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guppy-software [2021/07/08 08:10] – created aorthguppy-software [2023/12/06 06:42] (current) aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 5.0.11+  * Version: 6.5.7
   * Added: July, 2021   * Added: July, 2021
-  * Models/export/apps/guppy/5.0.11/data +  * UpdatedDecember, 2023
-  * Link: https://community.nanoporetech.com/downloads/guppy/release_notes+
  
 ===== Usage ===== ===== Usage =====
 +Guppy is only available on compute06 because this is the only node that has a GPU.
  
-See versions of guppy that are available: +//Note: guppy ships with some pre-configured models that set many basecalling parameters to sensible defaults. Please consult/opt/ont/guppy/data.// 
-<code>$ module avail guppy</code>+===== Installation ======
  
-Load one version into your environment and run it: 
-<code>$ module load guppy/5.0.11</code> 
- 
-**Note: guppy ships with some pre-configured models that set many basecalling parameters to sensible defaults. Please consult: /export/apps/guppy/5.0.11/data.** 
- 
-===== Installation ====== 
 Notes from the sysadmin during installation. Notes from the sysadmin during installation.
  
-<code>cd /tmp +<code>sudo dnf install https://hpc.ilri.cgiar.org/~jbaka/ONT-Dec2023/Software/ont-guppy-6.5.7-1.el8.x86_64.rpm</code>
-$ wget https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy_5.0.11_linux64.tar.gz +
-$ tar xf ont-guppy_5.0.11_linux64.tar.gz +
-$ sudo mkdir -p /export/apps/guppy +
-$ sudo cp -r ont-guppy /export/apps/guppy/5.0.11</code>+
  
 Run some test data using fourteen CPUs: Run some test data using fourteen CPUs:
  
-<code>cd /var/scratch +<code>mkdir -p /var/scratch/aorth/2022-05-24-guppy 
-mkdir -p /var/scratch/aorth/2021-07-01-guppy+cd /var/scratch/aorth/2022-05-24-guppy
 $ wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/nanopore_course_data/Data_Group1.tar.gz $ wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/nanopore_course_data/Data_Group1.tar.gz
-$ tar xf Data_Group1.tar.gz -C /var/scratch/aorth/2021-07-01-guppy +$ tar xf Data_Group1.tar.gz 
-$ guppy_basecaller --compress_fastq -i /var/scratch/aorth/2021-07-01-guppy/data/fast5_tiny/ -s /var/scratch/aorth/2021-07-01-guppy/data/basecall_tiny/ --cpu_threads_per_caller 14 --num_callers 1 -c dna_r9.4.1_450bps_hac.cfg+$ guppy_basecaller --compress_fastq -i data/fast5_tiny/ -s data/basecall_tiny/ --cpu_threads_per_caller 14 --num_callers 1 -c dna_r9.4.1_450bps_hac.cfg
 ... ...
-Caller time: 208271 ms, Samples called: 27619692, samples/s: 132614</code>+Caller time: 3281435 ms, Samples called: 27619692, samples/s: 8416.96</code>
  
 Run some test data using a GPU (currently only on compute06): Run some test data using a GPU (currently only on compute06):
  
-<code>$ guppy_basecaller --device "cuda:0" --compress_fastq -i /var/scratch/aorth/2021-07-01-guppy/data/fast5_tiny/ -s /var/scratch/aorth/2021-07-01-guppy/data/basecall_tiny/ -c dna_r9.4.1_450bps_hac.cfg+<code>$ srun --gres=gpu:v100:1 --partition=batch -w compute06 -n 1 -J guppy --pty bash 
 +$ guppy_basecaller --device "cuda:0" --compress_fastq -i data/fast5_tiny/ -s data/basecall_tiny/ -c dna_r9.4.1_450bps_hac.cfg
 ... ...
-Caller time: 2994 ms, Samples called: 27619692, samples/s: 9.22501e+06</code>+Caller time: 4366 ms, Samples called: 27619692, samples/s: 6.32609e+06</code>
guppy-software.1625731828.txt.gz · Last modified: 2021/07/08 08:10 by aorth