Comments (5)
This was fixed in the Bioconda recipe. New installs won't have this issue anymore.
from genomad.
Hi @flefler
This is very strange. Keras and Tensorflow are dependencies that should have been installed. Can you run these commands within the environment and send me the outputs?
python -c "import tensorflow as tf; print(tf.__version__)"
I think the problem here is that newer TensorFlow versions probably changed the way Keras is imported. If that's the case, you'll be able to fix the issue by installing an older version of TensorFlow (and I'll update geNomad accordingly).
from genomad.
Below is the output of the command
(genomad) [flefler@login12]$ python -c "import tensorflow as tf; print(tf.__version__)"
2024-05-25 01:23:06.695325: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: SSE4.1 SSE4.2 AVX AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2.16.1
Here are the versions of keras, tensonflow, and tensorboard in the conda environment. Not sure if this is useful, can provide full output of conda list
if helpful
# Name Version Build Channel
keras 3.3.3 pyhd8ed1ab_0 conda-forge
tensorboard 2.16.2 pyhd8ed1ab_0 conda-forge
tensorboard-data-server 0.7.0 py310h75e40e8_1 conda-forge
tensorflow 2.16.1 cpu_py310h49b650b_0 conda-forge
tensorflow-base 2.16.1 cpu_py310h224022f_0 conda-forge
tensorflow-estimator 2.16.1 cpu_py310hc6dcfef_0 conda-forge
from genomad.
Ok, so the problem is that geNomad is not compatible with keras >= 3
and tensorflow >= 2.16
. Can you downgrade to keras < 3
and tensorflow < 2.15
? I'll fix this in Bioconda so that future installs won't have this issue.
from genomad.
Great. Thank you for your help!
from genomad.
Related Issues (20)
- mmseqs2 error HOT 3
- Different protein number from genomad and pyrodigal-gv HOT 2
- Small (reference) data for testing HOT 9
- Error while classifying sequences HOT 6
- Error mmseqs prefilter HOT 4
- genomad annotate fastq file is empty or contains multiple entries HOT 3
- plasmid classified as virus? HOT 7
- Optimization Request for Analyzing Large Number of MAGs with geNomad HOT 5
- Fewer viral contigs identified from genomad vs virsorter2 HOT 4
- The question about --disable-nn-classification HOT 1
- Provirus detection in genomad vs checkv HOT 6
- Error mmseqs prefilter HOT 2
- Genetic codes HOT 2
- question about integrase identification during provirus identification HOT 3
- How to export the viral DNA gene sequence? HOT 5
- Number of contigs in the assembly HOT 1
- Chromosome classification result HOT 2
- Discrepancy in Output Counts in Genomad HOT 1
- line 19 in aggregated_classfication.py HOT 2
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 genomad.