[ensembl-dev] VEP segmentation fault error

Anja Thormann anja at ebi.ac.uk
Wed Mar 21 09:07:39 GMT 2018 

Dear Fazulur,

you are using column names in your dbNSFP argument list that are not contained in the 2.9. version. Please find the list of supported column names for version 2.9 here: https://drive.google.com/file/d/0B60wROKy6OqcdkFqMi1fNFJpZ0U/view <https://drive.google.com/file/d/0B60wROKy6OqcdkFqMi1fNFJpZ0U/view>

Kind regards,
Anja

> On 21 Mar 2018, at 08:31, Rehaman <ensemblfan at gmail.com> wrote:
> 
> Dear Anja Thormann,
> 
> Thanks a lot for confirmation.
> 
> I used the same and ran vep with both --custom annotation feature and dbNSFP plugin, it's working now.
> 
> I am getting few info lines while running vep. Please find below the same.
> 
> Use of uninitialized value in concatenation (.) or string at /ensembl-vep/cache/Plugins/dbNSFP.pm line 197.
> Use of uninitialized value in concatenation (.) or string at /ensembl-vep/cache/Plugins/dbNSFP.pm line 197.
> 
> Could you please let me know is there any issue with dbNSFP plugin.
> 
> Thanks In Advance
> Fazulur Rehaman
> 
> On Tue, Mar 13, 2018 at 5:28 PM, Anja Thormann <anja at ebi.ac.uk <mailto:anja at ebi.ac.uk>> wrote:
> Dear Fazulur,
> 
> you need to use dbNSFP version 2.9.2 for GRCh37 annotations. The most recent version of dbNSFP 3.5a supports annotations for GRCh37 and GRCh38. We updated the dbNSFP plugin accordingly for our coming release/93 to work with the new file from dbNSFP. Until the new release which is planned for April I suggest that you use dbNSFP version 2.9.2.
> 
> Regards,
> Anja
> 
>> On 13 Mar 2018, at 14:21, Rehaman <ensemblfan at gmail.com <mailto:ensemblfan at gmail.com>> wrote:
>> 
>> 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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <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 <mailto: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 <mailto: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
>>>>> 
>>>>> 
>>>>> _______________________________________________
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>>>> 
>>>> 
>>>> 
>>> 
>>> 
>>> 
>> 
>> 
>> 
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