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!
Cheers
CS
%%mothur
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
by
Patrick D. Schloss
Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org
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()