[proteowizard-support] problem with pwiz docker

[Zamboni N. <za...@im...>]

Hello,

I am trying to run msconvert in Ubuntu 18.04 using the "official" docker. It seems to work in the sense that the file is found by msconvert, but eventually it fails to load it (see below). I noticed that in the file path, the last slash / is converted to a backslash. Maybe that explains why the file isn't recognized.

Is this a bug? Is there a workaround?

Main thanks,
NIcola

nzadmin@imsb-nz-crazy:/mnt $ docker run -it --rm -v /mnt/repo:/mnt/repo chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert "/mnt/repo/2019-03-26_15:58:24_petrova8_05.d" --mzXML -v -z
format: mzXML
    m/z: Compression-Zlib, 64-bit
    intensity: Compression-Zlib, 32-bit
    rt: Compression-Zlib, 64-bit
ByteOrder_LittleEndian
indexed="true"
outputPath: .
extension: .mzXML
contactFilename:
runIndexSet:

spectrum list filters:

chromatogram list filters:

filenames:
  /mnt/repo\2019-03-26_15:58:24_petrova8_05.d

processing file: /mnt/repo\2019-03-26_15:58:24_petrova8_05.d
[MassHunterData::hasIonMobilityData()] Data file /mnt/repo\2019-03-26_15:58:24_petrova8_05.d does not exist

-
Prof. Dr. Nicola Zamboni
ETH Zurich
Institute of Molecular Systems Biology
Otto-Stern-Weg 3, HPM H45, 8093 Zurich
Phone +41 44 633 3141
http://www.imsb.ethz.ch/research/zamboni.html