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 installations include strainphlan, phylophlan, and hclust2.
$METAPHLAN_TEST_DATAAllocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive -c4 --mem=20g --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]$ 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]$ hclust2.py -c bbcry --top 0.25 \
-l --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). For example:
#!/bin/bash
module load metaphlan || exit 1
METAPHLAN_DB=/fdb/metaphlan/vOct22
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 |