[ensembl-dev] vep warning when using cache

Will McLaren wm2 at ebi.ac.uk
Thu Jun 11 11:40:16 BST 2015


Hi Guillermo,

The info.txt looks fine. My guess is something's gone wrong in the
conversion stage which has corrupted the column structure in one of the
converted files.

I downloaded the cache afresh and ran the convert_cache.pl script and I'm
afraid I don't see the same error.

I'd try

a) run convert_cache.pl again (you may need to add the --force_overwrite
option)

b) remove the existing one and download the cache again

Will


On 11 June 2015 at 08:21, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

>  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 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> 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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>
>
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