[ensembl-dev] hgvs in offline mode.

[Andrew Parton]

Hi Kurt,

Unfortunately the error is correct, you cannot use HGVS input format in offline mode.

If there’s something incorrect or unclear in our docs then I would like to update it, could you please point in the direction of the documentation you found?

Kind Regards,
Andrew



> On 4 Jan 2021, at 17:54, Kurt Hetrick <khetric1 at jhmi.edu> wrote:
> 
> Hello,
> 
> From reading the online documentation I was under the impression that one could use hgvs in offline mode provided that they pointed to the fasta file, but the error I received suggests otherwise. Am I missing something or is hgvs not possible in offline mode. Using GRCh37.
> 
> I am using a singularity image for ensemble 102 that I pulled from a docker image that I built using the dockerfile from your dockerhub page where I changed the base image from Ubuntu 18.04 to Ubuntu 16.04 and then built the cache locally.
> 
> export PERL5LIB=/mnt/resources/vep_data
> export PATH=$PATH:/mnt/resources/vep_data
>  
> singularity exec -B /mnt:/mnt /mnt/containers/vep-102.0.simg vep -i file2.txt -o test.vcf --fork 4 --cache --offline --refseq --force_overwrite --dir /mnt/resources/vep_data --fasta /mnt/research/tools/test/human_g1k_v37_decoy.fasta --hgvs --assembly GRCh37 --check_existing --dir_cache /mnt/resources/vep_data
> 2021-01-04 17:43:09 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this
>  
> -------------------- EXCEPTION --------------------
> MSG: ERROR: Cannot use HGVS format in offline mode
> STACK Bio::EnsEMBL::VEP::Parser::HGVS::new /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser/HGVS.pm:104
> STACK Bio::EnsEMBL::VEP::Parser::new /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm:151
> STACK Bio::EnsEMBL::VEP::Runner::get_Parser /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:805
> STACK Bio::EnsEMBL::VEP::Runner::get_InputBuffer /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:832
> STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:140
> STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:203
> STACK toplevel /opt/vep/src/ensembl-vep/vep:229
> Date (localtime)    = Mon Jan  4 17:43:09 2021
> Ensembl API version = 102
>  
> head -n 5 file2.txt
> NM_000492.4:c.-13_10del23
> NM_000492.4:c.-9_14del23
> NM_000492.4:c.-8G>C
> NM_000492.4:c.[1046C>T;3747delG]
> NM_000492.4:c.[1093_1094delCT;3705T>G]
>  
> Thanks in advance,
>  
> Kurt Hetrick
>  
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