final MultiQC taking a lot of memory yet not finished
Nobody has claimed this yet.
- Dominant language
- Nextflow
- Stars
- 14
- Forks
- 9
- PR merge metrics
- No merged PRs in 30d
Description
Description of the bug
The final MultiQC step after running 3 analysis (AE/AS/MAE) either fails at low memory (48GB; 64GB with export_plots true) or runs for 18 hours ++ and is not able to finish (128GB - 400GB; after 18 hours, the memory used was 280GB and still climbing with export_plots false).
Command used and terminal output
Relevant files
No response
System information
Nextflow v25, on Cambridge HPC, nf-core/drop 1.0.0
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 reproducing the final MultiQC step for the AE/AS/MAE analyses on Cambridge HPC, comparing the reported memory limits with export_plots enabled and disabled. Inspect the pipeline's final MultiQC entry point and collect command output and resource usage; done means identifying why memory keeps growing and confirming a fix or documented resource requirement.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, performance
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Active
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100