Purdue University

Commands

• concoct
• concoct_refine
• concoct_coverage_table.py
• cut_up_fasta.py
• extract_fasta_bins.py
• merge_cutup_clustering.py

Module

You can load the modules by:

module load biocontainers
module load concoct/1.1.0-py38

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run concoct on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=concoct
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers concoct/1.1.0-py38

cut_up_fasta.py final.contigs.fa -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.fa
concoct_coverage_table.py contigs_10K.bed SRR1976948_sorted.bam > coverage_table.tsv
concoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b concoct_output/