Purdue University

Commands

• average_nucleotide_identity.py
• genbank_get_genomes_by_taxon.py
• delta_filter_wrapper.py

Module

You can load the modules by:

module load biocontainers
module load pyani

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 Pyani on our clusters:

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

module --force purge
ml biocontainers pyani

average_nucleotide_identity.py -i tests/ -o tests/test_ANIm_output -m ANIm -g
average_nucleotide_identity.py -i tests/  -o tests/test_ANIb_output -m ANIb -g
average_nucleotide_identity.py -i tests/ -o tests/test_ANIblastall_output -m ANIblastall -g
average_nucleotide_identity.py -i tests/  -o tests/test_TETRA_output -m TETRA -g