[ensembl-dev] vep warning when using cache
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Fri Jun 12 14:32:51 BST 2015
Sorry Will I forgot to copy "-check_existing" from command (it was on
new line)
Regards,
Guillermo
On 12/06/15 15:26, Will McLaren wrote:
> That command shouldn't even execute the line of code that is reporting
> that warning. Please double check.
>
> Will
>
> On 12 June 2015 at 14:21, Guillermo Marco Puche
> <guillermo.marco at sistemasgenomicos.com
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
> Hi Will,
>
> This is the command:
>
> * variant_effect_predictor.pl
> <http://variant_effect_predictor.pl> -i example_GRCh38.vcf -o
> annotation_example_GRCh38.vcf -database -hgvs -cache
> -dir_cache /home/gmarco/ensembl_80/cache
>
> I've tried on another machine (machine2) and I dont' get the
> error. Gonna try to re-install the exact same version of Perl on
> both machines. If this continues failing then I've no idea what's
> going on.
> Tried both version of bioperl 1.2.3 and 1.6.1 on both machines and
> both work good on machine2 and show warnings on machine1.
> Tried both versions of tabix 0.2.5 and 0.2.6 on both machines and
> both work good on machine2 and show warnings on machine1.
>
> * Machine1 Warnings:
> This is perl 5, version 14, subversion 4 (v5.14.4) built for
> x86_64-linux
>
> * Machine2 NO warnings:
> This is perl 5, version 18, subversion 2 (v5.18.2) built for
> x86_64-linux-gnu-thread-multi (with 41 registered patches, see
> perl -V for more detail)
>
> Maybe it's not a perl issue. Then I've no clue what could be
> causing the issue.
>
> Regards,
> Guillermo.
>
>
>
>
> On 12/06/15 15:04, Will McLaren wrote:
>> 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
>> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>
>> Hi Will,
>>
>> Completely deleted cache, re-downloaded and ran
>> convert_cache.pl <http://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 <http://convert_cache.pl> I get:
>>
>> convert_cache.pl <http://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
>> <http://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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