Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-02-10T22:56:20.003Z
Answers.Text: Thank you, it worked. Just a general inquiry at the end.. Is ```samtools``` really necessary here? Thanks.
Answers.UserDisplayName: Dmitrii Trubetskoy
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-02-11T01:18:06.613Z
Answers.Text: From your script samtools does not seem to be necessary.
Answers.UserDisplayName: Phoenix Mu
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-02-10T21:35:10.410Z
Answers.LastActivityDate: 2021-02-10T21:35:10.410Z
Answers.UserDisplayName: Phoenix Mu
Body: <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>
  
Tags: <samtools><bowtie2><slurm>
Title: How to perform bowtie2 analysis with slurm?
ThreadText: # How to perform bowtie2 analysis with slurm?
  
  (Asked by: username_0 on 2021-02-10)
  
  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
  
  ```
  
  **Tags:** samtools, bowtie2, slurm
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-02-10. Score: 3 | Accepted answer
  
  It seems you do not have bowtie installed or loaded. Use `module load bowtie2` together when you load `samtools`.
  
  > **Comments:**
  > **username_0**: Thank you, it worked. Just a general inquiry at the end.. Is ```samtools``` really necessary here? Thanks.  
  > **username_1**: From your script samtools does not seem to be necessary.  
  
  ---
  
  