deepvariant cannot import name locked_file

Question

[372910137]

when i tried to install the DeepVariant (./build-prereq.sh) cannot import name locked_file

[GenoMax]

You should directly follow up with google cloud genomics support. While Dr. DePristo seems to have joined Biostars I don't think he is going to provide regular support for deepvariant here.

[alaincoletta]

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

There is also a post with benchmarks across various AWS instances here: https://blog.lifebit.ai/post/deepvariant/.

[GenoMax]

Tagging: arostami

[alaincoletta]

Hi Mark, we implemented the DeepVariant pipeline with Docker and Nextflow here

Lifebit integrate it the pipeline with example parameters

Would love your feedback on this.

Thanks!

Answer 1

[mdepristo]

First, it's better if you tag these posts with deepvariant so we get pinged by biostars that people are asking about DeepVariant. Second, I'd recommend you post this as an issue on github repo: https://github.com/google/deepvariant/issues with a bunch more details so we can reproduce and fix.

[dariober]

Just thought to let you know... Saddly, the "watched tag" feature of biostars is there but it doesn't work (see Biostars meta: Does "Watched tags" work? ). (If it works for you let me know, please!)