Partition error on SLURM only with fetchngs -
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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
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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