VEP variation cache

[DNAjunk]

Hi all

When running VEP with ensembl annoation files I get errors of the form "Could not find variation cache for Chromosome..."

I downloaded genome (ie. pao1, $name.fa) and annotation ($name.gff3) from ensembl ftp.
Then created the cache files according to the VEP tutorial:


sort -k1,1 -k4,4n $name.gff | bgzip > $name.gff.gz
tabix -p gff $name.gff.gz
./cufflinks/gffread $name.gff -T -o $name.gtf
perl gtf2vep.pl -i $name.gtf -f $name.fa -d 79 -s $name --dir variant_effect_predictor_version79/cache_files_
and move the cache files to the correct location manually.

Then mapped reads to the genome, ran freebayes (variants.vcf) and then vep with the following command:


perl variant_effect_predictor.pl --everything --offline --custom $name.gff.gz,$name-genes,gff,overlap,0 --format vcf -i variants.vcf -o variants.txt --species $name --dir_cache $VEP_DATA

I don't understand why I got this errors/warnings?

Attached is the vep log output.

Any help would be appreciated very much!

Thanks.