ERROR ~ Error executing process > 'pipeline:preprocess_ref_annotation'

[amir-tagh]

Ask away!

Hello,

I am trying to get the demo model to work using the following script on HPC and I get a couple of error Plus 4 more processes waiting for tasks… Doing reference based transcript analysis ERROR ~ Error executing process > 'pipeline:preprocess_ref_annotation'

can you please let me know how to solve this.

Thanks, Amir

Script:

!/bin/bash

SBATCH --job-name=MINI

SBATCH -n 5

SBATCH --partition=gpu

SBATCH --nodes=1

SBATCH --ntasks=1

SBATCH --cpus-per-task=20

SBATCH --gres=gpu:1

SBATCH --output=RNA-error.out

SBATCH --mail-type=ALL

SBATCH --time=3-00:00:00

SBATCH --mem=100G

ml nextflow/24.04.2 singularity/3.10.4

nextflow run epi2me-labs/wf-transcriptomes \ --de_analysis \ --direct_rna \ --fastq 'condition1_rep1.fastq.gz' \ --ref_annotation 'gencode.v22.annotation.chr20.gtf' \ --ref_genome 'hg38_chr20.fa' \ --sample_sheet 'sample_sheet.csv' \ -profile standard

[sarahjeeeze]

Is there any other info in the output/error message? Did it successfully complete any processes?

[amir-tagh]

RNA-error.txt

Hello, please see attached the error output. It does not look like any processes has been done. Thanks,

[sarahjeeeze]

Hey, have you installed docker in your environment? https://docs.docker.com/engine/install/ you can also use singularity if you prefer https://labs.epi2me.io/singularity/

[amir-tagh]

Hi I have installed both the dockr and the singularity. I will try with these. Thanks,

[sarahjeeeze]

Did you manage to get it to work?

[amir-tagh]

The HPC is down for a couple of days for maintenance I will give it a try when is running, thanks for the follow up.

[sarahjeeeze]

oh i realise this was a while ago now - did you get it to work in the end?