[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
Hi,
I'm using VEP release-79 with cache from
ftp://ftp.ensembl.org/pub/release-79/variation/VEP/homo_sapiens_merged_vep_79_GRCh37.tar.gz
.
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
/work/genomic/variantDbs/repeatMasker/repeatMasker_hg19.20150508.reformat.sorted.bed.gz,repeatMasker,bed,overlap,0
-i test.na12878.vcf -o vep_processed.vcf
Best regards,
Svein Tore Koksrud Seljebotn
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