HUMAnN
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. This process (functional profiling) aims to describe the metabolic potential of a microbial community and its members.
License
Free to use and open source under MIT License.
Available
Versions available in Puhti: 3.0.1, 3.6, 3.8, 3.9
Usage
In Puhti, HUMAnN is installed as containerized application. To activate it, run command:
module load humann
humann
By default HUMaN tries to check and update the MetaPhlAn database every time it's run. This will fail with containerized installation, so you will need to add command line option:
--metaphlan-options "--offline --bowtie2db /path/to/db"
To use CSC provided database use:
--metaphlan-options "--offline --bowtie2db $MPA"
CSC provides default versions of the HUMaN databases. You can use them by specifying:
--nucleotide-database $HUMANN_NUC
--protein-database $HUMANN_PROT
HUMAnN can utilize several CPU cores. To do this set --cpus-per-task to desired number.
In Puhti you can use up to 40 cores. Also remember to add option --threads to your HUMAnN
command. You can use variable $SLURM_CPUS_PER_TASK to automatically match the requested
number.
Example batch job script (use your actual project neame for --account)
#!/bin/bash -l
#SBATCH --job-name=humann
#SBATCH --account=project_123456
#SBATCH --partition=small
#SBATCH --time=01:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=10
#SBATCH --mem=20000
# Load HUMaN module
module load humann
# Dowload a test file
wget https://github.com/biobakery/humann/raw/master/examples/demo.fastq.gz
# Run HUMaN
humann --threads=$SLURM_CPUS_PER_TASK --input demo.fastq.gz --nucleotide-database $HUMANN_NUC --protein-database $HUMANN_PROT --metaphlan-options "--offline --bowtie2db $MPA" --output demo_out