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Set.logfile

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You may want to give your logfile a specific name or append a series of logfiles. The set.logfile command allows you to do this.

Default Options

mothur > set.logfile(name=myCollectLogfile)
mothur > read.otu(list=abrecovery.fn.list)
mothur > collect.single(label=0.03)

When you open myCollectLogfile you will see:

Mac version

Using ReadLine

mothur v.1.10.0
Last updated: 5/14/2010

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=myCollectLogfile)

mothur > read.otu(list=abrecovery.fn.list)

mothur > collect.single(label=0.03)
0.03

Output File Names: 
abrecovery.fn.sobs
abrecovery.fn.chao
abrecovery.fn.ace
abrecovery.fn.jack
abrecovery.fn.shannon
abrecovery.fn.np_shannon
abrecovery.fn.simpson


mothur > quit()

append

Now if you want to append other executions of mothur to the myCollectLogfile you can do so with the following commands:

mothur > set.logfile(name=myCollectLogfile, append=T)
mothur > read.otu(list=abrecovery.fn.list)
mothur > collect.single(label=0.10)


Now myCollectLogfile will look like:

Mac version

Using ReadLine

mothur v.1.10.0
Last updated: 5/14/2010

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=myCollectLogfile)

mothur > read.otu(list=abrecovery.fn.list)

mothur > collect.single(label=0.03)
0.03

Output File Names: 
abrecovery.fn.sobs
abrecovery.fn.chao
abrecovery.fn.ace
abrecovery.fn.jack
abrecovery.fn.shannon
abrecovery.fn.np_shannon
abrecovery.fn.simpson


mothur > quit()


*********************************************************************************

Mac version

Using ReadLine

mothur v.1.10.0
Last updated: 5/14/2010

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=myCollectLogfile, append=T)

mothur > read.otu(list=abrecovery.fn.list)

mothur > collect.single(label=0.10)
0.10

Output File Names: 
abrecovery.fn.sobs
abrecovery.fn.chao
abrecovery.fn.ace
abrecovery.fn.jack
abrecovery.fn.shannon
abrecovery.fn.np_shannon
abrecovery.fn.simpson


mothur > quit()