[ensembl-dev] Error message WARNING: Could not find variation cache

Svein Tore Koksrud Seljebotn s.t.seljebotn at medisin.uio.no
Thu May 14 09:48:10 BST 2015


I'm using VEP release-79 with cache from 

I tried to annotate some human exome data and I get the following error 
message in a separate file called {output_name}_warnings.txt:

"WARNING: Could not find variation cache for 20:63000001-64000000"

Looking at the files for this range inside the cache, I can see that 
those files contain almost not data. There are also other regions that 
are as small, while most are from 1MB and upwards.

My question, is this something I should worry about? Is my cache 
corrupted somehow?

Command line:
vep --cache --dir_cache=/work/genomic/funcAnnot/VEP/cache/ 
--fasta=/work/genomic/gatkBundle_2.5/human_g1k_v37_decoy.fasta --offline 
--sift=b --polyphen=b --ccds --hgvs --numbers --domains --regulatory 
--canonical --protein --biotype --gmaf --maf_1kg --maf_esp --pubmed 
--allow_non_variant --fork=4 --vcf --allele_number --no_escape 
--failed=1 --no_stats --merged --symbol -custom 
-i test.na12878.vcf -o vep_processed.vcf

Best regards,
Svein Tore Koksrud Seljebotn

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