owlcollab / owlcollab/owltools
map2slim memory requirements
Nobody has claimed this yet.
- Dominant language
- Java
- Stars
- 115
- Forks
- 34
- PR merge metrics
- No merged PRs in 30d
Description
Hi,
I'm trying to use the --map2slim functionality to map a gaf-file to metagenomics slim. It' s 90+ GB in size. The process owltools starts swapping and dies at 0,5 TB (Yes, Terabyte) memory usage. Any way around this (except splitting my file into X pieces after prototyping size vs. memory usage)?
Contributor guide
No contributing guide indexed for this repository
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 OWLTools --map2slim run with a representative GAF file and record memory use as the input grows. Trace the map2slim entry point to determine whether the 90+ GB input can be processed without exhausting memory; done means a verified implementation change or a documented supported limitation and workaround.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java
- Domain
- bioinformatics, tooling
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100