Differences

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--- guppy-software [2021/07/08 08:10] – aorth
+++ guppy-software [2023/12/06 06:42] (current) – aorth
@@ Line 6: / Line 6: @@
 ===== Information =====
-  * Version: 5.0.11
+  * Version: 6.5.7
   * Added: July, 2021
-  * Models: /export/apps/guppy/5.0.11/data
+  * Updated: December, 2023
-  * Link: https://community.nanoporetech.com/downloads/guppy/release_notes
 ===== 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.
-<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:
-<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
-$ 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):
-<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>