guppy¶
Description¶
A basecaller for data generated with equipment produced by Oxford Nanopore Technologies.
Environment Modules¶
Run module spider guppy to find out what environment modules are available for this application.
Environment Variables¶
- HPC_GUPPY_DIR - installation directory
- HPC_GUPPY_BIN - executable directory
- HPC_GUPPY_LIB - library directory
- HPC_GUPPY_EXE - examples directory
Additional Usage Information¶
Warning
Guppy can be orders of magnitude faster when using GPUs for basecalling compared to pure CPU runs. See GPU Access for more details on how to request GPUs on HiPerGator.
GPU Job Example¶
Here's a sample Guppy GPU script you might want to use as a starting point:
#!/bin/bash
#SBATCH --job-name=guppy
#SBATCH --output=guppy_%j.out
#SBATCH --time=12:00:00
#SBATCH --ntasks=1
#SBATCH --mem=10GB
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=MYEMAIL@ufl.edu
#SBATCH --partition=gpu
#SBATCH --gpus=geforce:1
date;hostname;pwd
module purge
module load cuda guppy
guppy_basecaller \
--recursive \
--input_path cool_project/minion_input/fast5 \
--save_path cool_project/minion_output/basecalls \
--flowcell FLO-MIN107 --kit SQK-LSK109 \
--device "auto"
date
Use jobnvtop and jobhtop tools from the UFRC environment module for a real-time look at GPU and CPU processes on the job node.
CPU Job Example¶
If you don't have access to GPUs then set
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=X
in the resources request section and use the corresponding guppy_basecaller arguments to set the number of basecallers and threads to use CPUs:
--cpu_threads_per_caller X --num_callers 1
Categories¶
phylogenetics