[ensembl-dev] vep warning when using cache
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Fri Jun 12 14:21:21 BST 2015
Hi Will,
This is the command:
* 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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