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MaAsLin FAQs

This page will host answers to questions posed to MaAsLin

Question 1: I am getting a possible input file error. How should the metadata be formatted?

Answer: Please review your tsv file to make sure there are no duplicated column names. It is important to note that MaAsLin does not recognize special characters (ie anything other than [a-z|A-Z|0-9] ) for unique column names as special characters will all be replaced with underscores for file naming purposes.

Question 2: Can I still run MaAsLin from the command line?

Answer: Yes, you can still run MaAsLin from the command line after you follow the install steps.

To run the demo on the command line ($MAASLIN_PATH = the location of the readme in the MaAsLin package):

$ Rscript $MAASLIN_PATH/R/Maaslin.R $MAASLIN_PATH/inst/extdata/maaslin_demo2.tsv maaslin_demo_output -i $MAASLIN_PATH/inst/extdata/

Question 3: Why are the parameters in the args file not applied to the MaAsLin run?

Answer: The args file is only used when running MaAsLin with sfle. MaAsLin no longer supports runs with sfle. Please provide the parameters from the args file on the command line or as options to the MaAsLin function.