Segmentation fault while using SLURM executor

[melian98]

I am using Nextflow to run sortmerna on some DNA sequence files using the slurm executor. My config file is as follows:

process {

executor = "slurm"
memory = "128GB"
time = "2h"
cpus = 4
clusterOptions = '--account=cluster_account --output=fastqc.out'

}


params {

reads = "$baseDir/raw_files/temp/*_R{1,2}.fastq.gz"
outdir = "$baseDir"

}

my nf file is as follows:

#!/usr/bin/env nextflow
process sortmerna {

        publishDir "$params.outdir/output/sortmerna"

        input:
        tuple val(sample_id), path(reads)

        output:
        file("*.gz")

        """
        sortmerna \
        --workdir $baseDir/sortmerna \
        --ref /home/tools/sortmerna/smr_v4.3_default_db.fasta \
        --reads $baseDir/raw_files/temp/${reads[0]} \
        --reads $baseDir/raw_files/temp/${reads[1]}
        """

}

workflow {

        reads_ch = Channel.fromFilePairs(params.reads, checkIfExists: true)

        sortmerna(reads_ch)
}

After running this. I receive the following error:

Command error:
  .command.sh: line 2:   535 Segmentation fault      (core dumped)

I have run the exact same command with sortmerna in SLURM without nextflow and the output was fine. This error only occurs when I try to run it using nextflow. I'm not sure how to approach this issue as the error message is quite vague. If there is any additional information that can help with diagnosing this, please let me know and I'd be happy to add it