DeepMicrobes

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UnicodeEncodeError: 'ascii' codec can't encode character '\ufeff' in position #

5

Hi DeepMicrobes developers and users, I'm excited to start using this tool on my dataset but I'm running into an error at the installation testing step. Here is the command...

Ahmed-Shibl

Running DeepMicrobes with TensorFlow 2.x

4

Hello, our GPU requires CUDA 11 and therefore I am stuck with using TensoFlow 2.x. I was trying to lift the code to TF2, but it seems I can't find...

Mashin6

Versioned release package for DeepMicrobes

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I'm working to make DeepMicrobes available on Bioconda. Please refer. -> https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository#creating-a-release I need your help creating a versioned release to use for the Bioconda recipe. Once DeepMicrobes is added...

jayramr

Trained weights not accesible

2

I was hoping to use your model on metagenomics data, but I did'nt want to train it from scratch but rather use the exact same model you generated in your...

ghost

How should I run this model in single-end mode?

8

stargazer-dot

AttributeError: module 'tensorflow' has no attribute 'logging'. Did you mean: '_logging'? - issue while creating tfrec

1

I am trying to convert my reference fasta to TFrec file for training, following instructions on: https://github.com/MicrobeLab/DeepMicrobes/blob/master/document/tfrecord.md It is able to shuffle the sequences, split but when the conversion starts...

Gayathri142

Model weights for training

2

Hi, Could you please elaborate a bit on the parameter '--model_dir', in the training part of the tool? Are there weights that come with the study, or do we have...

Gayathri142

Question about the size of the model

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Hi! May I know the size of the DeepMicrobes model (the best performing one)? Like how many trainable parameters are there? Thank you!

viccc17

Question about training a DeepMicrobes model to predict the taxonomy from phylum to species

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Hi! I have read the DeepMicrobes paper and it is great work! I'm planning to train the DeepMicrobes model using my data and I want it to predict the taxonomy...

Steven-GUHK

Error training a custom model

3

Hello, I am writing because I am trying to train a custom model for DeepMicrobes, and keep getting the same error whenever I try to train the model on the...

GiovanniFaldani