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Offline Usage of the Go Plugin

I'm using VEP in offline mode. I want to add the GO terms. From what I've read, it seems like I need the --database connection. But isn't there another way to run the GO plugin offline?

ensembl go-terms vep
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updated by tvrlisml • tvrlisml • written by mrymkdnz • mrymkdnz

1 answer

You will need to run the GO plugin with --database at least once in order to create the GO files for the first time. You can simply run VEP with any variant to generate the GO data, like so:

./vep --id rs699 --database --plugin GO

Afterwards, you can run your usual VEP command in the same directory and the available GO data will be automatically used by the plugin.

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updated by Ram Ram • written by Ben Moore Ben Moore

As I experienced the same problem, I tried to run the command you noted down. However, I get a warning message like:

WARNING: Failed to instantiate plugin GO: Modification of a read-only value attempted at /home/tvrl/Desktop/test/.snakemake/conda/a9885697a950c8db50bdcb37d8f2cb8c_/share/ensembl-vep-108.2-0/GO.pm line 327.

I use the latest version of the package and as far as I understand, I should get .gff file as the result of this command to be used in next runs. However I got two files as:

GO.pm_homo_sapiens_110_GRCh38.gff.lock
GO.pm_homo_sapiens_110_GRCh38.gff.tmp

How to fix this situation?

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updated by Ram Ram • written by tvrlisml • tvrlisml

Hi tvrlisml,

Those files are only temporary files and probably mean that the first run didn't finish. Could you please delete those files and try to generate them again with the command ./vep --id rs699 --database --plugin GO

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updated by Ram Ram • written by Ben Moore Ben Moore

Hi there,

Thanks for your quick response. After those files are generated, they remain empty with no lines even after the whole process is completed. I have tried removing them and running the command multiple times. However, even though I can reach the output file, .gff file is not created (nothing but these two blank temporary files). I thought there might be an issue with the perl module of GO plugin as it gives a warning message while process is in progress.

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written by tvrlisml • tvrlisml

It seems the VEP code is trying to modify a read-only variable that newer versions of Perl simply refuse to do. There is a PR to fix this (VEP_plugins#625), which will be available for next VEP release.

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written by Ben Moore Ben Moore

Thank you for the information. I will be waiting for this to be fixed

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written by tvrlisml • tvrlisml

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