From the humann home page:

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). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question "What are the microbes in my community-of-interest doing (or capable of doing)?"

• GitHub
• Home page

• Module Name: humann (see the modules page for more information)
• humann is a multithreaded application
• Reference data in /fdb/humann/
• humann depends on metaphlan reference data in /fdb/metaphlan. These are used by default, but users can bring their own versions and use the option: --metaphlan-options "--bowtie2db /path/to/db"
• Example data in $HUMANN_TEST_DATA

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive -c12 --mem=24g --gres=lscratch:100
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load humann
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 ~]$ cp -r ${HUMANN_TEST_DATA:-none} demo
[user@cn3144 ~]$ humann --threads $SLURM_CPUS_PER_TASK --input demo/demo.fastq --output demo.out
Creating output directory: /lscratch/46116226/demo.out
Output files will be written to: /lscratch/46116226/demo.out

Running metaphlan ........

Found g__Bacteroides.s__Bacteroides_dorei : 57.96% of mapped reads
Found g__Bacteroides.s__Bacteroides_vulgatus : 42.04% of mapped reads

Total species selected from prescreen: 2

Selected species explain 100.00% of predicted community composition

Creating custom ChocoPhlAn database ........

Running bowtie2-build ........

Running bowtie2 ........

Total bugs from nucleotide alignment: 2
g__Bacteroides.s__Bacteroides_vulgatus: 1274 hits
g__Bacteroides.s__Bacteroides_dorei: 1318 hits

Total gene families from nucleotide alignment: 548

Unaligned reads after nucleotide alignment: 87.6571428571 %

Running diamond ........

Aligning to reference database: uniref90_201901b_full.dmnd

Total bugs after translated alignment: 3
g__Bacteroides.s__Bacteroides_vulgatus: 1274 hits
g__Bacteroides.s__Bacteroides_dorei: 1318 hits
unclassified: 1599 hits

Total gene families after translated alignment: 815

Unaligned reads after translated alignment: 80.6190476190 %

Computing gene families ...

Computing pathways abundance and coverage ...

Output files created:
/lscratch/46116226/demo.out/demo_genefamilies.tsv
/lscratch/46116226/demo.out/demo_pathabundance.tsv
/lscratch/46116226/demo.out/demo_pathcoverage.tsv

[user@cn3144 ~]$ ls -lh demo.out
total 168K
-rw-r--r-- 1 user group 104K Dec 11 12:25 demo_genefamilies.tsv
drwxr-xr-x 2 user group 4.0K Dec 11 12:25 demo_humann_temp
-rw-r--r-- 1 user group 1.4K Dec 11 12:25 demo_pathabundance.tsv
-rw-r--r-- 1 user group 1.3K Dec 11 12:25 demo_pathcoverage.tsv
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. humann.sh). For example:

#! /bin/bash

module load humann/3.9.0 || exit 1
cd /lscratch/$SLURM_JOB_ID || exit 1
cp $HUMANN_TEST_DATA/demo.fastq .
mkdir out

# for humann version 2 modules, this command would be humann2
humann --threads $SLURM_CPUS_PER_TASK \
  --input demo.fastq \
  --output out

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] humann.sh

Create a swarmfile (e.g. humann.swarm). For example:

humann --input sample1.bam --output sample1.out
humann --input sample2.bam --output sample2.out
humann --input sample3.bam --output sample3.out

Submit this job using the swarm command.

swarm -f humann.swarm -g 10 -t 4 --module humann/3.9.0