The "--spec-out" argument has problems with output files that are not in the "Quandenser_output/consensus_spectra" folder.
Using "--spec-out Quandenser_output/consensus_spectra/myOutput.mzML" (assuming "Quandenser_output" is the specified output directory) works, but using just "--spec-out myOutput.mzML" results in the error "Error: could not create output directory at Quandenser_output/consensus_spectra".
The problem probably lies in the construction of the maracluster command line arguments which contains the argument "--output-folder Quandenser_output/consensus_spectra" and expects the consensus spectrum file in that same directory.
The "--spec-out" argument has problems with output files that are not in the "Quandenser_output/consensus_spectra" folder.
Using "--spec-out Quandenser_output/consensus_spectra/myOutput.mzML" (assuming "Quandenser_output" is the specified output directory) works, but using just "--spec-out myOutput.mzML" results in the error "Error: could not create output directory at Quandenser_output/consensus_spectra".
The problem probably lies in the construction of the maracluster command line arguments which contains the argument "--output-folder Quandenser_output/consensus_spectra" and expects the consensus spectrum file in that same directory.