[ensembl-dev] vep warning when using cache

Fri Jun 12 14:04:17 BST 2015

Just to clarify, what command are you running that gives the original
error/warning?

I can't recreate the issue, sorry!

Will

On 11 June 2015 at 12:28, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

>  Hi Will,
>
> Completely deleted cache, re-downloaded and ran convert_cache.pl as you
> suggest in b) warnings still appear.
>
> If I try to reprocess again a cache already processed with
> convert_cache.pl I get:
>
> convert_cache.pl -d /share/references/vep -s homo_sapiens -v 80_GRCh38
> --force_overwrite
> 2015-06-11 13:25:43 - Processing homo_sapiens
> 2015-06-11 13:25:43 - Processing version 80_GRCh38
> 2015-06-11 13:25:43 - Processing _var cache type
> [>                                                          ]    [ 2%
> ]ERROR: tabix failed
> [ti_index_core] the file out of order at line 300
>
> First run on fresh cache doesn't fail.
> I've tried with tabix 0.2.5 and tabix 0.2.6 both versions have the exact
> same results.
>
> As I said I'm getting warnings when using cache *even if I don't index it
> *previously with convert_cache.pl
>
> Regards,
> Guillermo.
>
>
> On 11/06/15 12:40, Will McLaren wrote:
>
> 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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>
>
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