Dorado is a basecaller for Oxford Nanopore reads.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ sinteractive --gres=gpu:v100x:1,lscratch:200 --mem=16g --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 ~]$ module load dorado/0.5.3 [user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID [user@cn3144 ~]$ cp -rL "${DORADO_TEST_DATA:-none}" input [user@cn3144 ~]$ ls -lh input -rw-r--r--. 1 user group 20G Jun 2 17:21 reads.pod5 [user@cn3144 ~]$ # emits unaligned bam by default [user@cn3144 ~]$ dorado basecaller --device cuda:all ${DORADO_MODELS}/dna_r9.4.1_e8_sup@v3.3 input > output.bam [user@cn3144 ~]$ ls -lh output.bam -rw-r--r-- 1 user group 2.1G Jun 2 20:02 output.bam [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. dorado.sh). For example:
#!/bin/bash set -e module load dorado/0.5.3 cd /lscratch/$SLURM_JOB_ID cp -rL "${DORADO_TEST_DATA:-none}" input dorado basecaller --device cuda:all ${DORADO_MODELS}/dna_r9.4.1_e8_sup@v3.3 input > output.bam
Submit this job using the Slurm sbatch command.
sbatch --cpus-per-task=6 --mem=16g --gres=lscratch:50,gpu:v100x:1 dorado.sh