Difference between revisions of "Applications/guppy"
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* Description: Local accelerated base calling for Nanopore data. | * Description: Local accelerated base calling for Nanopore data. | ||
| − | * Version: guppy 3.1.5 | + | * Version: guppy 3.1.5 to 6.4.2 |
| − | * Modules: guppy/cpu/3.1.5 (CPU) | + | * Modules: guppy/cpu/3.1.5 (CPU) to guppy/cpu/6.4.2 (CPU) |
| + | * Modules: guppy/gpu/3.1.5 (GPU) to guppy/gpu/6.4.2 (GPU) | ||
* Licence: Free, open-source | * Licence: Free, open-source | ||
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module purge | module purge | ||
module load cuda/10.1.168 | module load cuda/10.1.168 | ||
| − | module load guppy/gpu/4 | + | module load guppy/gpu/6.4.2 |
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 | 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 | ||
| Line 42: | Line 43: | ||
For applications that require this information: | For applications that require this information: | ||
| − | * | + | * NVidia A40 is at least 6.0 (GPU01 to GPU04) |
| − | * P100 is 6.0 | + | * NVidia P100 is 6.0 (GPU05) |
Revision as of 15:05, 13 December 2022
Contents
Application Details
- Description: Local accelerated base calling for Nanopore data.
- Version: guppy 3.1.5 to 6.4.2
- Modules: guppy/cpu/3.1.5 (CPU) to guppy/cpu/6.4.2 (CPU)
- Modules: guppy/gpu/3.1.5 (GPU) to guppy/gpu/6.4.2 (GPU)
- Licence: Free, open-source
- Note: guppy version 3 will be removed from service soon
Usage Examples
Using the GPU as an accelerator 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 to 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/6.4.2 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:
- NVidia A40 is at least 6.0 (GPU01 to GPU04)
- NVidia P100 is 6.0 (GPU05)
Further Information
- https://community.nanoporetech.com/ (login required)