When running the pipeline and supplying PSMs filtered at 1% FDR, mokapot does not train any SVM since the number of PSMs is already optimal given the standard arguments --trainFDR=0.01 and --testFDR=0.01.
These FDR thresholds are already configurable when calling the run_mokapot module directly, but cannot be changed when running the pipeline or the GUI.
When running the pipeline and supplying PSMs filtered at 1% FDR, mokapot does not train any SVM since the number of PSMs is already optimal given the standard arguments
--trainFDR=0.01and--testFDR=0.01.These FDR thresholds are already configurable when calling the
run_mokapotmodule directly, but cannot be changed when running the pipeline or the GUI.