Comments (7)
Hi @motroy,
Thank you very much! I think it should be straight-forward to add porechop (via --trim
). I honestly haven't added it because I use Dragonflye with Bactopia (https://github.com/bactopia/bactopia/) and Bactopia runs porechop in a previous step. More importantly, if you have nanopore tool recommendations, please pass them my way.
For using GPUs with medaka, I think so, but I currently don't have access to GPUs for testing. Is it as simple as specifying --device
(https://github.com/nanoporetech/medaka/blob/master/medaka/medaka.py#L410)?
Cheers,
Robert
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@motroy for medaka and gpus can you confirm just --device
is needed?
from dragonflye.
Also nevermind on the GPU, looking at the readme looks like tensorflow-gpu
would be needed instead of tensorflow
Would you be wiling to test for me?
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Hi @rpetit3,
sorry for the very belated response.
re: porechop, we use the defaults (though there are some parameters that look to be potentially useful), however for demultiplexing there are recommendations in the repo (https://github.com/rrwick/Porechop#barcode-demultiplexing) for stringent or lenient binning that may be useful.
re: medaka, we have yet to use it on GPU :) but we can help with testing
from dragonflye.
No worries!
I released v1.0.8 yesterday which added porechop via --trim
, there is also --trimopts
to feed additional parameters to Porechop. Not sure if you'll be able to use it for demultiplexing though.
I also updated the Bioconda recipe to include tensorflow-gpu
, which I think "should" allow you to use your GPU for the medaka steps.
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Hi @rpetit3,
- I have successfully completed a run with the latest release (v1.0.8) using both --trim and --trimopts.
- I have also successfully completed a run with the latest release (v1.0.8) using medaka with a GPU (GeForce RTX 2080; CUDA Version: 11.0; NVIDIA-SMI 450.66).
Of note, we ran dragonflye
in a singularity
container (built from biocontainers/dragonflye:1.0.8--hdfd78af_0) and initially ran into an error with tensorflow
:
tensorflow/stream_executor/cuda/cuda_driver.cc:313] failed call to cuInit: UNKNOWN ERROR (303)
The error was resolved by setting CUDA_VISIBLE_DEVICES=0
and using the --nv
flag in singularity
(from this issue). Running with docker
may require setting the docker
parameter --runtime=nvidia
(as mentioned in the referred issue).
thanks for your help and very useful tool,
great work,
regards,
Yair
from dragonflye.
That's awesome! Glad you were able to get it working with the GPU!
I'm going to add a note to the README and point it to this comment.
I'm going to go ahead and close this, please feel free to reopn
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