Problems when trying to use ensembl-vep

Question

[langziv]

Hi. I've been using ensembl-vep through Docker before and managed to use it, but now I'm encountering difficulties.
I'm running the commands as instructed in the ensembl-vep page.
After running the commands

docker pull ensemblorg/ensembl-vep

and

mkdir $HOME/vep_data

I run

docker run -t -i -v $HOME/vep_data:/data ensemblorg/ensembl-vep INSTALL.pl -a cf -s homo_sapiens -y GRCh38

which resulted in the following output:

  - getting list of available cache files


- downloading https://ftp.ensembl.org/pub/release-110/variation/indexed_vep_cache/homo_sapiens_vep_110_GRCh38.tar.gz
Cannot open Local file /opt/vep/.vep/tmp/homo_sapiens_vep_110_GRCh38.tar.gz: No such file or directory
 at /opt/vep/src/ensembl-vep/INSTALL.pl line 1315.
Cannot open Local file /opt/vep/.vep/tmp/CHECKSUMS: No such file or directory
 at /opt/vep/src/ensembl-vep/INSTALL.pl line 1319.
 - unpacking homo_sapiens_vep_110_GRCh38.tar.gz
tar (child): /opt/vep/.vep/tmp/homo_sapiens_vep_110_GRCh38.tar.gz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
ERROR: Failed to unpack file /opt/vep/.vep/tmp/homo_sapiens_vep_110_GRCh38.tar.gz

I tried expending file permissions but that didn't work.
What can be done?
Thanks.

[dthorbur]

Is there a particular reason you need to use VEP in a docker container? There is a conda release available that could be easier to use, and I've not encountered any problems with using that.

[langziv]

I found that using Docker eliminates the need to install multiple modules, as happens when using perl ensembl-vep without a container.
I'll try using conda.
Thanks.

[langziv]

Didn't work. I installed ensembl-vep in conda and followed the instruction to no avail.

[tomas4482]

I won't recommend using conda for installation. The environment is somehow very difficult to set up. Conda will always fail to recognize some perl modules in my case (but strangely, I did sucessfully install it by conda two years ago...Some releases must have changed and cannot work anymore). Docker is the only option for easier installation, despite it is still difficult to use when my data is not in /vep_data...

Answer 1

[A@Ensembl]

Hi,

Please could you try installing the cache manually as per the instructions here (https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#docker)?

# Install the new cache through the VEP INSTALL.pl script (see "Cache installation" section above)
docker run -t -i -v $HOME/vep_data:/data ensemblorg/ensembl-vep INSTALL.pl -a c

# Or install the cache manually
cd $HOME/vep_data
curl -O https://ftp.ensembl.org/pub/release-110/variation/vep/homo_sapiens_vep_110_GRCh38.tar.gz
tar xzf homo_sapiens_vep_110_GRCh38.tar.gz

Please let me know if you face any issues.

Best wishes, Ensembl Outreach team

[langziv]

The second suggestion worked once I run the commands as root. Thanks.
Now I can't figure out why the ensembl-vep command doesn't work:

$ sudo docker run -v $HOME/vep_data:/data ensemblorg/ensembl-vep   vep --cache --offline --format vcf --vcf --force_overwrite     
  --input_file input/1000123_23191_0_0.g.vcf       --output_file output/my_output.vcf
-------------------- EXCEPTION --------------------
MSG: ERROR: File "input/1000123_23191_0_0.g.vcf" does not exist

STACK Bio::EnsEMBL::VEP::Parser::file /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm:237
STACK Bio::EnsEMBL::VEP::Parser::new /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm:131
STACK Bio::EnsEMBL::VEP::Runner::get_Parser /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:802
STACK Bio::EnsEMBL::VEP::Runner::get_InputBuffer /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:829
STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:136
STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:200
STACK toplevel /opt/vep/src/ensembl-vep/vep:46
Date (localtime)    = Wed Aug  2 15:41:03 2023
Ensembl API version = 110
---------------------------------------------------

[Ben Moore]

Hi langziv - from the error message, it seems that the input file "input/1000123_23191_0_0.g.vcf" does not exist