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Error Raw #194

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Error Raw#194

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@enryH
enryH
opened on Apr 7, 2025

Is there any way how to find out more details what exactly went wrong? I ran

mono ThermoRawFileParser1.4.5/ThermoRawFileParser.exe -i=20220830_JL-4884_Forster_Ecoli_DMSO_rep2_EG-2.raw -f=2 -o=./ --logging=1
2025-04-07 15:31:12 INFO Started parsing 20220830_JL-4884_Forster_Ecoli_DMSO_rep2_EG-2.raw
2025-04-07 15:31:12 ERROR RAW file cannot be processed because of an error - ThermoFisher.CommonCore.RawFileReader.Facade.RawFileLoader
2025-04-07 15:31:12 INFO Processing completed 1 errors, 0 warnings

I tried both using the quantms docker container as well as locally (above).

Dataset: https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/

Activity

  1. caetera commented on Apr 7, 2025

    @caetera
    caetera
    on Apr 7, 2025
    Contributor

    Hi @enryH,

    this error usually means that the file is corrupted. The file size is about two times smaller compared to other replicates in the dataset - I guess, it was broken during transfer or acquisition.
    I tried to use MSConvert on it with no success - I am afraid there is nothing to do here.

    We will need to look into more human-understandable error reporting, though

  2. enryH commented on Apr 8, 2025

    @enryH
    enryH
    on Apr 8, 2025
    Author

    Thanks for looking into it Vladimir! I just got confirmation from Caroline that she also could not open the first two raw files, exactly the ones I tested... Remindes me to be more random in selecting my test data...

    Should we close for now?

  3. enryH
    closed this as completedon Apr 8, 2025

  4. caetera commented on Apr 9, 2025

    @caetera
    caetera
    on Apr 9, 2025
    Contributor

    I pushed a commit for the upcoming release #193 which should provide cleaner error messages for such cases.

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