sc.pp.combat runtime/out of memory
Open
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 2.6k
- Forks
- 779
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 27
Description
I have a dataset with around 400K observations -- I wanted to perform batch correction using sc.pp.combat, but I'm getting out of memory errors after running for a couple hours with > 2 TB of memory.
My understanding was that combat used a dense matrix, which requires a lot of memory.
Why is this? Are there suggestions for workarounds here?
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 at the sc.pp.combat entry point and investigate its behavior on datasets around 400K observations, focusing on the reported out-of-memory condition despite more than 2 TB of memory. Reproduce or characterize the failure, then document a confirmed cause and practical workaround for large datasets.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, performance
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100