Comments (5)
iiSeymour
commented on September 25, 2024
Hey @studyfranco
The OpenVino branch is still a work in process and I would expect a few issues until it's merged. The issue you are seeing is related to preparing the training data only so if you just want to try basecalling with the OpenVino backend you can ignore this error for now.
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studyfranco
commented on September 25, 2024
Hey @iiSeymour
Thank you for the rapid reply. I do what you suggest, and I try to create my basecall.
bonito basecaller dna_r9.4.1 --save-ctc --use_openvino --reference possibleSeq.mmi /mnt/Data/Team_projects/fast5_pass > basecalls.sam
But I obtain this error:
> loading model
Traceback (most recent call last):
File "/home/sysfate/.conda/envs/bonito/bin/bonito", line 33, in <module>
sys.exit(load_entry_point('ont-bonito', 'console_scripts', 'bonito')())
File "/home/sysfate/.conda/envs/bonito/bonito/bonito/__init__.py", line 39, in main
args.func(args)
File "/home/sysfate/.conda/envs/bonito/bonito/bonito/basecaller.py", line 30, in main
use_openvino=args.use_openvino,
File "/home/sysfate/.conda/envs/bonito/bonito/bonito/util.py", line 332, in load_model
model = Model(toml.load(config))
File "/home/sysfate/.conda/envs/bonito/bonito/bonito/model.py", line 81, in __init__
self.stride = config['block'][0]['stride'][0]
KeyError: 'block'
I am a little bit lost now, what do you suggest ?
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iiSeymour
commented on September 25, 2024
Ah that's my fault, I've pushed a new pre-trained model in preparation for v0.3.0 next week that has a different config.
Can you delete the dna_r9.4.1 directory in bonito/models and swap the model URL here to "nas0uhf46fd1lh2jndhx2a54a9vvhxp4.zip" then run bonito download --models again.
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studyfranco
commented on September 25, 2024
I followed your instructions. With my next try I obtain this error:
> loading model
Traceback (most recent call last):
File "/home/sysfate/.conda/envs/bonito/bin/bonito", line 33, in <module>
sys.exit(load_entry_point('ont-bonito', 'console_scripts', 'bonito')())
File "/home/sysfate/.conda/envs/bonito/bonito/bonito/__init__.py", line 39, in main
args.func(args)
File "/home/sysfate/.conda/envs/bonito/bonito/bonito/basecaller.py", line 30, in main
use_openvino=args.use_openvino,
File "/home/sysfate/.conda/envs/bonito/bonito/bonito/util.py", line 346, in load_model
model = OpenVINOModel(model, half, dirname)
File "/home/sysfate/.conda/envs/bonito/bonito/bonito/openvino/model.py", line 19, in __init__
model_name = model.config['model'] + ('_fp16' if half else '')
TypeError: unsupported operand type(s) for +: 'dict' and 'str'
inside model.config['model'] you have {'package': 'bonito.ctc'}
What are your suggestion ?
Thank you lot of for your help !
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dkurt
commented on September 25, 2024
Hi!
openvino-python 2021.1 requires numpy==1.16.3, but you'll have numpy 1.19.2 which is incompatible.
Please try an updated version of the branch. I modified requirements.txt so it installs numpy==1.16.3.
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