Biowulf High Performance Computing at the NIH
Azimuth on Biowulf

Azimuth: Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load Azimuth
[+] Loading Azimuth 2.0 ...
[user@cn3144 ~]$ python
Python 2.7.14 |Anaconda, Inc.| (default, Mar 27 2018, 17:29:31)
[GCC 7.2.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import azimuth.model_comparison
>>> import numpy as np
>>> sequences = np.array(['ACAGCTGATCTCCAGATATGACCATGGGTT', 'CAGCTGATCTCCAGATATGACCATGGGTTT', 'CCAGAAGTTTGAGCCACAAACCCATGGTCA'])
>>> amino_acid_cut_positions = np.array([2, 2, 4])
>>> percent_peptides = np.array([0.18, 0.18, 0.35])
>>> predictions = azimuth.model_comparison.predict(sequences, amino_acid_cut_positions, percent_peptides)
No model file specified, using V3_model_full
>>> for i, prediction in enumerate(predictions):
...     print sequences[i], prediction
...
ACAGCTGATCTCCAGATATGACCATGGGTT 0.672298196907
CAGCTGATCTCCAGATATGACCATGGGTTT 0.687944237021
CCAGAAGTTTGAGCCACAAACCCATGGTCA 0.659245390401
>>> quit()

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. Azimuth.sh). For example:

#!/bin/bash
module load Azimuth
python my_Azimuth.py

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] Azimuth.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. Azimuth.swarm). For example:

python my_Azimuth.py
python my_Azimuth.py
python my_Azimuth.py
python my_Azimuth.py

Submit this job using the swarm command.

swarm -f Azimuth.swarm [-g #] [-t #] --module Azimuth
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module Azimuth Loads the Azimuth module for each subjob in the swarm