How to perform bowtie2 analysis with slurm? I am trying to run my alignment script that works locally, using SBATCH.
Official manual for bowtie2 says I can use samtools for that. However when I run the following script I have an error
line 22: bowtie2: command not found

Below is the script:
#!/bin/bash

#SBATCH --time=05:00:00
#SBATCH --account=def-myaccount
#SBATCH --mem=200000M
#SBATCH --mail-user=mymail@gmail.com
#SBATCH --mail-type=All


module load nixpkgs/16.09  intel/2018.3
module load samtools/1.9



for FILE in *R1_001.fastq.gz;

do
        BASENAME=${file%%_R1_001.fastq.gz*}

        NUM=`echo $FILE | sed 's/_S.*$//'`

        bowtie2 -x cov_nastya -U $FILE -S ${NUM}exit.sam

done
It seems you do not have bowtie installed or loaded. Use module load bowtie2 together when you load samtools.