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Software Requirements
an initial python venv
bonito has a very specific requirement on pytorch 1.10.0, so depending on the base CUDA version we'll look at setting up one of these two:
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could look at the web server version
Bonito
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Use threads and redirect STDOUT to a file (line 6)
Bonito Standalone
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#!/bin/bash -l #PBS -N bonito-gpu #PBS -l select=1:ncpus=8:mem=32gb:ngpus=1:gputype=A100 #PBS -l walltime=72:00:00 #Change to folder where the job was submitted cd $PBS_O_WORKDIR # Run Bonito - check paths and parameters are correct singularity exec -B /work/ont --nv docker://ghcr.io/eresearchqut/bonito:v0.0.5 bonito \ basecaller dna_r9.4.1_e8_sup@v3.3 \ ./example_fast5 \ --modified-bases 5mC \ --reference ./reference/GCA_000001405.15_GRCh38_no_alt_analysis_set.mmi \ --recursive \ --alignment-threads 4 | \ samtools view -u | samtools sort -@ 4 > ./bonito_test/bam/HG002_as_test.bam # Run samtools index singularity exec -B /work/ont --nv docker://ghcr.io/eresearchqut/bonito:v0.0.5 \ samtools index HG002_as_test.bam |
Clair3
Clair3 is available in a nextflow pipeline:
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