metaphlan.submit

#!/bin/bash
#SBATCH --mem=20gb
#SBATCH --time=168:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --job-name=metaphlan
#SBATCH --error=metaphlan.%J.err
#SBATCH --output=metaphlan.%J.out
#SBATCH --partition=batch

module purge
module load metaphlan/4.0

# The indexed CHOCOPhlAnSGB database is already downloaded on our clusters
# This database can be accessed with the variable $METAPHLAN_BOWTIE2_DB once the MetaPhlAn module is loaded

# Run MetaPhlAn
# Here, input paired-end reads are the output reads generated with KneadData
# Please modify these paths according to your data location
metaphlan ./kneaddata_output_demo1/demo1.R1_kneaddata_paired_1.fastq,./kneaddata_output_demo1/demo1.R1_kneaddata_paired_2.fastq \
    --input_type fastq --nproc 8 \
    --bowtie2out demo1_metagenome_bowtie2.bz2 \
    -s demo1_metagenome_sam.bz2 \
    -o demo1_profiled_metagenome_marker_counts.txt

# Zipped *_sam.bz2 files can be unzipped with:
# bzip2 -d demo1_metagenome_sam.bz2

# If needed, output files from multiple samples can be merged with:
# merge_metaphlan_tables.py *_profiled_metagenome_marker_counts.txt > all_metaphlan_output.txt