PeptideshakerCLI for two percolator xml files, identification files not found

[Jannik Schneider]

Hey,

I wanted to run the cli tool but I am getting the error "No identification file found." . I tried different approaches but I am always getting this error no matter if I provide a list like -identification_files "file1.xml, file2.xml" or if I move my files to a folder and provide the folderpath like -identification_files path/to/folder . I wanted to read in two xml files that came from percolator.

Thanks for your time and help

[Harald Barsnes]

Hi!

It would seem like PeptideShaker is not able to read the input files you are giving it. As far as I can remember we do not support the Percolator xml output files and I'm afraid we do not have any immediate plans to do so. Is there any chance that you can convert your xml files to mzIdentML?

Best regards,

Harald