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Difference between revisions of "Set.logfile"

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  mothur > quit()
 
  mothur > quit()
  
 +
==To shut off logging==
 +
You can shut off mothur's logging features by running the following:
  
 +
mothur > set.logfile(name=silent)
 +
 +
==Revisions==
 +
* 1.40.0 Updates to mothur's log file management.  [https://github.com/mothur/mothur/issues/377 #377]
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Latest revision as of 19:08, 2 October 2018

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 > collect.single(list=abrecovery.fn.list, 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 > collect.single(list=abrecovery.fn.list, 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 > collect.single(list=abrecovery.fn.list, 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 > collect.single(list=abrecovery.fn.list, 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 > collect.single(list=abrecovery.fn.list, 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()

To shut off logging

You can shut off mothur's logging features by running the following:

mothur > set.logfile(name=silent)

Revisions

  • 1.40.0 Updates to mothur's log file management. #377