search

Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
Apache License 2.0
449 stars 151 forks source link

Docker v111.0 and. v112.0 got error bgzip not found in path #1693

Closed barbarian1803 closed 3 months ago

barbarian1803 commented 3 months ago

Describe the issue

Error when running VEP docker version 111.0 and 112.0: MSG: ERROR: bgzip not found in path The same script works when running docker version v110.1. It works when compress_output parameter is not specified. The docker for v110 use ubuntu 18 but for 111 and 112 use ubuntu:22.04. I suspect this is the cause.

Parameters

compress_output bgzip

Additional information

Please fill in the following sections to help us find the source of your issue as quickly as possible.

System

Full error message

-------------------- EXCEPTION --------------------
MSG: ERROR: bgzip not found in path

STACK Bio::EnsEMBL::VEP::BaseRunner::get_output_file_handle /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:206
STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:202
STACK toplevel /opt/vep/src/ensembl-vep/vep:46
Date (localtime)    = Thu Jun  6 03:20:29 2024
Ensembl API version = 111
---------------------------------------------------
nuno-agostinho commented 3 months ago

Hi @barbarian1803,

bgzip is indeed part of the Docker images, so I am not sure why you are getting that error. Can you show me the command that you are using to get that error?

Also, could you try running the following command and sending me the output?

docker run -ti ensemblorg/ensembl-vep:release_112.0 bgzip

Thank you and sorry for the inconvenience.

Best regards, Nuno

barbarian1803 commented 3 months ago

Hi,

That is the weird part. I have tried your command and it shows the bgzip command is there. I have also run it on other linux machine and it works fine. The environment that shows error is using podman so I am not sure that is the cause although the old version v110 works just fine.

nuno-agostinho commented 3 months ago

Hi @barbarian1803,

In that case, the issue appears to be related to using the Docker image in Podman. Unfortunately, we do not provide support for Podman.

As a workaround, you can manually bgzip the resulting uncompressed file from VEP.

Don’t hesitate to ask if you have more questions or want to chat about this further.

Cheers, Nuno