[ensembl-dev] vep warning when using cache

[Guillermo Marco Puche]

Hi Will,

This is info.txt content in [cache_dir]/homo_sapiens/80_GRCh38/info.txt


# CACHE UPDATED 2015-06-11 09:12:21
sift    b
cell_types 
HeLa-S3,GM06990,U2OS,CD4,IMR90,HL-60,HepG2,Lymphoblastoid,CD133,CD36,K562,GM12878,HUVEC,NHEK,H1ESC,MultiCell,K562b,NH-A,HSMM,HMEC,A549,AG04449,AG04450,AG09309,AG09319,AG10803,Caco-2,Chorion,CMK,GM10847,GM12801,GM12864,GM12865,GM12872,GM12873,GM12874,GM12875,GM12891,GM12892,GM15510,GM18505,GM18507,GM18526,GM18951,GM19099,GM19193,GM19238,GM19239,GM19240,H7ESC,H9ESC,HAEpiC,HCF,HCM,HCPEpiC,HCT116,HEEpiC,HEK293b,HEK293,HepG2b,HGF,HIPEpiC,HNPCEpiC,HRCEpiC,HRE,HRPEpiC,Jurkat,LHSR,MCF7,Medullo,Melano,NB4,NHBE,NHDF-neo,NHLF,NT2-D1,Panc1,PanIslets,PFSK1,SAEC,SKMC,SKNMC,SKNSHRA,Th1,Th2,WERIRB1,RPTEC,ProgFib,HSMMtube,Osteobl,MCF10A-Er-Src,HPAEpiC,Fibrobl,GM12878-XiMat,BJ,NHDF-AD,Monocytes-CD14+,DND-41
var_type    tabix
user    ensro
host    genebuild9
variation_cols 
chr,variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,pubmed,AFR,AMR,EAS,EUR,SAS,AA,EA
port    3306
build    all
polyphen    b
regulatory    1
assembly    GRCh38
species    homo_sapiens
source_polyphen    2.2.2
source_sift    sift5.2.2
source_COSMIC    71
source_ESP    20141103
source_gencode    GENCODE 22
source_HGMD-PUBLIC    20144
source_genebuild    2014-07
source_regbuild    13.0
source_assembly    GRCh38.p2
source_dbSNP    142
source_ClinVar    20150306

Regards,
Guillermo

On 10/06/15 20:41, Guillermo Marco Puche wrote:
> Hi Will,
>
> I got the exact same warnings with 79_GRCh38 cache (indexed previosuly 
> with convert_cache)
> Then I decided to try with 80_GRCh38 cache and API version 80. I 
> didn't index it and I'm getting the same warnings. Tomorrow I'll index 
> 80_GRCh38 cache and report "info.txt".
>
> Regards,
> Guillermo.
>
> El 10/06/2015 a las 17:59, Will McLaren escribió:
>> Hi Guillermo,
>>
>> Did you say you had run convert_cache.pl <http://convert_cache.pl> in 
>> an earlier email?
>>
>> This may be the issue here. Can you send on the content of the file 
>> [cache_dir]/homo_sapiens/80_GRCh37/info.txt
>>
>> It may be you need to re-run the convert_cache script, possibly after 
>> downloading the original cache again.
>>
>> Will
>>
>> On 10 June 2015 at 15:40, Guillermo Marco Puche 
>> <guillermo.marco at sistemasgenomicos.com 
>> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>
>>     Dear devs,
>>
>>     I'm experiencing the following warnings when using vep local
>>     cache with variant_effect_predictor script:
>>
>>         Argument "-/C" isn't numeric in numeric eq (==) at /share/apps/src/ensembl_80-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 6218.
>>
>>         Use of uninitialized value in split at /share/apps/src/ensembl_80-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 6223.
>>
>>
>>     If no cache is used warnings disappear.
>>
>>     Input VCF: example_GRCh38.vcf  (inside
>>     https://github.com/Ensembl/ensembl-tools/archive/release/80.zip)
>>     Cache downloaded from:
>>     ftp://ftp.ensembl.org/pub/release-80/variation/VEP/homo_sapiens_vep_80_GRCh38.tar.gz
>>
>>     Best regards,
>>     Guillermo.
>>
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