[ensembl-dev] vep warning when using cache
Will McLaren
wm2 at ebi.ac.uk
Fri Jun 12 14:26:16 BST 2015
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> wrote:
> 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> 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.
>>>>
>>>> _______________________________________________
>>>> Dev mailing list Dev at ensembl.org
>>>> Posting guidelines and subscribe/unsubscribe info:
>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>> Ensembl Blog: http://www.ensembl.info/
>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>>
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150612/0a29776a/attachment.html>
More information about the Dev
mailing list