Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

There are bugs in version 1.6 #764

Closed
ColinR01 opened this issue Jan 19, 2024 · 4 comments
Closed

There are bugs in version 1.6 #764

ColinR01 opened this issue Jan 19, 2024 · 4 comments
Assignees

Comments

@ColinR01
Copy link

Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6/docs/FAQ.md:

Describe the issue:
When variant is not detected, the program will freeze in the last step;

Setup

  • Operating system:Centos7.6
  • DeepVariant version: 1.6
  • Installation method (Docker, built from source, etc.): singularity
  • Type of data: (sequencing instrument, reference genome, anything special that is unlike the case studies?) PACBIO-SMART;A reference sequence for a normal person;

Steps to reproduce:

  • Command: /bin/singularity run -B /work/:/work/ /work/deepvariant.sif /opt/deepvariant/bin/run_deepvariant --model_type=PACBIO --ref=human_geneA_reference.fa --reads=reference.align.bam --output_vcf=out.vcf --output_gvcf=out.gvcf --num_shards=32
  • Error trace: Last line: I0119 11:43:53.450599 47012502976320 call_variants.py:623] Complete: call_variants(Stuck at this step).

Does the quick start test work on your system?
Please test with https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-quick-start.md.
Is there any way to reproduce the issue by using the quick start?

Any additional context:

deepvariant_1.6.pdf

@kishwarshafin
Copy link
Collaborator

@ColinR01 ,

Is it possible to provide the input files to reproduce this result?

@pichuan
Copy link
Collaborator

pichuan commented Jan 30, 2024

I believe @kishwarshafin was able to reproduce the issue and is currently looking into a fix.
Keeping this open for now.

@kishwarshafin
Copy link
Collaborator

Hi @ColinR01 ,

Please try the following docker that has the patch incorporated that should fix your issue:

docker pull google/deepvariant:CL602468145
docker pull google/deepvariant:CL602468145-gpu

@kishwarshafin
Copy link
Collaborator

@ColinR01 , Can you please try the v1.6.1 docker? If the issue isn't resolved, please feel free to reopen this bug.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants