FastQC uses only 10 cores in a 32 core server
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- Dominant language
- Nextflow
- Stars
- 230
- Forks
- 142
- Avg merge
- 13h 41m
- Merged PRs (30d)
- 1
Description
Description of feature
Despite specifying 32 cores through Slurm and Nextflow config, FastQC uses only 10 threads/cores, that is 1 thread per FASTQ file, even though there are more than 10 FASTQ files and 10 cores that can be utilized in parallel.
This behavior has been noticed with other tasks as well.
It will be very helpful if FastQC and other tools can use M threads = M FASTQ or intermediate files, where, M < N cores.
Max job request options
max_cpus : 32
max_memory : 240.GB
System information
Version of nf-core/atacseq: 2.1.2
Nextflow version: v24.10.3
Container enginer: Singularity
Executor: Slurm
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 by tracing the FastQC task and its CPU settings in nf-core/atacseq 2.1.2, then compare the Slurm and Nextflow configuration with the observed 10-thread limit. Done should demonstrate that FastQC can use the requested available parallelism and clarify whether the same behavior affects other tasks.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100