title: Variant Calling Pipeline Parallelization: ERROR - "sbatch: not found Error submitting jobscript (exit code 127)"
body: <p>I developed a pipeline written in Snakemake for genome variant calling analysis.
  I'm trying to <a href="https://github.com/ray2g/vcall_biodata/blob/master/vcall-pipe2_cluster.snake" rel="nofollow noreferrer">parallelize it now</a>, in order to be ran in a HPC cluster with multiple nodes.</p>
  <p>I have a <a href="https://github.com/ray2g/vcall_biodata/blob/master/config_pipeline2_cluster.yaml" rel="nofollow noreferrer">configuration file</a> (yaml) where the paths of the files are defined.</p>
  <p>When I execute the pipeline with the command:</p>
  <pre><code>shifter --volume=/home/ubuntu/vcall_docker_gatk4_bottle/:/mnt/  \
  --image=docker:ray2g/vcall_biodata:1.5.1 \
  snakemake --snakefile /mnt/vcall-pipe3_cluster.snake \
  -p /mnt/genome/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta.sa \
  -j 24 \
  --cluster 'sbatch -p {params.partition} --mem {resources.mem_mb}mb --cpus-per-task {resources.cpus}' \
  --forceall
  </code></pre>
  <p>I'm getting this ERROR:</p>
  <pre><code>Building DAG of jobs...
  Using shell: /bin/bash
  Provided cluster nodes: 24
  Unlimited resources: cpus, mem_mb
  Job counts:
          count   jobs
          1       bwa_index
          1
  
  [Wed Jan 27 14:30:40 2021]
  Job 0: Building index -&gt; /mnt/genome/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta.sa
  
  bwa index /mnt/genome/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta
  /bin/sh: 1: sbatch: not found
  Error submitting jobscript (exit code 127):Shutting down, this might take some time.
  </code></pre>
  <p>Any one could help me ?</p>