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Published 20 hours ago • verified publisher icon google

locale setting failed with latest docker image.

Open yangyxt opened this issue 2 years ago • 4 comments

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) image

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:

yangyxt avatar Sep 19 '22 04:09 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 ?

pichuan avatar Sep 19 '22 17:09 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 ?

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.

yangyxt avatar Sep 21 '22 05:09 yangyxt

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!

pichuan avatar Sep 21 '22 05:09 pichuan

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.

yangyxt avatar Sep 21 '22 06:09 yangyxt

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

pichuan avatar Oct 20 '22 00:10 pichuan