Error with geNomad v1.8.0, missing tensorflow.keras about genomad

[apcamargo]

This was fixed in the Bioconda recipe. New installs won't have this issue anymore.

[apcamargo]

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).

[flefler]

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

[apcamargo]

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.

[flefler]

Great. Thank you for your help!