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?

[sarahjeeeze]

Closing through lack of response, please feel free to re-open if you are still having trouble getting it to work