Ensembl Beta was the name of the site which is now the Ensembl Data Platform. Known bugs from before August 2026 are listed below. This list will not be updated further, please see the lists from the latest integrated release.
Known bugs as of August 2026:
| Incorrect paths in the the new FTP structure JSON index | |
| Affects: Live site | Expected fix: within four releases |
| Description: There are incorrect paths in the new FTP structure JSON index – species.new_ftp_structure.json These may be due to incorrect dates for a directory, or due to an error in the file compression pipeline for that species data. Please take note of this when parsing the new FTP structure documentation and folders. | |
| Workaround: No current workaround. | |
| Assembly statistics not being shown for species without chromosome level assembly | |
| Affects: Live site | Expected fix: within two releases |
| Description: Due to a display issue, assembly statistics are not being shown on the species homepage. This affects genomes with assembly levels that are not chromosome level (e.g. scaffold). e.g. https://beta.ensembl.org/species/ff7a2ba3-b5ce-4c24-b452-c0b56fcf16fa | |
| Description: No current workaround. | |
| Incorrect date directories in the new FTP structure for variation and homology data | |
| Affects: FTP | Expected fix: within two releases |
| Description: Due to a processing error, directories of dates for homology and variation data are incorrect for the new FTP structure released in June 2026. These directories have inconsistent dates. For example: The directory containing the homology file for Homo sapiens GRCh38 is incorrectly named: Index of /pub/ensemblorganisms/GCA/000/001/405/29/ensembl/2025_12/homology/2023_10_18 The homology file in this directory is from the 2025_12 update, so the correct path should be : https://ftp.ebi.ac.uk/pub/ensemblorganisms/GCA/000/001/405/29/ensembl/2025_12/homology/2026_04_09/ Please take caution of this when developing with the new FTP structure. | |
| Workaround: No current workaround. | |
| Issue in the automatic superseding of partial releases | |
| Affects: Partial releases | Expected fix: Autumn 2026 |
| Description: A web bug is causing partial releases which are meant to be superseded to persist if these have already been selected or if accessed via a saved URL. In future, when a partial release for a given genome is updated, it will redirect to the latest version of that data, and the previous versions will no longer be available. Data files for all releases remain available from the new Ensembl FTP site – https://ftp.ebi.ac.uk/pub/ensemblorganisms/ | |
| Workaround: The latest versions for partial releases may be selected by searching in the Species Selector | |
| Geneset FTP dumps are missing for select species | |
| Affects: Integrated Release 2025-02, Partial releases | Expected fix: Autumn 2026 |
| Description: Geneset files on the new Ensembl FTP are missing for a selected number of genomes for the following organisms: Ovis aries Strigamia maritima Donax variegatus Yponomeuta padella Drosophila melanogaster Chrysolina graminis Melanotaenia boesemani Bruchidius varius, Xestobium rufovillosum Bruchidius varius, Crassostrea angulata Calliactis parasitica | |
| Workaround: No current workaround | |
| Missing data from Western wild mouse SPRET_EiJ_v3 GCA_921997135.2 in release 2025-02 | |
| Affects: Integrated Release 2025-02 | Expected fix: N/A, may be suppressed |
| Description: Due to missing data, gene visualisations in apps may fail for Western wild mouse SPRET_EiJ_v3 GCA_921997135.2. This will be resolved in a future release and this release version may be suppressed from the site. | |
| Workaround: No current workaround | |
| Norway rat mRatBN7.2 genome in Integrated release 2025-02 is broken | |
| Affects: Integrated Release 2025-02 | Expected fix: N/A, will be suppressed |
| Description: Due to a site error, the Norway rat mRatBN7.2 genome from the 2025-02 Integrated release is not working correctly. This genome will be suppressed from site features to prevent use. There is a more up to date release of Norway Rat mRatBN7.2 from the 2025-07-14 partial release: https://beta.ensembl.org/species/d6c51c59-4863-4c1f-a738-bb838afa868e | |
| Workaround: Please make use of the Norway Rat mRatBN7.2 from the 2025-07-14 partial release: https://beta.ensembl.org/species/d6c51c59-4863-4c1f-a738-bb838afa868e | |
