maaslin2.submit

#!/bin/bash
#SBATCH --mem=20gb
#SBATCH --time=168:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --job-name=maaslin2
#SBATCH --error=maaslin2.%J.err
#SBATCH --output=maaslin2.%J.out
#SBATCH --partition=batch

module purge
module load maaslin2/0.3

# Running the demo example from https://github.com/biobakery/Maaslin2#run-a-demo
# MaAsLin2 uses metadata and output from HUMAnN as input
# If needed, please normalize your HUMAnN output using humann_renorm_table 

# Input .tsv files are in ./data in these examples
# Please modify these paths according to your data location
# Please modify the arguments, as well as --fixed_effects and --random_effects, based on your data
Maaslin2.R --fixed_effects="diagnosis,dysbiosis" \
    --random_effects="site,subject" \
    --standardize=FALSE \
   ./data/HMP2_taxonomy.tsv ./data/HMP2_metadata.tsv test_maaslin2_output