[ensembl-dev] VEP dbNSFP error

Abhishek Nag abhishek at well.ox.ac.uk
Sun May 26 15:47:26 BST 2019

Dear Anja,

Thanks for responding to my email.

The header line that is returned on running tabix -H seems fine.

Here is the VEP command that I'm running:

/apps/well/ensembl-tools/93/ensembl-vep/vep -i variants.txt -o output.txt --cache --dir /home/VEP/ --plugin dbNSFP,/home/VEP/Plugins/dbNSFP4.0b2a.txt.gz,ALL --tab --force_overwrite --port 3337

The /home/VEP/ path contains the Plugins subdirectory (which contains the dbNSFP4.0b2a.txt.gz file) as well as the cache folder homo_sapiens.

Thanks for your help!


From: Dev [dev-bounces at ensembl.org] on behalf of Anja Thormann [anja at ebi.ac.uk]
Sent: Thursday, May 23, 2019 3:52 PM
To: Ensembl developers list
Subject: Re: [ensembl-dev] VEP dbNSFP error

Dear Abhishek,

could you please run tabix -H dbNSFP4.0b2a.txt.gz and let me know if it returns the header line starting with #chr  pos(1-based)..? If that is the case could you please let me know who exactly your are running the VEP command together with the dbNSFP plugin command? If the header is returned correctly I’m wondering if the dbNSFP file path is maybe not found correctly by the plugin.


On 23 May 2019, at 13:53, Abhishek Nag <abhishek at well.ox.ac.uk<mailto:abhishek at well.ox.ac.uk>> wrote:


I have been trying to use the dbNSFP database to annotate my variants. Currently, I'm trying to use the latest version of the database (v4.0), but I have also tried using the version 3.5. With both versions, I'm getting the following error message whenever I'm trying to run it -

Failed to instantiate plugin dbNSFP: ERROR: Could not read headers from dbNSFP4.0b2a.txt.gz

When I zcat the database file, I am able to read the header line, which was obtained from one of the chromosome files, as suggested in the online manual.

The formatting steps for the database (including tab indexing) seem to have gone fine, so I'm not sure where the problem is. Also, I am being able to use the other VEP Plugins just fine; for now, I'm getting this error messge with only the dbNSFP plugin.

It would be great if I could have some pointers regarding where the issue might be.

Many Thanks
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