mothurmagic not working

Hello mothur forum! I am somewhat new to computers, and for some reason am running into problems with my mothurmagic in ipy notebook. My notebook is in the mothur forum and everything is where it should be in the mothur folder. I even ran mothur via terminal and got make.contigs to work. Another thing is that mothur works in the ipy notebook, giving me responses when I send for make.contigs(help) and even gives me back responses when I input commands. I input the following commands and the log file gets output, but it doesn’t seem to run anything. Any help would be appreciated as I have no idea what it could be at this point!

mothur > set.dir(output=/Users/chrissugai/Desktop/mothur/analysis)
mothur > set.dir(input=/Users/chrissugai/Desktop/mothur/data)
mothur > make.contigs(file=stability.files, processors=1)
mothur > summary.seqs(fasta=stability.trim.contigs.fasta)

Mac version

Using ReadLine

Running 64Bit Version

mothur v.1.37.6
Last updated: 6/20/2016

Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type ‘help()’ for information on the commands that are available

Type ‘quit()’ to exit program
Script Mode

mothur > set.logfile(name=mothur.ipython.86497.logfile)

mothur > mothur > set.dir(output=/Users/chrissugai/Desktop/mothur/analysis)

mothur > mothur > set.dir(input=/Users/chrissugai/Desktop/mothur/data)

mothur > mothur > make.contigs(file=stability.files, processors=1)

mothur > mothur > summary.seqs(fasta=stability.trim.contigs.fasta)

mothur > quit()

Are you including the “mothur >” part in you notebook? You shouldn’t include those. Other than that, what isn’t working?