[ensembl-dev] VEP return error

KingWai Lau KingWai.Lau at icr.ac.uk
Fri Nov 30 11:08:57 GMT 2012


Ok, I will download the Ensemble API 65 and wait for your email.

Thanks for everything!

Best,
King Wai

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: 30 November 2012 11:06
To: Ensembl developers list
Subject: Re: [ensembl-dev] VEP return error

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<mailto: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> [mailto: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<mailto: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> [mailto: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<mailto: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> [mailto: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<mailto: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<http://variant_effect_predictor.pl> --host ensembldb.ensembl.org<http://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<http://variant_effect_predictor.pl:161>

STACK toplevel /home/cancgene/klau/software/vep/2.3/variant_effect_predictor/variant_effect_predictor.pl:66<http://variant_effect_predictor.pl:66>

Ensembl API version = 65


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This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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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 the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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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 the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
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