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:


#SBATCH --time=05:00:00
#SBATCH --account=def-myaccount
#SBATCH --mem=200000M
#SBATCH [email protected]
#SBATCH --mail-type=All

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

for FILE in *R1_001.fastq.gz;


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

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


1 Answer 1


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

  • $\begingroup$ Thank you, it worked. Just a general inquiry at the end.. Is samtools really necessary here? Thanks. $\endgroup$ Commented Feb 10, 2021 at 22:56
  • $\begingroup$ From your script samtools does not seem to be necessary. $\endgroup$
    – Phoenix Mu
    Commented Feb 11, 2021 at 1:18

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