Bioinformatics Center

User Tools

Site Tools

You are here: home » guides » slurm » basics
guides:slurm:basics

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision Both sides next revision
guides:slurm:basics [16.10.2020 10:47]
Juha Kekäläinen 		guides:slurm:basics [03.03.2021 13:45]
Administrator
Line 47: Line 47:
 ``` ```
 **[sbatch](https://slurm.schedmd.com/sbatch.html)** command submits the job to the job queue and executes the **[bash script](https://en.wikipedia.org/wiki/Bash_(Unix_shell)**.  **[sbatch](https://slurm.schedmd.com/sbatch.html)** command submits the job to the job queue and executes the **[bash script](https://en.wikipedia.org/wiki/Bash_(Unix_shell)**. 
 +
 +Here is an another example on how to analyze variants.
 +
 +```
 +#!/bin/bash
 +#SBATCH --ntasks 1          # Number of task
 +#SBATCH --time 00:30:00     # Runtime 30min
 +#SBATCH --mem 2000          # Reserve 2 GB RAM for the job
 +#SBATCH --partition serial  # Partition to submit
 +
 +module load bcftools # load modules
 +
 +# filter variants and calculate stats
 +bcftools filter --include'%QUAL>20' calls.vcf.gz | bcftools stats --output calls_filtered.stats 
 +```
 +
 +Submit the job to computing queue with the **[sbatch](https://slurm.schedmd.com/sbatch.html)** command.
 +
 +```
 +sbatch variants.sbatch
 +```
  
  
guides/slurm/basics.txt · Last modified: 27.11.2023 12:40 by Administrator

Page Tools