Kraken2¶
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
Kraken2 is available as a module on Apocrita.
Usage¶
To run the default installed version of Kraken2, simply load the kraken2
module:
module load kraken2
For usage documentation, run kraken2 -h.
Example job¶
Do not use --memory-mapping
Kraken2 has a --memory-mapping flag which is not suitable for cluster use
and puts enormous strain on the storage infrastructure, as it avoids loading
your database into RAM and instead uses it directly from disk.
Please do not use it and instead let Kraken2 fully load your database into RAM (the default behaviour).
Please check your database size and ensure you request enough RAM (plus an additional allowance to allow for overhead) to load the entire database into RAM before Kraken2 runs.
Serial job¶
Here is a Kraken2 example job running on 1 core and 5GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=5G
module load kraken2
kraken2 --db example2_db \
--threads ${NSLOTS} \
input_file