set.logfile
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 [`https://mothur.org`](https://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 [`https://mothur.org`](https://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 [`https://mothur.org`](https://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