Failed to convert mzml files from .wiff, because of Illegal characters in path

[FabRiols]

Hi guys,

I try using MS convert to convert a .wiff file to .mzml files, as I do all time.
However, this time something went wrong with Analyst software (Sciex acquisition soft.) when generating the very first acquisition, called blank, and makes MCconvert fail:

"Starting...
Opening file "D:\Analyst Data\Projects\20231122_P-22069_S-Perocchi_ALS_CSF_Plate04\Data\SLA Batch - 20231123 - 1.wiff" for read...
Failed - System.ArgumentException: error generating output filename for input file 'D:\Analyst Data\Projects\20231122_P-22069_S-Perocchi_ALS_CSF_Plate04\Data\SLA Batch - 20231123 - 1.wiff' and output run id 'SLA Batch - 20231123 - 1-Blank_10
Blank_10
Blank_10
Blank_10
blank_0000' ---> System.ArgumentException: Illegal characters in path."

This issue is specific to that sample. So my question, is it possible to skip this particular sample, so the software can manage the rest?
Thank you very much for your help!
Best wishes,
Fabien

[brendanx67]

To me, that looks like there are newline characters in a sample name inside your WIFF file. The file is: Data\SLA Batch - 20231123 - 1.wiff And the sample name is: "Blank_10 Blank_10 Blank_10 Blank_10 blank_0000" And MSConvert is trying to create a separate mzML file for each sample in your WIFF file by using the naming strategy: <wiff-basename>-<sample-name>.mzML I am not sure what this code currently does to remove invalid path characters from the <sample-name> but it seems that code needs to be improved to include \n and \r and any other invalid path characters it may have omitted. I am sure this will be a relatively straightforward fix that can be released soon. In the meantime, if SCIEX offers any ability to edit sample names in a WIFF file, you could fix this on your side. And probably you should look into how you created such an odd and undesirable sample name in the first place and avoid doing it again. Thanks for posting your issue so clearly.

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On Fri, Nov 24, 2023 at 12:51 AM FabRiols ***@***.***> wrote: Hi guys, I try using MS convert to convert a .wiff file to .mzml files, as I do all time. However, this time something went wrong with Analyst software (Sciex acquisition soft.) when generating the very first acquisition, called blank, and makes MCconvert fail: "Starting... Opening file "D:\Analyst Data\Projects\20231122_P-22069_S-Perocchi_ALS_CSF_Plate04\Data\SLA Batch - 20231123 - 1.wiff" for read... Failed - System.ArgumentException: error generating output filename for input file 'D:\Analyst Data\Projects\20231122_P-22069_S-Perocchi_ALS_CSF_Plate04\Data\SLA Batch - 20231123 - 1.wiff' and output run id 'SLA Batch - 20231123 - 1-Blank_10 Blank_10 Blank_10 Blank_10 blank_0000' ---> System.ArgumentException: Illegal characters in path." This issue is specific to that sample. So my question, is it possible to skip this particular sample, so the software can manage the rest? Thank you very much for your help! Best wishes, Fabien — Reply to this email directly, view it on GitHub <#2786>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACYBWUEOURY6SCXMSW2OVGLYGBNZ7AVCNFSM6AAAAAA7YZODWKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAYDSMZTG43TQOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[chambm]

Thanks for the report. I forgot to update MSConvertGUI's logic when I did msconvert's.