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guides:slurm:array-job [05.03.2020 16:07] Juha Kekäläinen |
guides:slurm:array-job [18.10.2024 14:09] (current) Administrator |
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# SLURM Job Array | # SLURM Job Array | ||
- | [SLURM job array](https:// | + | [SLURM job array](https:// |
- | Below we have an example of fastqc quality analysis for multiple fastq nucleotide files. It scans for the " | + | Below we have an example of [fastqc](https:// |
Each job has 5 minutes of runtime and the job has 500 MB of RAM reserved. | Each job has 5 minutes of runtime and the job has 500 MB of RAM reserved. | ||
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#SBATCH --time 5 # Runtime in minutes. | #SBATCH --time 5 # Runtime in minutes. | ||
#SBATCH --mem=500 | #SBATCH --mem=500 | ||
- | #SBATCH --partition | + | #SBATCH --partition |
#SBATCH --output fastq_%A_%a.out.out | #SBATCH --output fastq_%A_%a.out.out | ||
#SBATCH --error fastqc_%A_%a.err | #SBATCH --error fastqc_%A_%a.err | ||
- | ##SBATCH --mail-user username@uef.fi | + | #SBATCH --mail-user username@uef.fi |
- | ##SBATCH --mail-type ALL # ALL will alert you of job beginning, completion, failure etc | + | #SBATCH --mail-type ALL # ALL will alert you of job beginning, completion, failure etc |
#SBATCH --array=1-100%3 | #SBATCH --array=1-100%3 | ||
- | # Make sure that the results exists | + | # Make sure that the results |
mkdir -p ./results/ | mkdir -p ./results/ | ||
# Load required modules | # Load required modules | ||
- | module load fastqc/0.11.7 | + | module load fastqc/0.12.1 |
# Search all the fastq files from the " | # Search all the fastq files from the " | ||
file=$(ls ./ | file=$(ls ./ | ||
- | # Run quality analysis | + | # Run quality analysis |
fastqc -o ./results/ $file | fastqc -o ./results/ $file | ||
``` | ``` | ||
- | Submit the job to computing queue with **"sbatch"** command. | + | Submit the job to computing queue with **sbatch** command. |