Major The "Classify Sequences with CLARK" element has two modes: CLARK and CLARK-l. It can be chosen with the "Classification tool" parameter. In CLARK-l mode some parameters become invisible, because they don't have sense for this mode, e.g. "K-mer length". But the value of this parameter is still passed to the tool process.
Check all parameters of the element. The hidden parameters shouldn't be passed to the process.