Comments (5)
iiSeymour
commented on June 23, 2024
1
Guppy sounds like the best option at this time, all downloads are here.
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iiSeymour
commented on June 23, 2024
Hey @dcopetti
It looks like you are using Anaconda which is not something I use myself. This StackOverflow link has a few suggestions and I suspect it's a conflict between using mix of conda and pip. What do you get if you run the following two commands?
$ conda list | grep pandas
$ python3 -m pip list | grep pandas
The pandas dependency comes from optuna which is used only for bonito tune and is not a requirement for basecalling so a quick workaround would be to remove the import of tune from bonito/__init__.py.
Yes, you will need to unpack the reads from the .tar before you can basecall.
HTH,
Chris.
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dcopetti
commented on June 23, 2024
Hi Chris,
Thank you for the feedback.
The two commands result in:
(py36) bash-4.2$ python --version
Python 3.6.9 :: Anaconda, Inc.
(py36) bash-4.2$ conda list | grep pandas
pandas 1.0.3 py36h0573a6f_0
(py36) bash-4.2$ python3 -m pip list | grep pandas
pandas 1.0.3
I tried removing the import of tune:
try:
from bonito import train
modules.extend(['train'])
except ImportError:
pass
and for now it works:
(py36) bash-4.2$ bonito basecaller
usage: bonito basecaller [-h] [--device DEVICE] [--weights WEIGHTS]
[--beamsize BEAMSIZE] [--half]
model_directory reads_directory
bonito basecaller: error: the following arguments are required: model_directory, reads_directory
however, when I run it I get this error:
(py36) bash-4.2$ bonito basecaller dna_r9.4.1 reads2/
> loading model
Traceback (most recent call last):
File "/home/copettid/anaconda3/envs/py36/bin/bonito", line 8, in <module>
sys.exit(main())
File "/home/copettid/anaconda3/envs/py36/lib/python3.6/site-packages/bonito/__init__.py", line 39, in main
args.func(args)
File "/home/copettid/anaconda3/envs/py36/lib/python3.6/site-packages/bonito/basecaller.py", line 19, in main
model = load_model(args.model_directory, args.device, weights=int(args.weights), half=args.half)
File "/home/copettid/anaconda3/envs/py36/lib/python3.6/site-packages/bonito/util.py", line 186, in load_model
model.to(device)
File "/home/copettid/anaconda3/envs/py36/lib/python3.6/site-packages/torch/nn/modules/module.py", line 425, in to
return self._apply(convert)
File "/home/copettid/anaconda3/envs/py36/lib/python3.6/site-packages/torch/nn/modules/module.py", line 201, in _apply
module._apply(fn)
File "/home/copettid/anaconda3/envs/py36/lib/python3.6/site-packages/torch/nn/modules/module.py", line 201, in _apply
module._apply(fn)
File "/home/copettid/anaconda3/envs/py36/lib/python3.6/site-packages/torch/nn/modules/module.py", line 201, in _apply
module._apply(fn)
[Previous line repeated 3 more times]
File "/home/copettid/anaconda3/envs/py36/lib/python3.6/site-packages/torch/nn/modules/module.py", line 223, in _apply
param_applied = fn(param)
File "/home/copettid/anaconda3/envs/py36/lib/python3.6/site-packages/torch/nn/modules/module.py", line 423, in convert
return t.to(device, dtype if t.is_floating_point() else None, non_blocking)
File "/home/copettid/anaconda3/envs/py36/lib/python3.6/site-packages/torch/cuda/__init__.py", line 196, in _lazy_init
_check_driver()
File "/home/copettid/anaconda3/envs/py36/lib/python3.6/site-packages/torch/cuda/__init__.py", line 101, in _check_driver
http://www.nvidia.com/Download/index.aspx""")
AssertionError:
Found no NVIDIA driver on your system. Please check that you
have an NVIDIA GPU and installed a driver from
http://www.nvidia.com/Download/index.aspx
do I need to have GPUs to run bonito?
From running lshw -short I get this:
system Computer
/0 bus Motherboard
/0/0 memory 976GiB System memory
/0/1 processor Intel(R) Xeon(R) Platinum 8168 CPU @ 2.70GHz
I have 48 CPUs in this virtual machine
Thanks,
Dario
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iiSeymour
commented on June 23, 2024
Bonito can run on the CPU with --device cpu however it's more for validation and I wouldn't recommend calling a large batch of reads on the CPU as PyTorch will only use a single core. Even heavily optimized CPU runtimes that use all cores are significantly slower than a single GPU so my recommendation would be to run on GPU if you can. Also, see #10.
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dcopetti
commented on June 23, 2024
thanks.
At this point I would switch to another basecaller that I can run on my own with CPUs:
is Guppy the best out there now? If so, where can I download it? I don't find it in Github or in the ONT community pages
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Related Issues (20)
- Model versions HOT 1
- how to cite bonito in my paper? HOT 2
- Optimise training batch_size HOT 2
- Running the example from the README.md doesn't work
- Update for remora 3.0.0 trained model?
- how bonito normalize raw signals when save-ctc HOT 1
- how to calibrate CTC-CRF model base qualities? HOT 1
- Short basecalled R9.4.1 reads using both trained and default models in bonito, but not in guppy
- Bonito Train missing dataset.py HOT 5
- RNA002 model
- RNA004 Does not output any CTC data HOT 3
- bonito basecaller max_reads HOT 1
- Bonito export for dorado error HOT 6
- Feature request: export the list of reads used to train a model
- bonito WASM
- Training data for R10.4, 4 and 5kHz? HOT 3
- Chunks.npy and Dataset.py not being generated HOT 2
- how to best fine tune a model with different references HOT 12
- Applying INT8 quantization, just like in Dorado HOT 2
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