ITADN

Partition error on SLURM only with fetchngs -

#343OpenDollyCM 创建于 2025-04-09
bug
D
DollyCMcommented
### 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 ```console 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
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