[ensembl-dev] VEP segmentation fault error
Rehaman
ensemblfan at gmail.com
Wed Mar 21 11:15:52 GMT 2018
Dear Anja Thormann,
Thanks a lot.
I have checked that, I have given dbNSFP column name *"chr" *as* "#chr"*.
Now it got fixed. I am not getting info messages.
Thanks & Regards
Fazulur Rehaman
On Wed, Mar 21, 2018 at 12:07 PM, Anja Thormann <anja at ebi.ac.uk> wrote:
> 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
>
> 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> 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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>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>
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