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

References:

• Paper

• guppy Main Site

• Module Name: guppy (see the modules page for more information)
• Multithreaded/GPU
• Example files in /usr/local/apps/guppy/2.3.1/data

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 ~]$

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

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