[ensembl-dev] VEP segmentation fault error
Rehaman
ensemblfan at gmail.com
Wed Mar 14 04:26:37 GMT 2018
Dear Laurent,
Thanks a lot for quick response and I will use the same till new release.
Thanks & Regards
Fazulur Rehaman
On Tue, Mar 13, 2018 at 5:28 PM, Anja Thormann <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> 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> 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
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>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
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