nf-core / nf-core/fetchngs

Partition error on SLURM only with fetchngs -

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bug
Dominant language
Nextflow
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202
Forks
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Avg merge
1d 18m
Merged PRs (30d)
15

Description

Description of the bug

Hi,
I am using the following script to download SRA data and it gives me a partition error despite indicating the partition explicitly. When I do bash .command.run, it gives no error. Can you kindly help fixing this problem?

Script used: submit_job.sh

#!/bin/bash
#SBATCH --ntasks=4
#SBATCH --partition=epyc2 <<<---- Valid Partition requested!
#SBATCH --time=4-00:00:00
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=32GB
#SBATCH --output=xiangData_download.out
#SBATCH --error=xiangData_download.err
#SBATCH --job-name=xiangData_download
#SBATCH --mail-type=END,FAIL

#Load required modules
module load Nextflow/24.04.4

#Setup directory structure. Make sure the path does not have '/' at the end.
OUTDIR="Xiang2023_PRJNA852547_SHAPEdata";

#Run pipeline
nextflow run nf-core/fetchngs
-resume
-profile unibe_ibu singularity
--input sra_list.csv
--download_method sratools
--outdir $OUTDIR

date

Error:

Caused by:
Failed to submit process to grid scheduler for execution

Command executed:

sbatch .command.run

Command exit status:
1

Command output:
sbatch: error: invalid partition specified: pibu_el8
sbatch: error: Batch job submission failed: Invalid partition name specified

Command used and terminal output
sbatch submit_job.sh
Relevant files

#sra_list.csv contains following input:

PRJNA852547

System information

N E X T F L O W ~ version 24.04.4
nf-core/fetchngs v1.12.0
Hardware: HPC
Executor: SLURM
Container: Singularity

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with submit_job.sh and compare its requested epyc2 partition with the generated .command.run that fails on pibu_el8. Read how the unibe_ibu profile is applied when running nf-core/fetchngs v1.12.0, using the reported sbatch error as the reproduction. Done means the fetchngs processes submit to the intended valid partition without the invalid pibu_el8 error.

Written by the indexing model from the issue text.

Assessment

Tech stack
shell
Domain
infrastructure
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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