Purdue University

Commands

• kaiju
• kaiju-addTaxonNames
• kaiju-convertMAR.py
• kaiju-convertNR
• kaiju-excluded-accessions.txt
• kaiju-gbk2faa.pl
• kaiju-makedb
• kaiju-mergeOutputs
• kaiju-mkbwt
• kaiju-mkfmi
• kaiju-multi
• kaiju-taxonlistEuk.tsv
• kaiju2krona
• kaiju2table
• kaijup
• kaijux

Module

You can load the modules by:

module load biocontainers
module load kaiju

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 Kaiju on our clusters:

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

module --force purge
ml biocontainers kaiju

kaiju -t kaijudb/nodes.dmp \
     -f kaijudb/refseq/kaiju_db_refseq.fmi \
    -i input_1.fastq -j input_2.fastq
     -z 24