• bonito on GitHub

• Module Name: bonito (see the modules page for more information)
• This software is GPU accelerated
• Example files in $BONITO_TEST_DATA

Models available

Use

$ bonito download --models --show

to see all available models. Note that models are included in the install already. fast: fast model hac: high accuracy sup: super high accuracy

Allocate an interactive session and run the program. Note that 0.3.6 runs on p100 GPUs but >=0.5.0 requires v100 or newer. Sample session:

[user@biowulf]$ sinteractive --gres=lscratch:50,gpu:v100x:1 --mem=12g --cpus-per-task=6
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144]$ module load bonito/0.7.2
[user@cn3144]$ cp -rL ${BONITO_TEST_DATA:-none}/* .
[user@cn3144]$ ls -lh
total 4.0K
drwxr-xr-x 3 user group 4.0K Feb  8 11:07 Zymo-GridION-EVEN-BB-SN
[user@cn3144]$ find Zymo-GridION-EVEN-BB-SN -name '*.fast5' -printf '.' | wc -c
160000
[user@cn3144]$ ### basecalling command for bonito 0.3.6
[user@cn3144]$ bonito basecaller --fastq --recursive \
                    --device cuda dna_r9.4.1 Zymo-GridION-EVEN-BB-SN > reads.fastq
> loading model
> calling: 20829 reads [49:08,  7.08 reads/s]
...
[user@cn3144]$ ### basecalling command for bonito >=0.5.0
[user@cn3144]$ bonito basecaller --recursive --device cuda \
    dna_r9.4.1_e8_hac@v3.3 Zymo-GridION-EVEN-BB-SN | gzip -c - > reads.fastq.gz
> loading model dna_r9.4.1_e8.1_hac@v3.3
> completed reads: 160000
> duration: 0:24:34
> samples per second 4.7E+06
> done

[user@cn3144]$ ### basecalling command for bonito >=0.7.1
[user@cn3144]$ bonito basecaller --recursive --device cuda \
    dna_r9.4.1_e8_hac@v3.3 Zymo-GridION-EVEN-BB-SN | gzip -c - > reads.fastq.gz
> reading fast5
> outputting unaligned fastq
> loading model dna_r9.4.1_e8_hac@v3.3
> completed reads: 160000
> duration: 0:23:39
> samples per second 4.9E+06
> done

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Current versions of bonito achieved ~110 reads/s on a V100X GPU with the hac model. The basecaller does not scale to more than 1 GPU

Create a batch input file (e.g. bonito.sh), which uses the input file 'bonito.in'. For example:

#!/bin/bash
wd=$PWD

module load bonito/0.7.2 || exit 1
cd /lscratch/$SLURM_JOB_ID || exit 1
cp -rL ${BONITO_TEST_DATA:-none}/* .
bonito basecaller --recursive --device cuda \
    dna_r9.4.1_e8_hac@v3.3 Zymo-GridION-EVEN-BB-SN | gzip -c - > reads.fastq.gz
mv reads.fastq $wd

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=12g --gres=gpu:v100x:1,lscratch:50 bonito.sh

Create a swarmfile (e.g. bonito.swarm). For example:

bonito basecaller --fastq --recursive --device cuda dna_r9.4.1_e8_hac@v3.3 run1 > reads1.fastq
bonito basecaller --fastq --recursive --device cuda dna_r9.4.1_e8_hac@v3.3 run2 > reads2.fastq

Submit this job using the swarm command.

swarm -f bonito.swarm -g 12 -t 6 --gres=gpu:v100x:1 --module bonito/0.7.2