From the metaphlan documentation:
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling. MetaPhlAn relies on ~1.1M unique clade-specific marker genes identified from ~100,000 reference genomes (~99,500 bacterial and archaeal and ~500 eukaryotic), allowing:
- unambiguous taxonomic assignments;
- accurate estimation of organismal relative abundance;
- species-level resolution for bacteria, archaea, eukaryotes and viruses;
- strain identification and tracking;
- orders of magnitude speedups compared to existing methods;
- metagenomic strain-level population genomics
Metaphlan versions >3 include strainphlan, phylophlan, and hclust2.
$METAPHLAN_TEST_DATA
metaphlan --install --bowtie2db /data/$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.
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 metaphlanwhere
| -g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
| -t # | Number of threads/CPUs required for each process (1 line in the swarm command file). |
| --module metaphlan | Loads the metaphlan module for each subjob in the swarm |