, Venkatraman, Vidya wrote:
>
> Hi
>
> I am using the following command and I get some messages around regarding the peakpicking syntax: [msconvert] no files found matching "true"
>
> [msconvert] no files found matching "1-"
>
> #msconvert command
>
> *sudo /hpc/apps/docker/0.0.1/bin/dockerwrap run -e WINEDEBUG=-all -v /common/venkatramanv/Data/Test/msconvertdocker:/data 
> chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:x64 wine msconvert /data/file.raw --mzML --64 --zlib --filter "peakPicking true 1-" -o 
> file2.mzML*
>
> This is how my log looks:
>
> [msconvert] no files found matching "true"
>
> [msconvert] no files found matching "1-"
>
> format: mzML
>
>     m/z: Compression-Zlib, 64-bit
>
> intensity: Compression-Zlib, 64-bit
>
> rt: Compression-Zlib, 64-bit
>
> ByteOrder_LittleEndian
>
> indexed="true"
>
> outputPath: file2.mzML
>
> extension: .mzML
>
> contactFilename:
>
> runIndexSet:
>
> spectrum list filters:
>
> peakPicking
>
> chromatogram list filters:
>
> filenames:
>
> /data\file.raw
>
> processing file: /data\file.raw
>
> calculating source file checksums
>
> writing output file: file2.mzML\file.mzML
>
> Even though a mzML is generated, I am not sure if the peakpicking filter is applied. I have not seen the first 2 lines before with 
> msconvert on windows. Can you please advise on the right way to use peakpicking filter with the docker container?
>
>
> Regards
>
> *Vidya Venkatraman*
>
> *Bioinformatics Lead*
>
> *–––––––––––––––––––––––––––––––––––––––––––––––––––
> **Cedars-Sinai Medical Center*
>
> *Advanced Clinical Biosystems Research Institute*
>
> 8700 Beverly Blvd., Davis Building, 2089, Los Angeles, CA 90048
> *(*310.423.2998*|*7310.423.2833*|****vid...@cs... <mailto:vid...@cs...>**
>
> *From:* Venkatraman, Vidya
> *Sent:* Tuesday, March 05, 2019 4:20 PM
> *To:* 'su...@pr...' <su...@pr...>
> *Subject:* Question about peakpicking filter
>
> Hi
>
> I am using the following command and
>
> #msconvert
>
> sudo /hpc/apps/docker/0.0.1/bin/dockerwrap run -e WINEDEBUG=-all -v /common/venkatramanv/Data/Test/msconvertdocker:/data 
> chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:x64 wine msconvert /data/file.raw --mzML --64 --zlib --filter "peakPicking true 1-" -o 
> file2.mzML
>
> This is how my log looks:
>
> *Vidya Venkatraman*
>
> *Bioinformatics Lead*
>
> *–––––––––––––––––––––––––––––––––––––––––––––––––––
> **Cedars-Sinai Medical Center*
>
> *Advanced Clinical Biosystems Research Institute*
>
> 8700 Beverly Blvd., Davis Building, 2089, Los Angeles, CA 90048
> *(*310.423.2998*|*7310.423.2833*|****vid...@cs... <mailto:vid...@cs...>**
>
>
>
> _______________________________________________
> proteowizard-support mailing list
> pro...@li...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-support