[ensembl-dev] <External> Re: release 105 MySQL protein domain data severely truncated

Eric Engelhard eric.engelhard at regeneron.com
Sat Jan 22 19:09:59 GMT 2022

Hell Marc,

Yes, the protein domain issues for both human and mouse have been resolved. Thank you and any additional team members involved for the rapid response and fix.


From: Dev <dev-bounces at ensembl.org> On Behalf Of mchakiachvili
Sent: Friday, January 21, 2022 7:27 AM
To: Ensembl developers list <dev at ensembl.org>
Subject: <External> Re: [ensembl-dev] release 105 MySQL protein domain data severely truncated


Hello again,

files for both homo_sapiens and mus_musculus have been regenerated anew today, and published onto the FTP.

Please can you confirm that this resolve your issue?

Thanks for your support.


On Thu, 2022-01-20 at 17:14 +0000, mchakiachvili wrote:

Hello Eric,

Thanks for your message, we are aware of some troubles with truncated files for some of our current FTP.

We are correcting those when they arise. We'll surely fix those dumps quickly and let you know when the expected files are restored.

Sorry for the inconvenience caused.


On Thu, 2022-01-20 at 16:24 +0000, Eric Engelhard wrote:
Hello Ensembl team,

I am working from Ensembl MySQL downloads and have discovered that protein domain data from ftp://ftp.ensembl.org/pub/current_mysql/homo_sapiens_core_105_38/<https://urldefense.com/v3/__ftp:/ftp.ensembl.org/pub/current_mysql/homo_sapiens_core_105_38/__;!!ODpDvJZr5w!Sldr6zpX7noerjYVZDfvSGgeSqBmqJqTExtB7QP3DuKZSrjPYARUQNsaxF6aTI8Bg33M$>
and ftp://ftp.ensembl.org/pub/current_mysql/mus_musculus_core_105_39/<https://urldefense.com/v3/__ftp:/ftp.ensembl.org/pub/current_mysql/mus_musculus_core_105_39/__;!!ODpDvJZr5w!Sldr6zpX7noerjYVZDfvSGgeSqBmqJqTExtB7QP3DuKZSrjPYARUQNsaxF6aTCDyF8wY$> is severely truncated. This is directly impacting the Core Perl API, which is only able to extract
domain information for about 20 proteins. Specifically, the interpro.txt.gz files for each data set are empty files. I am still comparing other files against release 104 for size

Is this a know issue?


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Marc Chakiachvili

Ensembl Production Project Leader - Genomics Technology Infrastructure

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom
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