Commands

• alpha_diversity.py
• beta_diversity.py
• combine_kreports.py
• combine_mpa.py
• extract_kraken_reads.py
• filter_bracken.out.py
• fix_unmapped.py
• kreport2krona.py
• kreport2mpa.py
• make_kreport.py
• make_ktaxonomy.py

Module

You can load the modules by:

module load biocontainers
module load krakentools/1.2

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 krakentools on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=krakentools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers krakentools/1.2

extract_kraken_reads.py -k myfile.kraken -t 2 -s1 SRR5043021_1.fastq -s2 SRR5043021_2.fastq -o extracted1.fq -o2 extracted2.fq