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.

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_Ensembl]

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