aparton
commented
3 years ago Hi @PeterG188,
I suspect this is caused by VEP being unable to find your personal copy of the cache file. With your current set up then VEP will be looking for an unzipped 102 cache within the folder that you've specified in --dir_cache, i.e. it will be looking for /nobackup/b7000371/WORKING_DATA/SourceFiles/VEPHSCache/homo_sapiens/102_GRCh38. Does this folder exist?
If it does not, then unzipping your cache file in /nobackup/b7000371/WORKING_DATA/SourceFiles/VEPHSCache should setup the cache file as expected. Alternatively, you can do this with the VEP installer by running:
perl INSTALL.pl --auto c --CACHEDIR /nobackup/b7000371/WORKING_DATA/SourceFiles/VEPHSCache --SPECIES homo_sapiens --ASSEMBLY GRCh38
If there's anything else we can do to help, please let us know.
Kind Regards, Andrew
Hello Everybody, Our group are currently developing a script for variant calling within a gene on Rocket. As part of such we are including a VEP section for pathogenicity prediction etc. While this worked previously with an older version of VEP, we are now receiving error messages when using such with the pipeline effectively ending at the VCF stage. Below is a copy of the script used, followed by the error message we receive
module load VEP/102.0-foss-2019a-Perl-5.28.1
vep --cache --cache_version 102 --offline --use_given_ref --format vcf --tab --SIFT b --PolyPhen b --biotype --numbers \ --dir_cache /nobackup/b7000371/WORKING_DATA/SourceFiles/VEPHSCache \ -i /nobackup/b7000371/WORKING_DATA/PMS2_Variants/vcf/SampleExonMIPs202012/${Sample}.vcf \ -o $NFVEPDir/${Sample}.txt
filter_vep -filter "(Gene is ENSG00000122512) and (Feature is ENST00000265849)" \ -i $NFVEPDir/${Sample}.txt \ -o $FVEPDir/${Sample}.txt
MSG: ERROR: No cache found for homo_sapiens, version 102
STACK Bio::EnsEMBL::VEP::CacheDir::dir /mnt/storage/apps/eb/software/VEP/102.0-foss-2019a-Perl-5.28.1/modules/Bio/EnsEMBL/VEP/CacheDir.pm:328 STACK Bio::EnsEMBL::VEP::CacheDir::init /mnt/storage/apps/eb/software/VEP/102.0-foss-2019a-Perl-5.28.1/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227 STACK Bio::EnsEMBL::VEP::CacheDir::new /mnt/storage/apps/eb/software/VEP/102.0-foss-2019a-Perl-5.28.1/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /mnt/storage/apps/eb/software/VEP/102.0-foss-2019a-Perl-5.28.1/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /mnt/storage/apps/eb/software/VEP/102.0-foss-2019a-Perl-5.28.1/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /mnt/storage/apps/eb/software/VEP/102.0-foss-2019a-Perl-5.28.1/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:170 STACK Bio::EnsEMBL::VEP::Runner::init /mnt/storage/apps/eb/software/VEP/102.0-foss-2019a-Perl-5.28.1/modules/Bio/EnsEMBL/VEP/Runner.pm:132 STACK Bio::EnsEMBL::VEP::Runner::run /mnt/storage/apps/eb/software/VEP/102.0-foss-2019a-Perl-5.28.1/modules/Bio/EnsEMBL/VEP/Runner.pm:203 STACK toplevel /mnt/storage/apps/eb/software/VEP/102.0-foss-2019a-Perl-5.28.1/vep:229 Date (localtime) = Fri Feb 5 11:31:20 2021 Ensembl API version = 102
I have a personal copy of the homo_sapiens (V102) cache saved locally, and have tried running the script without the '--offline' option, but nothing seems to correct this issue. Does anybody know how to resolve this issue so that VEP will run effectively?
Thanks