HUMAnN 3

Introduction

HUMAnN 3.0 is the next iteration of HUMAnN, the HMP Unified Metabolic Analysis Network. HUMAnN is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data.

For more information please check its website: https://huttenhower.sph.harvard.edu/humann/

Versions

  • 3.0.0

  • 3.6

Commands

  • humann

  • humann3

  • humann3_databases

  • humann_barplot

  • humann_benchmark

  • humann_build_custom_database

  • humann_config

  • humann_databases

  • humann_genefamilies_genus_level

  • humann_infer_taxonomy

  • humann_join_tables

  • humann_reduce_table

  • humann_regroup_table

  • humann_rename_table

  • humann_renorm_table

  • humann_split_stratified_table

  • humann_split_table

  • humann_test

  • humann_unpack_pathways

Database

Full ChocoPhlAn, UniRef90, EC-filtered UniRef90, UniRef50, EC-filtered UniRef50, and utility_mapping databases have been downloaded for users.

Module

You can load the modules by:

module load biocontainers
module load humann/3.0.0

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run HUMAnN3 on our cluster:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=humann
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers humann/3.0.0
# Check the database and config by:
humann_config --print

humann --threads 24 --input examples/demo.fastq --output demo_output --metaphlan-options "--bowtie2db /depot/itap/datasets/metaphlan"