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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.