Comments (1)
ksahlin
commented on August 19, 2024
Hi @pre-mRNA,
No solution that would yield identical results. Reducing the number of cores seems like the best option.
Another alternative is to use the parameter --use_NAM_seeds (based on strobemer seeds), which has a fixed peak memory roughly equivalent to using uLTRA with 18 cores (at least on human genome) - and this option is also faster. Then you should be able to specify --t 48.
However, this parameter does not guarantee identical alignments. I observed that uLTRA's alignments with --use_NAM_seeds were a tiny bit worse than default on the datasets I tried with. The --use_NAM_seeds uses StrobeMap instead of slaMEM to find matches. StrobeMap is automatically installed if you installed uLTRA through conda. For details about --use_NAM_seeds, see section "New since v0.0.4" in the readme.
from ultra.
Related Issues (20)
- ultra installation and run error HOT 7
- CIGAR string starts/ends with N HOT 7
- Mapping with uLTRA without GTF? HOT 3
- Cigar is None HOT 2
- BUG -4294967296 HOT 8
- a bug of `--alignment_threshold` HOT 1
- Out of bound reads HOT 13
- Genomes FASTA/GTF files needed to run the evaluation HOT 4
- Can not access local variable 'read_mems_tmp' when using --use_NAM_seeds HOT 2
- Error: invalid feature coordinates (end<start!) at line: HOT 1
- Bug with uLTRA align : TypeError: bad argument type for built-in operation HOT 3
- UnboundLocalError: local variable 'i' referenced before assignment HOT 4
- Can I use ultra to align est to references HOT 1
- Failed in building index HOT 1
- KeyError when running test pipeline HOT 3
- How to control minimap 2 parameters during uLTRA alignment HOT 6
- uLTRA + SQANTI3 HOT 2
- Non-absolute paths don't resolve HOT 5
- Python bindings? HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from ultra.