Humann

Introduction

Humann is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads).

Versions

• 3.8

Commands

• humann

• humann3

• humann3_databases

• humann_associate

• humann_barplot

• humann_benchmark

• humann_build_custom_database

• humann_config

• humann_databases

• humann_genefamilies_genus_level

• humann_humann1_kegg

• humann_infer_taxonomy

• humann_join_tables

• humann_reduce_table

• humann_regroup_table

• humann_rename_table

• humann_renorm_table

• humann_rna_dna_norm

• humann_split_stratified_table

• humann_split_table

• humann_strain_profiler

• humann_test

• humann_unpack_pathways

Example job

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=humann      # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load humann/XXXX        ### Latest version is recommended.