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No function of Docker container for DeepVariant

Hi,

I tried to install the docker container for DeepVariant as it is described in the documentation. But when I execute the commands in the container nothing happens. It does not even print an error message. dmesg gives me the following line after the execution of ./opt/deepvariant/bin/make_examples: traps: python[44779] trap invalid opcode ip:7f87f0fe6891 sp:7ffcc9fbf3d0 error:0 in libtensorflow_framework.so[7f87f0bff000+c00000] Sadly, I could not find any helpful information on the internet regarding this output.

Could anyone help me to make the software run?

Thanks,

Tobi

deepvariant
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updated by alaincoletta alaincoletta • written by Tobi • Tobi

Hi Tobi,

Could you please let us know what OS and environment you are using for running the docker image?

Thanks, Asha

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written by arostami • arostami

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

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written by GenoMax GenoMax

Hi Asha,

I'm using an Ubuntu 16.04 to run the docker image. The computer has 24 cores and 48 GB of RAM so this should be enough I guess. I am not using a GPU.

Does this help you or do you need more information?

Best, Tobi

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written by Tobi • Tobi

Thanks for providing the info, Tobi. This is very strange and it should work with Ubuntu 16. I haven't seen this error before, but it looks like there may be a hardware configuration issue.

  • Could you please confirm that you can run the regular binaries (outside of docker) following the quick start instructions? https://github.com/google/deepvariant/blob/r0.4/docs/deepvariant-quick-start.md
  • Could you please retry with IMAGE_VERSION=0.4.1 (just released)?
  • Lastly, can you try running a simple python program (shown below) inside the docker image? I want to ensure that tensorflow can properly run in your environment.

Sample test code:

import tensorflow as tf
def main(argv=()):
  print 'ok'
if __name__ == '__main__':
  tf.app.run()
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written by arostami • arostami

I tested a few things but sadly I got no positive results:

  • the regular binaries do not run correctly outside of docker. When I run them nothing happens and using dmesg I get a similar error to the one I get inside of docker.
  • Using the new image version changes nothing. Neither when using docker nor when not using it.
  • While your test code runs on the machine without docker, inside of the docker container the import line gives me Illegal instruction (core dumped)...

Now I do not have any Idea what I could change to make DeepVariant run. I will also have a look at this issue, I think it is related to my case.

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written by Tobi • Tobi

Sadly, the linked issue did not help me. Therefore I need further help. For now I will try it on another machine.

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written by Tobi • Tobi

1 answer

Hi Tobi, we implemented the DeepVariant pipeline with Docker and Nextflow here https://lifebit.page.link/gnbR . You can try it with example parameters.

Would love your feedback on this.

Thanks!

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written by alaincoletta alaincoletta

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