Conda: dv_make_example.py execution error.

Hi,

I had trouble running Deepvariant using conda.

I ran the following command.

dv_make_examples.py --sample {MY_SAMPLE} --ref {MY_FASTA}.fasta --reads {MY_BAM}.bam --logdir ./log/ --examples examples/

and I got an error like this:

ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s sh: 1: unzip: not found
Traceback (most recent call last):
  File "/opt/conda/envs/deepvariant/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/opt/conda/envs/deepvariant/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/opt/conda/envs/deepvariant/share/deepvariant-0.10.0-3/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 252, in <module>
  File "/opt/conda/envs/deepvariant/share/deepvariant-0.10.0-3/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 187, in Main
  File "/opt/conda/envs/deepvariant/share/deepvariant-0.10.0-3/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 138, in GetRepositoriesImports
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/Bazel.runfiles_qwsw52c7/runfiles'
parallel: This job failed:
/opt/conda/envs/deepvariant/bin/python /opt/conda/envs/deepvariant/share/deepvariant-0.10.0-3/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref E.coli_K12_MG1655.fa --reads SRR1770413.bam --examples examples//[e-mail] --task 0

When I installed unzip by conda install, the command worked fine.

When using conda to install deepvariant, should it not have to be installed together?

Thanks,

[chapmanb]

Thanks for reporting back and sorry my guess wasn’t very helpful for resolving the problem. I’m a bit confused as to why it doesn’t get unzip as a requirement since it’s listed in the host dependencies in the conda recipe (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/deepvariant/meta.yaml#L28). On the next iteration of the recipe we could add it to the run requirements to try and avoid this. In the short term, does adding unzip to your conda package install for the environment when building the Docker container avoid the issue and get things running? If you have other missing dependencies please let us know and we could have a similar treatment to fix them. Hope this helps.

[yiolino]

@chapmanb Thank you for your reply. I have seen the conda recipi. It is indeed strange. Maybe there’s something wrong with my running environment. OK, I’ll deal with it by installing unzip directly in apt or conda. Thanks a lot!