[ensembl-dev] Could not find variation cache for
Schmucki, Roland
roland.schmucki at roche.com
Fri Jun 5 13:52:52 BST 2015
Dear Will
Thank you very much for the quick response.
I would like to post this issue to the public Ensembl mailing list.
Here is a brief description of the problem I encountered:
When running VEP with ensembl annotation files I get errors of the form
"Could not find variation cache for Chromosome..."
I downloaded a genome (i.e. pao1, $name.fa) and annotation ($name.gff3)
from Ensembl ftp and 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.
This all seem to have worked fine without any error or warning messages.
Then I mapped the reads to the genome, ran Freebayes (variants.vcf with
2700 variants) and at the very end applied 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
The variable VEP_DATA points to the corresponding cache file:
with the following files (creation date and file size) there in:
$VEP_DATA/pao1/79/Chromosome/
292135 Jun 5 09:10 3000001-4000000.gz
294904 Jun 5 09:10 1000001-2000000.gz
290186 Jun 5 09:10 1-1000000.gz
290763 Jun 5 09:10 5000001-6000000.gz
284789 Jun 5 09:10 2000001-3000000.gz
292462 Jun 5 09:10 4000001-5000000.gz
78483 Jun 5 09:10 6000001-7000000.gz
When I run VEP I get the following errors and warnings (See attached log
file for all details):
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
etc.
I don't understand why I got this errors/warnings?
Thanks a lot for any advice!
Best,
R.
PS: there is an output file generated with variant annotations of the form:
#Uploaded_variation Location Allele Gene Feature
Feature_type Consequence cDNA_position CDS_position Pro
tein_position Amino_acids Codons Existing_variation Extra
Chromosome_2415_G/T Chromosome:2415 T gene:PA0005
transcript:AAG03395 Transcript downstream_gene_variant -
- - - - -
IMPACT=MODIFIER;pao1-genes=gene:PA0002,exon_Chromosome:2056-3159,CDS:AAG03392,transc
However, no amino acid changes are found which is unlikely.
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2015-06-05 09:13:34 - INFO: Disabling --hgvs; using --offline and no FASTA file found
2015-06-05 09:13:34 - Starting...
2015-06-05 09:13:34 - Read 2675 variants into buffer
2015-06-05 09:13:34 - Checking for existing variations
] [ 0% ]
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:6000001-7000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:6000001-7000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:6000001-7000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:6000001-7000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:6000001-7000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:6000001-7000000
WARNING: Could not find variation cache for Chromosome:3000001-4000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:6000001-7000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:2000001-3000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:5000001-6000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
WARNING: Could not find variation cache for Chromosome:1000001-2000000
WARNING: Could not find variation cache for Chromosome:1-1000000
WARNING: Could not find variation cache for Chromosome:4000001-5000000
2015-06-05 09:13:34 - Reading transcript data from cache and/or database
2015-06-05 09:13:35 - Retrieved 5678 transcripts (0 mem, 5678 cached, 0 DB, 0 duplicates)
2015-06-05 09:13:35 - Analyzing chromosome Chromosome
2015-06-05 09:13:35 - Caching custom annotations
2015-06-05 09:13:36 - Retrieved 1514 custom annotations (1514 pao1-genes)
2015-06-05 09:13:36 - Analyzing custom annotations
2015-06-05 09:14:12 - Processed 2675 total variants (70 vars/sec, 70 vars/sec total)
2015-06-05 09:14:12 - Wrote stats summary to TEST.txt_summary.html
2015-06-05 09:14:12 - See TEST.txt_warnings.txt for details of 132 warnings
2015-06-05 09:14:12 - Finished!
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