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.
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"