We will be hosting mothur and R workshops throughout 2018. Learn more.

Batch mode

From mothur
Jump to: navigation, search

In batch mode you can supply a file with a list of commands that you want mothur to run. This would be useful if you have a set of analyses that you know you are going to run and don't want to have to wait for them to run. For example the batch file could look like:

cluster(column=final.dist, count=final.count_table, cutoff=0.03)
collect.single()
rarefaction.single() 

To run mothur in batch mode enter the name of the batch file after the program name. For example:

escriba:AmazonData pschloss$ ../mothur/mothur batchfile

If you want to enter any comments in the batch file, simply make sure that the first character on the line is a pound (i.e. #) character:

#This is a batch file for running the equivalent of dotur
cluster(column=final.dist, count=final.count_table, cutoff=0.03)
collect.single()
rarefaction.single()

Of related interest is the command line mode.