[ensembl-dev] missing Motif features file for v107 - Homo_sapiens.GRCh38.motif_features.gff.gz

[ilsley at ebi.ac.uk]

Hi Julie,

 

The tabix file for 107 is now available. Please let us know if there are any further issues.

 

Best wishes,

Garth

 

From: Dev <dev-bounces at ensembl.org> On Behalf Of Julie Sullivan
Sent: 26 October 2022 16:45
To: Ensembl developers list <dev at ensembl.org>
Subject: Re: [ensembl-dev] missing Motif features file for v107 - Homo_sapiens.GRCh38.motif_features.gff.gz

 

That would be perfect. :) thanks so much!

 

On Wed, 26 Oct 2022 at 13:18, Garth Ilsley <ilsley at ebi.ac.uk <mailto:ilsley at ebi.ac.uk> > wrote:

Hi Julie,

Indeed, you noticed quickly!

No problem, we can generate a tabix file and add it to the ftp. Would it 
be OK if we aimed for the end of the week?

Garth

On 2022-10-26 12:38, Julie Sullivan wrote:
> I see the file is back in
> https://ftp.ensembl.org/pub/release-107/regulation/homo_sapiens/MotifFeatures/
> 
> Thanks so much!
> 
> Can I be a difficult customer and also ask for the tabix file also?
> (the TBI file).
> 
> "Homo_sapiens.GRCh38.motif_features.gff.gz.tbi"
> 
> Apologies, I should have asked for this file in my first email, but I
> forgot I needed both! Thanks!!
> 
> On Mon, 24 Oct 2022 at 14:16, Julie Sullivan
> <julie.sullivan at gmail.com <mailto:julie.sullivan at gmail.com> > wrote:
> 
>> Hi Garth!
>> 
>> Yes, that's the file I need! I will check back in a week.
>> 
>> Thanks so much!! :)
>> 
>> On Mon, 24 Oct 2022 at 12:34, <ilsley at ebi.ac.uk <mailto:ilsley at ebi.ac.uk> > wrote:
>> 
>>> Dear Julie,
>>> 
>>> Thank you for letting us know. The file
>>> homo_sapiens.GRCh38.motif_features.gff.gz is missing from this
>>> directory, and we plan to restore it for 107. Unfortunately, we
>>> need to regenerate this file, which will take about a week. The
>>> file for 108 is also missing (a known issue), but this one will be
>>> fixed more quickly, hopefully by tomorrow.
>>> 
>>> Is homo_sapiens.GRCh38.motif_features.gff.gz the file you are
>>> looking for? (We aren’t planning on placing the chromosome
>>> specific files there, as these duplicate information from the main
>>> file, and we aim to avoid unnecessary disk storage.)
>>> 
>>> Best wishes,
>>> 
>>> Garth
>>> 
>>> From: Dev <dev-bounces at ensembl.org <mailto:dev-bounces at ensembl.org> > On Behalf Of Julie Sullivan
>>> Sent: 24 October 2022 11:52
>>> To: dev at ensembl.org <mailto:dev at ensembl.org> 
>>> Subject: [ensembl-dev] missing Motif features file for v107 -
>>> Homo_sapiens.GRCh38.motif_features.gff.gz
>>> 
>>> I see all the files in the previous release:
>>> 
>>> 
>> 
> https://ftp.ensembl.org/pub/release-106/regulation/homo_sapiens/MotifFeatures/
>>> 
>>> But I don't see them in version 107:
>>> 
>>> 
>> 
> https://ftp.ensembl.org/pub/release-107/regulation/homo_sapiens/MotifFeatures/
>>> [1]
>>> 
>>> Have they been moved? If not, can they be restored?
>>> 
>>> Thanks!
>>> 
>>> Julie_______________________________________________
>>> Dev mailing list    Dev at ensembl.org <mailto:Dev at ensembl.org> 
>>> Posting guidelines and subscribe/unsubscribe info:
>>> https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
>>> Ensembl Blog: http://www.ensembl.info/
> 
> 
> Links:
> ------
> [1] 
> https://ftp.ensembl.org/pub/release-107/regulation/homo_sapiens/MotifFeatures/
> _______________________________________________
> Dev mailing list    Dev at ensembl.org <mailto:Dev at ensembl.org> 
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