Problem with step 11, run Percolator about mhcquant HOT 3 CLOSED

Hi @HeshamElAbd,

Thanks for trying MHCquant!
I never encountered this issue before. What kind of MS instrument are you using? Or do you have some special symbols in the filename by any chance?

Feel free to take this conversation to the #mhcquant channel in the nf-core slack: https://nf-co.re/join

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Hi @Leon-Bichmann
Thank you very much for the great software and thanks a lot for your help.
Okay, that is interesting, so for the type of machine, it. The file name is made from ASCII chars. At first, I used the mzML files, but then comet throws an error that the file is not indexed, so I used the following command to index the file using openMS FileFilter -peak_options:indexed_file true -in inputfile_.mzML -out_.mzML.

I re-started the pipeline with the indexed file everything went well until the percolator step, so I am really puzzled by the error, I will try it with different experiments and see the results. Also, I will move the message to MHCquant as well.

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Although we did not figure out the cause of the problem we suspect it is something related to file indexing and working with an unindexed mzML file. Nevertheless, this problem can be resolved by using .raw files directly, i.e. letting the pipeline do the conversion implicitly.

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