Biowulf High Performance Computing at the NIH
guppy on Biowulf

Guppy is a basecaller from Oxford Nanopore Technologies. Guppy can use both CPUs or GPUs.

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 guppy

[user@cn3144 ~]$ guppy_basecaller --input_path raw_fast5_dir --config dna_r9.4_450bps.cfg --save_path output_dir 

[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. guppy.sh). For example:

#!/bin/bash
set -e
module load guppy
guppy_basecaller --input_path raw_fast5_dir --config dna_r9.4_450bps.cfg --save_path output_dir

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] guppy.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. guppy.swarm). For example:

guppy_basecaller --input_path indir1 --config dna_r9.4_450bps.cfg --save_path outdir1
guppy_basecaller --input_path indir2 --config dna_r9.4_450bps.cfg --save_path outdir2
...etc...

Submit this job using the swarm command.

swarm -f guppy.swarm [-g #] [-t #] --module guppy
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 guppy Loads the guppy module for each subjob in the swarm