text: user6948: I am trying to run the following script on slurm to extract information from .sam files. While everything is perfect on my local machine with the samtools version 1.11, it does not work on slurm. I have this error:
  samtools: command not found
  
  That means slurm cannot understand the module if I am not mistaken. What would be a solution here?
  #!/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/1.11 # this is what I tried first
  module spider samtools/1.11 # this does not help either...
  
  
  for FILE in *.sam;
  
  do
  
  
          NUM=`echo $FILE | sed -r 's/.sam//' | sed -r 's/nastya//'`
  
  #         echo "$FILE" ;
  
  
          samtools flagstat -O tsv $FILE > file${NUM}.txt
  
  done
  
  
  user7153: I would start with:
  module avail
  
  Then look to see (a) if there is a samtools module avilable and (b) exactly what it's called.
  If it's called samtools/1.11 then:
  module load samtools/1.11
  
  Should work, if it doesn't speak to your sys admin.
  
original_text: 6948: <p>I am trying to run the following script on slurm to extract information from .sam files. While everything is perfect on my local machine with the samtools version 1.11, it does not work on slurm. I have this error:</p>
  <pre><code>samtools: command not found
  </code></pre>
  <p>That means slurm cannot understand the module if I am not mistaken. What would be a solution here?</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/1.11 # this is what I tried first
  module spider samtools/1.11 # this does not help either...
  
  
  for FILE in *.sam;
  
  do
  
  
          NUM=`echo $FILE | sed -r 's/.sam//' | sed -r 's/nastya//'`
  
  #         echo &quot;$FILE&quot; ;
  
  
          samtools flagstat -O tsv <span class="math-container">$FILE &gt; file$</span>{NUM}.txt
  
  done
  </code></pre>
   7153: <p>I would start with:</p>
  <pre><code>module avail
  </code></pre>
  <p>Then look to see (a) if there is a samtools module avilable and (b) exactly what it's called.</p>
  <p>If it's called samtools/1.11 then:</p>
  <pre><code>module load samtools/1.11
  </code></pre>
  <p>Should work, if it doesn't speak to your sys admin.</p>
  