VEP in containers. "Chromosome 1 not found in annotation sources..." error about ensembl-vep HOT 4 CLOSED

Hi @migrau,

Thanks for your query!

I tried to re-produce the issue with input that you provided but failed. The issue seems to be with cache - can you try deleting the cache dir and re-downloading it again.

Best regards,
Nakib

from ensembl-vep.

Hi nakib103,
I realised it was a problem with the folders hierarchy, maybe something changed in the last versions. In v109, specifying --dir /workspace/datasets/vep/ works (the v109 cache is in /workspace/datasets/vep/homo_sapiens/109_GRCh38). But when downloading the v110, the folder created /workspace/datasets/vep/homo_sapiens/110.0_GRCh38 contains two sublevels more: /workspace/datasets/vep/homo_sapiens/110.0_GRCh38/homo_sapiens/110_GRCh38/. If I specify /workspace/datasets/vep/homo_sapiens/110.0_GRCh38/, vep works correctly.

from ensembl-vep.

Hi @migrau,

The cache directory structure is same between 109 and 110 -

$ tar -tf homo_sapiens_vep_109_GRCh38.tar.gz | head -n 4
homo_sapiens/109_GRCh38/
homo_sapiens/109_GRCh38/1/
homo_sapiens/109_GRCh38/1/1-1000000.gz
homo_sapiens/109_GRCh38/1/1-1000000_reg.gz

$ tar -tf homo_sapiens_vep_110_GRCh38.tar.gz | head -n 4
homo_sapiens/110_GRCh38/
homo_sapiens/110_GRCh38/1/
homo_sapiens/110_GRCh38/1/1-1000000.gz
homo_sapiens/110_GRCh38/1/1-1000000_reg.gz

And as you can see it has structure such as - <species>/<version>_<assembly>/<chromosome>/<cache_files>. So when you gave the -c 110.0_GRCh38/ in your download command it extracted the cache files with the above folder structure under /workspace/datasets/vep/homo_sapiens/110.0_GRCh38.

If you had given -c /workspace/datasets/vep than you would expect the cache files under /workspace/datasets/vep/ same as 109.

Hope that answers your question.

Best regards,
Nakib

from ensembl-vep.

Thanks, nakin103. I didn't download the tar.gz directly but using the singularity exec ensembl-vep_110.0.sif INSTALL.pl -c 110.0_GRCh38/ -a cf -s homo_sapiens --ASSEMBLY GRCh38 command, and for some reason, the directory structure inside the downloaded folder is different, as I said.
109_GRCh38 contains all the files and folders (e.g. LRG_, Homo_sapiens.GRCh38.dna.toplevel.fa.gz) but 110.0_GRCh38 contains two subfolders more homo_sapiens/110_GRCh38, before all the files and folders (e.g. LRG_, Homo_sapiens.GRCh38.dna.toplevel.fa.gz)
Anyway, it is solved now, thanks!

from ensembl-vep.