[ensembl-dev] VEP return error

Will McLaren wm2 at ebi.ac.uk
Fri Nov 30 11:05:54 GMT 2012


OK, no problem.

Yes, if you download API 65 again it should be OK. You won't need to
download the script part (2.3) again as this has not changed.

I will send another email when the fixed cache file is available for
download.

Cheers

Will


On 30 November 2012 11:01, KingWai Lau <KingWai.Lau at icr.ac.uk> wrote:

> I am stuck with 65 because there are many things are linked to it.
> Certainly will get kill if I change to 68.****
>
> ** **
>
> Should I download the the API 2.3 again and wait a few hours for you to
> re-generate the cache?****
>
> ** **
>
> Many thanks for your help!! It is much appreciated!****
>
> ** **
>
> Best,****
>
> King Wai****
>
> ** **
>
> *From:* dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] *On
> Behalf Of *Will McLaren
> *Sent:* 30 November 2012 10:23
>
> *To:* Ensembl developers list
> *Subject:* Re: [ensembl-dev] VEP return error****
>
> ** **
>
> Hello again,****
>
> ** **
>
> I've managed to find the email trail for this issue as it cropped up
> before.****
>
> ** **
>
> It seemed there were a couple of issues, one with the cache file for
> features on chromosome Y, and one where there were insertions or deletions
> falling within a transcription factor binding motif.****
>
> ** **
>
> I have patched in the fix for the second problem to the CVS tree for API
> version 65, but for the first problem I would need to re-generate the cache
> file which will take me a few hours.****
>
> ** **
>
> What is the reason you are stuck with Ensembl 65? If it is because you
> don't have system admin rights to install a newer API, the INSTALL.pl
> script does not need admin rights; it only downloads the necessary API
> files locally within your user area.****
>
> ** **
>
> Cheers****
>
> ** **
>
> Will****
>
> ** **
>
> On 30 November 2012 10:11, KingWai Lau <KingWai.Lau at icr.ac.uk> wrote:****
>
> I don’t know how to capture the line. Are there any way I can capture the
> error and work my way back, please advice.****
>
>  ****
>
> King Wai****
>
>  ****
>
> *From:* dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] *On
> Behalf Of *Will McLaren
> *Sent:* 30 November 2012 10:05****
>
>
> *To:* Ensembl developers list
> *Subject:* Re: [ensembl-dev] VEP return error****
>
>  ****
>
> If you can find a line of input that reproduces the error, then I can run
> it through a debug process here.****
>
>  ****
>
> That would be great!****
>
>  ****
>
> Thanks****
>
>
> Will****
>
>  ****
>
> On 30 November 2012 10:01, KingWai Lau <KingWai.Lau at icr.ac.uk> wrote:****
>
> Hi,****
>
>  ****
>
> Unfortunately, we are stuck with Ensemble 65. By now, I tried VEP 2.2 –
> 2.7, they return the same error. Any there anything I can do/provide so
> that you can help?****
>
>  ****
>
> Best,****
>
> King Wai****
>
>  ****
>
> *From:* dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] *On
> Behalf Of *Will McLaren
> *Sent:* 30 November 2012 09:51
> *To:* Ensembl developers list
> *Subject:* Re: [ensembl-dev] VEP return error****
>
>  ****
>
> Hello,****
>
>  ****
>
> Have you tried updating your API installation?****
>
>  ****
>
> I seem to recall at least one other user encountering this problem (though
> I can't seem to find reference to it in my email records), and I think it
> was fixed by a patch to the API.****
>
>  ****
>
> I would also recommend that you always use the latest version of the
> script - this is now 2.7. If you use 2.7 you _must_ have the appropriate
> version of the API installed - for 2.7 this is 69. You can see the
> corresponding versions here:
> http://www.ensembl.org/info/docs/variation/vep/vep_script.html#download***
> *
>
>  ****
>
> To make it easier, you can run the INSTALL.pl script supplied in the
> script download archive, which will install/update the API to the
> appropriate version for the script.****
>
>  ****
>
> Regards****
>
>  ****
>
> Will McLaren****
>
> Ensembl Variation****
>
>  ****
>
> On 30 November 2012 09:16, KingWai Lau <KingWai.Lau at icr.ac.uk> wrote:****
>
> Dear sir/Madam,****
>
>  ****
>
> We are having difficulty to use variant effect predictor. We have Ensembl
> API 65, homo_sapiens_vep_65_sift_polyphen.tar.gz, VEP v2.3. we use the
> following command, and got an error. We have tried VEP 2.4, 2.6. Do you
> have any ideas how to solve it?****
>
>  ****
>
>  ****
>
>  ****
>
> perl variant_effect_predictor.pl --host ensembldb.ensembl.org --user
> anonymous --port 5306 --db_version 65 --cache --dir /vep --sift b
> --polyphen b --ccds --hgvs --hgnc --regulatory --canonical --protein
> --check_existing --check_alleles --quiet --no_progress --force_overwrite
> --format vcf --custom FACT5728.vcf.gz,samtools,vcf,exact,0 --input_file
> FACT5728.vcf -o FACT5728.csv****
>
> 2012-11-29 17:17:20 - Retrieved 5000 custom annotations (5000 samtools)***
> *
>
>  ****
>
> -------------------- EXCEPTION --------------------****
>
> MSG: Sequence NNNNNNNNNNNNNNNNNNN contains invalid characters: Only Aa Cc
> Gg Tt accepted STACK
> Bio::EnsEMBL::Funcgen::BindingMatrix::relative_affinity
> /home/apps/ensembl/ensembl65/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/BindingMatrix.pm:296
> ****
>
> STACK
> Bio::EnsEMBL::Variation::MotifFeatureVariationAllele::motif_score_delta
> /home/apps/ensembl/ensembl65/ensembl-variation/modules/Bio/EnsEMBL/Variation/MotifFeatureVariationAllele.pm:169
> ****
>
> STACK Bio::EnsEMBL::Variation::Utils::VEP::vf_to_consequences
> /home/apps/ensembl/ensembl65/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm:927
> ****
>
> STACK Bio::EnsEMBL::Variation::Utils::VEP::get_all_consequences
> /home/apps/ensembl/ensembl65/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm:816
> ****
>
> STACK main::main
> /home/cancgene/klau/software/vep/2.3/variant_effect_predictor/
> variant_effect_predictor.pl:161****
>
> STACK toplevel
> /home/cancgene/klau/software/vep/2.3/variant_effect_predictor/
> variant_effect_predictor.pl:66****
>
> Ensembl API version = 65****
>
>  ****
>
>
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> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> Company Limited by Guarantee, Registered in England under Company No.
> 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>
> This e-mail message is confidential and for use by the addressee only. If
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> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> Company Limited by Guarantee, Registered in England under Company No.
> 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>
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> the message is received by anyone other than the addressee, please return
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