locale setting failed with latest docker image.

[yangyxt]

Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.4/docs/FAQ.md:

Describe the issue:
According to the running log: the setlocale failed when trying to change LC_ALL to 'en_US.UTF-8'

Setup

• Operating system: CentOS7
• DeepVariant version: 1.4.0
• Installation method (Docker, built from source, etc.): docker pull
• Type of data: (sequencing instrument, reference genome, anything special that is unlike the case studies?) DNA seq

Steps to reproduce:

• Command:

• singularity run
  -B "/paedyl01/disk1/yangyxt,/usr/lib/locale"
  --env LANG="en_US.UTF-8"
  --env LC_ALL="C"
  --env LANGUAGE="en_US.UTF-8"
  --env LC_CTYPE="UTF-8"
  ......

• Error trace: (if applicable)
  

Does the quick start test work on your system?
Please test with https://github.com/google/deepvariant/blob/r0.10/docs/deepvariant-quick-start.md.
Is there any way to reproduce the issue by using the quick start?

Any additional context:

[pichuan]

Hi @yangyxt ,
can you try a command like:
https://github.com/google/deepvariant/blob/r1.4/docs/deepvariant-quick-start.md#notes-on-singularity ?

[yangyxt]

Hi @yangyxt , can you try a command like: https://github.com/google/deepvariant/blob/r1.4/docs/deepvariant-quick-start.md#notes-on-singularity ?

Thanks for the response. I tried a command without --env argument in the very beginning and the warning logs were still what is in the screenshot above. Then I started to alter the env variable with --env argument and still got the same warning messages.

[pichuan]

If i recall correctly, there might be warnings but it didn't seem to affect the run.
Can you confirm whether you're actually getting unexpected results or not? Thank you!

[yangyxt]

Yes. I didn't get unexpected results when only warning messages are shown. I just wonder whether the warning message would affect the results in some hidden way that I'm not aware of. So I tried to remove the warning message and ended up finding out it's somehow due to the lack of a dependency, locale, in the docker image.

[pichuan]

Thanks @yangyxt . Good to know that you're not seeing strange behaviors despite the warning messages. I'll close this issue now.