text: user6948: 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
  
  
  user4766: It seems you do not have bowtie installed or loaded. Use module load bowtie2 together when you load samtools.
  
original_text: 6948: <p>I am trying to run my alignment script that works locally, using <code>SBATCH</code>.</p>
  <p>Official manual for <code>bowtie2</code> says I can use <code>samtools</code> for that. However when I run the following script I have an error</p>
  <pre><code>line 22: bowtie2: command not found
  </code></pre>
  <p>Below is the script:</p>
  <pre><code>#!/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 <span class="math-container">$FILE -S $</span>{NUM}exit.sam
  
  done
  </code></pre>
   4766: <p>It seems you do not have bowtie installed or loaded. Use <code>module load bowtie2</code> together when you load <code>samtools</code>.</p>
  