ThermoRawFileParser produces files, which can not be processed with msconvert
See original GitHub issueWhen converting raw file to mzML with ThermoRawFileParser:
$ mono /opt/ThermoRawFileParser/ThermoRawFileParser.exe -f=2 -m=0 -i=170413_12mix_DIA_14.raw -b=170413_12mix_DIA_14.mzML -p
The mscovert can not process the converted file, but gives an error message about invalid cvParam
$ msconvert 170413_12mix_DIA_14.mzML --32 --zlib --filter "peakPicking false 1-" --mzXML -o ./
Invalid cvParam accession "1003145
I am not sure if this is a problem is in use-case or in ThermoRawFileParser or in msconvert (ProteoWizard release: 3.0.18344)
The raw file can be found from https://www.ebi.ac.uk/pride/archive/projects/PXD008738
Issue Analytics
- State:
- Created 2 years ago
- Reactions:1
- Comments:13 (3 by maintainers)
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Ok thanks for all the input, I’ll release a new version later today.
@nielshulstaert Yes, I think we have to release some sort of quick-fix for now. I was not expecting this small change will have such a huge effect. @martenson I agree that I should have been more aware of downstream tools when implementing the change.![Sorry](https://media.giphy.com/media/cjzkCDL3jZTZB6ki1B/giphy.gif)
It would be nice, however, to let the developers of the downstream tools aware that the change is to be implemented soon. Display some sort of warning, but I cannot come with a good idea how that is to be implemented