Guppy on GPU

Guppy basecalling may take days even when multi-threaded. Instead, you can run it on a GPU and turn days into hours.

Code Block (bash)

module load cuda/11.7 ont-guppy/4.5.2_gpu 
salloc -p gpu -q gpu --gres=gpu:A100 --cores=16


(0)-(user@maestro-3004:/pasteur/appa/scratch/user)-> guppy_basecaller basecall --input_path fast5 --save_path fastest --flowcell FLO-MIN106  --kit SQK-LSK109  --compress_fastq  --device=auto 
ONT Guppy basecalling software version 4.5.2+bcc53d3
config file:        /opt/gensoft/exe/ont-guppy/4.5.2_gpu/data/dna_r9.4.1_450bps_hac.cfg
model file:         /opt/gensoft/exe/ont-guppy/4.5.2_gpu/data/template_r9.4.1_450bps_hac.jsn
input path:         fast5
save path:          fastest
chunk size:         2000
chunks per runner:  512
minimum qscore:     9
records per file:   4000
fastq compression:  ON
num basecallers:    4
gpu device:         auto
kernel path:        
runners per device: 4
Found 485 fast5 files to process.
Init time: 1910 ms

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
*****^C