Comments (3)
Hi @youngDouble,
so the log output is hanging at "Epoch 77"? Since you are running with nohup, are you sure that the process is still running? It could have crashed, for example on unsufficient memory. Can you try running the training again?
I would also suggest running with less epochs, e.g. 100, since the accuracy seems quite high already on epoch 77. Also, if you want to try reserving part of training data for validation, you can set "validation_size" in your JSON file. For example, you can use "validation_size": 0.2 for validating your model on 20% of your data. Then, both training and validation metrics will be shown during training.
from deepbgc.
Also, please see the updated README section on training: https://github.com/Merck/deepbgc#train-deepbgc-on-your-own-data
You can upgrade DeepBGC to version 0.1.10 to be able to provide your trained model for detection and classification like so:
deepbgc pipeline \
mySequence.fa \
--detector path/to/myDetector.pkl \
--classifier path/to/myClassifier.pkl
from deepbgc.
Thank you for your reply, as you said, it is a problem with insufficient memory. After adjusting the parameters(validation_size
and num_epochs
), it can work.
It seems that the training process uses a lot of memory (more than 256G), I have delivered the task to the cluster.
from deepbgc.
Related Issues (20)
- Where I can get the code of e-deepBGC? HOT 1
- bug in get_proteins_by_id affecting pfam annotator HOT 4
- Visualization HOT 1
- run Deepbgc in fungal genomes HOT 1
- WARNING: Tensor flow backened message when running deepbgc info into the CLI HOT 1
- how to get a cluster?
- installation error HOT 1
- how to create negative samples? HOT 1
- fit_generator
- what "inhibitor" means???
- Could deepBGC be used for special gene clusters?
- Hmmer and Prodigal Package Access Problem HOT 1
- Bugs for protein input HOT 1
- running "deepbgc info" issue
- Use https instead of ftp protocol for Pfam database download HOT 1
- Looking for individual genes
- ImportError: Missing required dependencies ['numpy'] HOT 1
- User Warning
- deepbgc info crash - same as Issue #39
- ValueError: End location (8780) must be greater than or equal to start location (9428)
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 deepbgc.