[ensembl-dev] VEP segmentation fault error

Tue Mar 13 14:21:03 GMT 2018

Dear Laurent,

Thanks a lot for your suggestions. I am able to use  --custom annotation
feature without errors now. And I had tried with --keep_csq option too.

Now I want to add dbNSFP annotations using dbNSFP plugin. As per
documentation I installed plugins and downloaded dbNSP files.

Here is my command:

*vep -i  examples/homo_sapiens_GRCh37.vcf -cache --offline --dir
ensembl-vep/cache --assembly GRCh37 --plugin
dbNSFP,dbNSFP3.3a.txt.gz,hg19_chr,genename,cds_strand,refcodon,codonpos,codon_degeneracy,Ancestral_allele,AltaiNeandertal,Denisova,Ensembl_geneid,Ensembl_transcriptid,Ensembl_proteinid,aapos,SIFT_score,SIFT_converted_rankscore,SIFT_pred,Uniprot_acc_Polyphen2*

And I am getting below error:

*Use of uninitialized value $readme_file in concatenation (.) or string at
/gpfs/software/genomics/vep/ensembl-vep/cache/Plugins/dbNSFP.pm line 157.*
*Use of uninitialized value in concatenation (.) or string at
/gpfs/software/genomics/vep/ensembl-vep/cache/Plugins/dbNSFP.pm line 197.*

I come across below post related to this plugin and it was mentioned like
dbNSFP plugin is only compatible with GRCh38 build. And I am working on
GRCh37.

*http://lists.ensembl.org/pipermail/dev/2016-February/011680.html
<http://lists.ensembl.org/pipermail/dev/2016-February/011680.html>*

Could you please suggest me how to proceed further.

Thanks In Advance
Fazulur Rehaman

On Tue, Mar 6, 2018 at 2:53 PM, Rehaman <ensemblfan at gmail.com> wrote:

> Dear Laurent,
>
> Thanks for your suggestions on annotated vcf and I will try the same and
> let you know the status.
>
> Thanks & Regards
> Fazulur Rehaman
>
> On Tue, Mar 6, 2018 at 12:09 PM, Laurent Gil <lgil at ebi.ac.uk> wrote:
>
>> Dear Fazulur,
>>
>> If you re-annotate a VCF file which has been already annotated by VEP, it
>> will add all the annotations.
>>
>> However you have 2 options when you run VEP on your already VEP-annotated
>> VCF file:
>> 1 - The default behaviour si to replace the "old" annotation (CSQ) by a
>> "new" annotation
>> 2 - You can keep the "old" annotation (CSQ) in the new VCF output and
>> thus you will have 2 annotations per line, using the option "--keep_csq"
>>
>> I hope it makes sense.
>>
>> Best regards,
>>
>> Laurent
>> Ensembl Variation
>>
>> On 06/03/2018 07:10, Rehaman wrote:
>>
>> Dear Laurent,
>>
>> I have one more doubt regarding the vep annotations. I ran vep already
>> without gnomAD annotations before and I want to add the same now. Can I run
>> the same on annotated vcf file. Does it add again all the annotations or
>> only gnomAD frequencies. Since we already have 1000g Allele frequencies,
>> sift b scores etc in our annotated vcf. Does it add again into new
>> annotated vcf.
>>
>> Could you please suggest me.
>>
>> Thanks & Regards
>> Fazulur Rehaman
>>
>> On Tue, Mar 6, 2018 at 7:28 AM, Rehaman <ensemblfan at gmail.com> wrote:
>>
>>> Dear Laurent,
>>>
>>> Thanks a lot for documentation page and explanation on custom annotation
>>> feature.
>>>
>>> As "--everything" option contains other annotations (--sift b,
>>> --polyphen, --hgcs etc), can we use "--everything" and "--custom" (for
>>> missing gnomAD allele frequencies) options together with vep. Please
>>> confirm?
>>>
>>> Thanks & Regards
>>> Fazulur Rehaman
>>>
>>> On Mon, Mar 5, 2018 at 5:38 PM, Laurent Gil <lgil at ebi.ac.uk> wrote:
>>>
>>>> Dear Fazulur,
>>>>
>>>> You can see the explanations about the custom annotation options (i.e.
>>>> "exact" => "Annotation type"  and "0" => "Force report coordinates" flag)
>>>> in the VEP documentation page:
>>>>
>>>> http://www.ensembl.org/info/docs/tools/vep/script/vep_custom
>>>> .html#custom_options
>>>>
>>>> Best regards,
>>>>
>>>> Laurent
>>>>
>>>> On 05/03/2018 14:27, Rehaman wrote:
>>>>
>>>> Dear Laurent,
>>>>
>>>> I have installed  Bio:DB:HTS perl module and issue got resolved.
>>>> Thanks a lot.
>>>>
>>>> Could you please define what is "exact" and "0" custom annotation
>>>> feature.
>>>>
>>>> --custom gnomad.exomes.r2.0.1.sites.vcf.gz,gnomADg,*vcf,exact,0,*AF_AFR
>>>> ,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH
>>>>
>>>> Thanks In Advance
>>>> Fazulur Rehaman
>>>>
>>>> On Thu, Mar 1, 2018 at 9:58 AM, Rehaman <ensemblfan at gmail.com> wrote:
>>>>
>>>>> Dear Laurent,
>>>>>
>>>>> Thanks a lot for your response.
>>>>>
>>>>> It was a typo. Actually I have used "--" before the custom option
>>>>> while running vep.
>>>>>
>>>>> May be Segmentation fault error is due to Bio:DB:HTS perl module. I
>>>>> will run again after installing the same and let you know the status.
>>>>>
>>>>> Please suggest me if error is not related to module.
>>>>>
>>>>> Thanks & Regards
>>>>> Fazulur Rehaman
>>>>>
>>>>>
>>>>> On Wed, Feb 28, 2018 at 12:16 PM, Laurent Gil <lgil at ebi.ac.uk> wrote:
>>>>>
>>>>>> Dear Fazulur,
>>>>>>
>>>>>> Regarding your VEP command it looks like you missed to add "--"
>>>>>> before the "custom" option:
>>>>>>
>>>>>> *vep -i [vepdir]/examples/homo_sapiens_GRCh37.vcf -cache --ASSEMBLY
>>>>>> GRCh37 --fork 4 --custom
>>>>>> gnomad.exomes.r2.0.1.sites.vcf.gz,gnomADg,vcf,exact,0,AF_AFR,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH*
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Laurent
>>>>>> Ensembl Variation
>>>>>>
>>>>>> On 27/02/2018 19:04, Rehaman wrote:
>>>>>>
>>>>>> Dear Ensembl team,
>>>>>>
>>>>>> I am running VEP for GRCh37 assembly and as you mentioned some of
>>>>>> alleles may not get Allele frequencies and so I want to test custom
>>>>>> annotation optio
>>>>>>
>>>>>> I tried running vep with example vcf and getting "Segmentation Fault"
>>>>>> error.
>>>>>>
>>>>>> Command:
>>>>>>
>>>>>> *vep -i [vepdir]/examples/homo_sapiens_GRCh37.vcf -cache --ASSEMBLY
>>>>>> GRCh37 --fork 4 custom
>>>>>> gnomad.exomes.r2.0.1.sites.vcf.gz,gnomADg,vcf,exact,0,AF_AFR,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH*
>>>>>>
>>>>>> Could you please give me suggestions on this.
>>>>>>
>>>>>> Thanks & Regards
>>>>>> Fazulur Rehaman
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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/
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>>
>
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