High Memory consumption causes computer to freeze
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 302
- Forks
- 25
- PR merge metrics
- No merged PRs in 30d
Description
I'm trying to generate multiple transcriptomic datasets in parallel with different parameters (error model, coverage/depth, and sequence identity), however, Badread consumes a lot of memory while doing this and occasionally will cause my machine to freeze while running the simulation.
Is there a way to control the memory usage, or better optimize the process of simulating multiple datasets in parallel?
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
The issue names parallel transcriptomic dataset generation with varying error model, coverage/depth, and sequence identity, but it does not identify a file, test, or entry point. Start by reproducing the parallel simulation and measuring memory usage across those parameters. Done would require an agreed way to control or reduce memory use without freezing the machine.
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
- 25/100