• metaphlan github

• Module Name: metaphlan (see the modules page for more information)
• metaphlan uses multithreading. Please match the number of CPUs to the number of allocated cpus.
• Example files in $METAPHLAN_TEST_DATA
• We no longer provide metaphlan reference data since metaphlan3 requires these to be writable. This is not feasible in an HPC environment. Instead, users must install their own database the first time they run metaphlan. For example,

      	metaphlan --install --bowtie2db /data/$USER/mp_db
      

  Use the --bowtie2db option to point to where you want to install the database. Subsequent calls with the same option and argument will use the installed database.
• For the older version, metaphlan2, reference data is in /fdb/metaphlan/v20/

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

[user@cn3144]$ export METAPHLAN_DB=/data/$USER/mp_db

[user@cn3144]$ mkdir fasta

[user@cn3144]$ cp ${METAPHLAN_TEST_DATA:-none}/*.fasta.gz 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)
   metaphlan --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]$ exit
salloc.exe: Relinquishing job allocation 46116226

[user@biowulf]$

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

#!/bin/bash
module load metaphlan || exit 1
METAPHLAN_DB=/data/$USER/mp_db
fastq=/path/to/sample.fastq.gz
name=$(dirname $fastq)/$(basename $fastq .fastq.gz)
metaphlan --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:

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