Comments (5)
You can't use a full chip worth of Hifi reads as references. DeepConsensus is in the proof of concept stage, not meant for production yet. You can try this new tool, but there's no official support for it yet: https://github.com/PacificBiosciences/align-clr-to-ccs
from deepconsensus.
Hi @zhoudreames
As @armintoepfer indicates, DeepConsensus isn't yet scalable to run a full SMRT cell on an external machine. The v0.1 release still uses many systems that are efficient within Google's distributed systems, but are very inefficient when run on a single machine. We plan to improve this in future releases, but for now, it will be too slow for a full SMRT cell. If there is something you can use a targeted part of a sequence run, that might be better.
For the error you are encountering, I assume that this is in the pre-processing step? Thank you for pointing this out. This is one of the areas we will improve in the next release (potentially by using the tool that Armin linked). For now, to map the reads, you would need to use fewer reads for your input.
Thank you,
Andrew
from deepconsensus.
You can't use a full chip worth of Hifi reads as references. DeepConsensus is in the proof of concept stage, not meant for production yet. You can try this new tool, but there's no official support for it yet: https://github.com/PacificBiosciences/align-clr-to-ccs
thanks for your help
from deepconsensus.
Hi @zhoudreames
As @armintoepfer indicates, DeepConsensus isn't yet scalable to run a full SMRT cell on an external machine. The v0.1 release still uses many systems that are efficient within Google's distributed systems, but are very inefficient when run on a single machine. We plan to improve this in future releases, but for now, it will be too slow for a full SMRT cell. If there is something you can use a targeted part of a sequence run, that might be better.
For the error you are encountering, I assume that this is in the pre-processing step? Thank you for pointing this out. This is one of the areas we will improve in the next release (potentially by using the tool that Armin linked). For now, to map the reads, you would need to use fewer reads for your input.
Thank you,
Andrew
when will the next version releases ? How much do I need to split reads for the 500G menmory ? thanks~
from deepconsensus.
Hi @zhoudreames
I cannot give you an estimate for when the next version will be ready. With a fair amount of certainty, I will say likely more than 1 month from now and less than 6 months.
The changes in the next release will probably change the memory use, and I cannot now give you an estimate of memory at that time.
from deepconsensus.
Related Issues (20)
- no subreads available HOT 2
- Error: ModuleNotFoundError: No module named 'pandas._libs.interval' HOT 6
- Running deepconsensus results in "free(): invalid pointer" error HOT 15
- Missing majority of ZMWs after running lima to search for adapters HOT 4
- HPC resource managment not working with deepconsensus
- Use of samtools and awk to filter incorrect alignments. HOT 2
- Lower number of >Q30 average quality reads for v1.1 compared to v0.3 HOT 10
- Error detecting params.json using docker in debian (10) HPC HOT 2
- Installation from source file problem HOT 2
- lower quality and less reads in deepconsensus 1.0 output compared to ccs HOT 2
- python 3.9 HOT 2
- [Repeat] Running deepconsensus results in "free(): invalid pointer" error HOT 17
- QV for each ccs reads HOT 2
- Public raw train dataset availability HOT 2
- Cannot open/create ccs.bam file? HOT 6
- vRAM limit HOT 1
- the label without alignment HOT 5
- bam or fastq issue HOT 2
- Separate subreads for mixed samples? HOT 3
- GPU installation failure with pip HOT 3
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 deepconsensus.