not recognizing changes to parameters

[eam12]

I'm running metAMOS as a job submission (via PBS job script) to a computer cluster. However, runPipeline always runs the default parameters, no matter what parameters I change. For example, I want to use spades as my assembly tool, but the output is always with SOAPdenovo.

[aldembert]

Make sure that you are including the -a option with the assemblers that you want and also make sure that you are using the correct name of such assembler(remember its case sensitive)

[skoren]

Make sure you're running in a clean folder, without using force, it won't re-run an assembly if it already exists. Do you have the output as well as your PBS script/command, that would give information on available assemblers and what it is running, you can make it verbose by running with -v