Download refseq and nr_euk from http://kaiju.binf.ku.dk/server. Both files are very big (14GBs and 42 GBs). It is recommended to use wget for this.
Unzip with tar zxvf kaiju_db_nr_euk_2019-06-25.tgz. Because of the size of the file, upto ~100 GBs of RAM is used during this process. You should submit a job for this. Example of a jobscript for this step can be found here. This step takes a few hours to complete
3. Running Kaiju:
There are 3 required arguments kaiju -t nodes.dmp -f kaiju_db_*.fmi -i inputfile.fastq. nodes.dmp and kaiju_db_*.fmi are from step 2.
A jobscript we created for this step can be found here