[ensembl-dev] vep warning when using cache
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Thu Jun 11 12:28:46 BST 2015
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
> <http://convert_cache.pl> script and I'm afraid I don't see the same
> error.
>
> I'd try
>
> a) run convert_cache.pl <http://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
> <mailto: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
>>> <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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>>
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