Re: [proteowizard-support] Issue with Thermo RAW reader for Linux (msconvert)

[Robert M. F. <rfl...@gm...>]

Hi Simon,

For a CLI that "just works" on Linux (and other platforms), I've used
ThermoRawFileParser. It only needs a mono run time installed, which isn't
too bad to install on Linux.

https://github.com/compomics/ThermoRawFileParser

I've compared it against msconvert, and it generated very, very similar
output. I've used it to convert a large number of spectra.

Hope it helps.

Robert

On Sun, May 7, 2023, 7:32 AM SImon Michau <sim...@rw...>
wrote:

> Dear ProteoWizard Team,
>
> while working on a new Data Analysis Pipeline for Orbitrap in Linux I
> encountered a problem with msconvert when trying to convert a .raw file to
> .mzML using the command `msconvert data.RAW` (see log below).
>
> I also tried the same in Windows where it works flawless. Is there a
> workaround to make this work in Linux? And if not do you have any
> recommendations for raw to mzML conversion via CLI?
>
>
> ----------------------------------------------
> format: mzML
>     m/z: Compression-None, 64-bit
>     intensity: Compression-None, 32-bit
>     rt: Compression-None, 64-bit
> ByteOrder_LittleEndian
>  indexed="true"
> outputPath: .
> extension: .mzML
> contactFilename:
> runIndexSet:
>
> spectrum list filters:
>
> chromatogram list filters:
>
> filenames:
>   01_Run.RAW
>
> processing file: data.RAW
> *[ReaderFail] [Reader_Thermo::read()] Thermo RAW reader not implemented:
> Thermo DLLs only work on Windows*
> Error processing file data.RAW
> ----------------------------------------------
>
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