haotianteng / Chiron

A basecaller for Oxford Nanopore Technologies' sequencers
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Chiron file depreciated? #108

Closed KFeye closed 3 years ago

KFeye commented 3 years ago

Describe the bug Started training my dataset from ONT, had the following error:

To Reproduce python chiron/utils/raw.py --input ~/Desktop/YellowFast5Pass/ --output ~/Desktop/YellowBaseCalled/ --mode dna WARNING:tensorflow:From chiron/utils/raw.py:53: The name tf.gfile.Walk is deprecated. Please use tf.io.gfile.walk instead.

Traceback (most recent call last): File "chiron/utils/raw.py", line 169, in run(args) File "chiron/utils/raw.py", line 148, in run run_list(dirs,output_folder) File "chiron/utils/raw.py", line 111, in run_list extract(root_folder,output_folder) File "chiron/utils/raw.py", line 70, in extract total = total_errors) TypeError: update() got an unexpected keyword argument 'title' (base) Drs-iMac:Chiron dr.kristinafeyewaseen$

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haotianteng commented 3 years ago

Need to install older version of Tensorflow:

pip install tensorflow==1.15