parallel processing - Variant Calling Pipeline Parallelization: ERROR - "sbatch: not found Error submitting jobscript (exit code 127)"

Question

I developed a pipeline written in Snakemake for genome variant calling analysis. I'm trying to parallelize it now, in order to be ran in a HPC cluster with multiple nodes.

I have a configuration file (yaml) where the paths of the files are defined.

When I execute the pipeline with the command:

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

I'm getting this ERROR:

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 -> /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.

Any one could help me ?

question from:https://stackoverflow.com/questions/65921644/variant-calling-pipeline-parallelization-error-sbatch-not-found-error-submi

Answer 1

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