How to set the parameters for the slurm_singularity profile??

[zhenwenliu]

Hi, The following is my script sbatch to slurm platform, but I met some errors.

!/bin/bash

SBATCH -o hybpiper_cam.log

SBATCH -p scpu-p1

SBATCH -J hybpiper_cam

SBATCH --nodes=1

SBATCH --ntasks-per-node=28

ulimit -l unlimited ulimit -s unlimited nextflow run ~/biosoft/hybpiper-nf/hybpiper.nf -c ~/biosoft/hybpiper-nf/hybpiper.config -entry assemble -profile slurm_singularity --illumina_reads_directory ~/Ori_seq --targetfile_dna targetfile_fixed.fasta --cov_cutoff 4

Waiting for your useful suggestions. Thanks a lot ZW Liu

[chrisjackson-pellicle]

Hi @zhenwenliu,

As noted in the output you posted, Nextflow failed to submit the batch job because of an invalid account. I see you're using the profile slurm_singularity - have you updated that profile with the correct account name and other resource requests for your HPC as broadly described here? You can add options specific to your cluster using the Nextflow directive clusterOptions - see the profile gadi in the hybpiper.config file for an example.

Cheers,

Chris