• metaphlan Main Site: metaphlan.com

• Module Name: metaphlan (see the modules page for more information)
• metaphlan uses multithreading/processing. Please match the number of CPUs to the number of allocated cpus.
• Example files in $METAPHLAN_TEST_DATA
• Reference data in /fdb/metaphlan/

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

[user@biowulf]$ sinteractive -c4 --mem=8g --gres=lscratch:10
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]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144]$ module load metaphlan bowtie/2
[user@cn3144]$ mkdir fasta
[user@cn3144]$ cp $METAPHLAN_TEST_DATA/* fasta
[user@cn3144]$ ls -lh fasta
-rw-r--r-- 1 user group 690K Nov  4 13:11 SRS014459-Stool.fasta.gz
-rw-r--r-- 1 user group 608K Nov  4 13:11 SRS014464-Anterior_nares.fasta.gz
-rw-r--r-- 1 user group 704K Nov  4 13:11 SRS014470-Tongue_dorsum.fasta.gz
-rw-r--r-- 1 user group 748K Nov  4 13:11 SRS014472-Buccal_mucosa.fasta.gz
-rw-r--r-- 1 user group 696K Nov  4 13:11 SRS014476-Supragingival_plaque.fasta.gz
-rw-r--r-- 1 user group 687K Nov  4 13:11 SRS014494-Posterior_fornix.fasta.gz

[user@cn3144]$ for f in fasta/*.gz; do
                    name=$(basename $f .fasta.gz)
                    metaphlan2.py --nproc $SLURM_CPUS_PER_TASK --bowtie2out ${name}.bt2.bz2 \
                                  --input_type fasta --bowtie2db $METAPHLAN_DB $f > ${name}_profile.txt
                  done
[user@cn3144]$ merge_metaphlan_tables.py *_profile.txt > merged_abundance_table.txt
[user@cn3144]$ metaphlan_hclust_heatmap.py -c bbcry --top 25 --minv 0.1 \
                      -s log --in merged_abundance_table.txt \
                      --out abundance_heatmap.png

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Create a batch input file (e.g. metaphlan.sh), which uses the input file 'metaphlan.in'. For example:

#!/bin/bash
module load metaphlan || exit 1
fastq=/path/to/sample.fastq.gz
name=$(dirname $fastq)/$(basename $fastq .fastq.gz)
metaphlan2.py --nproc $SLURM_CPUS_PER_TASK --bowtie2out ${name}.bt2.bz2 \
              --input_type fastq --bowtie2db $METAPHLAN_DB $fastq > ${name}_profile.txt

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=12g metaphlan.sh

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

metaphlan2.py --nproc $SLURM_CPUS_PER_TASK --bowtie2out sample1.bt2.bz2 \
              --input_type fastq --bowtie2db $METAPHLAN_DB sample1.fastq.gz > sample1_profile.txt
metaphlan2.py --nproc $SLURM_CPUS_PER_TASK --bowtie2out sample2.bt2.bz2 \
              --input_type fastq --bowtie2db $METAPHLAN_DB sample2.fastq.gz > sample2_profile.txt
metaphlan2.py --nproc $SLURM_CPUS_PER_TASK --bowtie2out sample3.bt2.bz2 \
              --input_type fastq --bowtie2db $METAPHLAN_DB sample3.fastq.gz > sample3_profile.txt

Submit this job using the swarm command.

swarm -f metaphlan.swarm -g 12 -t 6 --module metaphlan