Re: [proteowizard-support] Question about peakpicking filter

[Venkatraman, V. <Vid...@cs...>]

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 | 7 310.423.2833 |*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 | 7 310.423.2833 |*vid...@cs...<mailto:vid...@cs...>