[ensembl-dev] Variant effect predictor: regulatory information and MATRIX/HIGH_INF_POS

A. P. Levine a.levine at ucl.ac.uk
Thu Oct 6 12:50:13 BST 2011


Dear Will,

I have downloaded the up-to-date APIs and it is working perfectly.

Thank you very much for your help.

Adam

Adam P. Levine

-----Original Message-----
From: wmclaren at gmail.com [mailto:wmclaren at gmail.com] On Behalf Of Will McLaren
Sent: 06 October 2011 11:10
To: A. P. Levine
Cc: dev at ensembl.org
Subject: Re: [ensembl-dev] Variant effect predictor: regulatory information and MATRIX/HIGH_INF_POS

Hi Adam,

I haven't seen this error before; perhaps you have APIs of different versions? Can you check that all of your API modules are up to date (version 64) and try again?

Cheers

Will

On 6 October 2011 11:01, A. P. Levine <a.levine at ucl.ac.uk> wrote:
> Dear Will,
>
> Thank you very much for your reply. MATRIX and HIGH_INF_POS are working online with the test input that you provided.
>
> With respect to the regulatory feature annotation, you were correct; I did not have ensembl-functgenomics in my src directory. I have downloaded it. However, now when I run the script I get the following error message:
>
> "DBD::mysql::st execute failed: Unknown column 'fs.experiment_id' in 'field list' at src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line 523, <GEN0> line 2026."
>
> Do you know what the problem might be?
>
> Thank you very much.
>
> Adam
>
> Adam P. Levine
>
>
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