Difference between revisions of "Applications/guppy"
From HPC
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* Description: Local accelerated basecalling for Nanopore data. | * Description: Local accelerated basecalling for Nanopore data. | ||
* Version: guppy 3.1.5 and 4.0.14 | * Version: guppy 3.1.5 and 4.0.14 | ||
| − | * Modules: guppy/cpu/3.1.5 (CPU), guppy/gpu/3.1.5 (GPU), guppy/cpu/4.0.14 (CPU), guppy/gpu/4.0.14 (GPU) | + | * Modules: guppy/cpu/3.1.5 (CPU), guppy/gpu/3.1.5 (GPU), guppy/cpu/4.0.14 (CPU), guppy/gpu/4.0.14 (GPU), guppy/gpu/4.2.2 |
* Licence: Free, open-source | * Licence: Free, open-source | ||
| + | |||
| + | * '''Note''' : guppy version 3 will be removed from service soon | ||
==Usage Examples== | ==Usage Examples== | ||
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#SBATCH --gres=gpu:tesla:2 | #SBATCH --gres=gpu:tesla:2 | ||
#SBATCH --exclusive | #SBATCH --exclusive | ||
| − | |||
module purge | module purge | ||
| − | module load cuda/ | + | module load cuda/10.1.168 |
| − | module load guppy/gpu/ | + | module load guppy/gpu/4.2.2 |
| − | |||
| − | guppy_basecaller --input_path /home/user/ | + | guppy_basecaller --input_path /home/user/folderIN --save_path /home/user/folderOUT --flowcell FLO-MIN106 --kit SQK-RPB004 --min_qscore 7 --qscore_filtering -x cuda:0 cuda:1 |
</pre> | </pre> | ||
Revision as of 09:39, 23 November 2021
Contents
Application Details
- Description: Local accelerated basecalling for Nanopore data.
- Version: guppy 3.1.5 and 4.0.14
- Modules: guppy/cpu/3.1.5 (CPU), guppy/gpu/3.1.5 (GPU), guppy/cpu/4.0.14 (CPU), guppy/gpu/4.0.14 (GPU), guppy/gpu/4.2.2
- Licence: Free, open-source
- Note : guppy version 3 will be removed from service soon
Usage Examples
Using the GPU as accelerators will make the analysis considerably faster (on large data sets). For small runs the CPU version is recommended and probably faster by removing the GPU overhead.
Important : guppy/gpu (GPU version) requires compute level of six or above, see examples below.
Batch example
This uses 2 GPUs presently on GPU05 (compute level is high than 6) which is required by guppy's minimum requirement.
#!/bin/bash #SBATCH -J guppy.job #SBATCH --exclusive #SBATCH -o gpu05.%j.out #SBATCH -e gpu05.%j.err #SBATCH -p gpu05 #SBATCH --gres=gpu:tesla:2 #SBATCH --exclusive module purge module load cuda/10.1.168 module load guppy/gpu/4.2.2 guppy_basecaller --input_path /home/user/folderIN --save_path /home/user/folderOUT --flowcell FLO-MIN106 --kit SQK-RPB004 --min_qscore 7 --qscore_filtering -x cuda:0 cuda:1
Compute capability
For applications that require this information:
- K40m is 3.5
- P100 is 6.0
Further Information
- https://community.nanoporetech.com/ (login required)