| Zimmermann’s shrew and Spiny mouse loaded incorrectly | |
| Affects: Ensembl beta | Expected fix: within two releases |
| Description: Data for Zimmermann’s shrew (Crocidura zimmermanni) and the Crete spiny mouse (Acomys minous) imported from Genoscope were loaded incorrectly and will contain missing or incorrect data. | |
| Workaround: Please use the older version of the genome: Zimmermann’s shrew (mCroZim1.1) https://beta.ensembl.org/species/183fb547-fe4f-483f-93a6-33e806d8ffb4 | |
| Broken Entity Viewer for some variants due to data mismatch | |
| Affects: Ensembl Beta | Expected fix: within eight beta releases |
| Description: The Entity Viewer page is broken for some variants. Example link: https://beta.ensembl.org/entity-viewer/t2t-chm13/variant:1:53345:rs1295930465?allele=1&view=transcript-consequences Example for expected page: https://beta.ensembl.org/entity-viewer/t2t-chm13/variant:1:53345:rs1295930465?allele=0 This is due to a version mismatch in transcript between core and variation data. | |
| Workaround: No workaround | |
| Genome Browser breaks for genomic patches | |
| Affects: Ensembl Beta | Expected fix: within the next four beta releases |
| Description: The Genome browser page breaks when pointed to a gene that is located in a patch region. Example: Select Human Grch38 and open the genome browser Search for gene ENSG00000285479The discovered gene is on a patch (HG1815_PATCH:312,916-1,046,066) | |
| Workaround: Point Genome Browser to the location of the gene instead of the gene ID: * broken: (https://beta.ensembl.org/genome-browser/grch38?focus=gene:ENSG00000285479) * works: (https://beta.ensembl.org/genome-browser/grch38?location=HG1815_PATCH:997023-1020218) | |
| Links to homologies data in FTP lead to incorrect directories | |
| Affects: Ensembl Beta | Expected fix: within the next two releases |
| Description: In many species the link to the homologies FTP dumps are broken on the site. For example: https://beta.ensembl.org/species/7c4e3698-a2c2-41e2-ac41-38323847c3e1 Leads to a folder which does not exist: https://ftp.ebi.ac.uk/pub/ensemblorganisms/Adineta_vaga/GCA_000513175.1/ Community/homology/2017_02 The files are present under the wrong directory. The correct directory is: https://ftp.ebi.ac.uk/pub/ensemblorganisms/Adineta_vaga/GCA_000513175.1/ community/homology/ Files can be found by going to the homology directory and browsing for the files. This bug should not be present for all new species, but the existing species will not be fixed immediately. | |
| Workaround: Revert to the GCA directory in the FTP link and follow the correct directory paths e.g. https://ftp.ebi.ac.uk/pub/ensemblorganisms/Adineta_vaga/GCA_000513175.1/ | |
| Missing data for Adineta vaga –Rotifer AMS_PRJEB1171_v1 | |
| Affects: Ensembl Beta | Expected fix: Within next two beta releases |
| Description: Due to incomplete loading, data for Adineta vaga –Rotifer AMS_PRJEB1171_v1 is missing from the site. Some data may load but it is likely incomplete. Until this issue is resolved data should be obtained from the main site https://metazoa.ensembl.org/Adineta_vaga/Info/Index | |
| Workaround: No current workaround in beta. Data is available via: https://metazoa.ensembl.org/Adineta_vaga/Info/Index | |
| Ensembl Beta FTP gff3 files are uncompressed | |
| Affects: Ensembl Beta | Expected fix: Existing files – within a few months time; new files – within the next two releases |
| Description: The gff3 files available via https://ftp.ebi.ac.uk/pub/ensemblorganisms/ are uncompressed due to a production system bug. Current uncompressed files will be fixed when the FTP structure is revised. New files generated within upcoming releases will be compressed. | |
| Workaround: No current workaround. | |
Previous bugs which have been resolved (last updated August 2026):
If you find that a bug in the list below is still occurring, please contact the Ensembl Helpdesk
| RESOLVED: Error in variant consequences for variants attached to IWGSC Wheat 2025_02 | |
| Affects: IWGSC Wheat 2025_02 | Expected fix: within two releases |
| Description: Due to a pipeline error, consequences for all of the variants in the attached variation dataset are “intergenic variant”. The pipeline has been corrected and the variants will be re-annotated with the correct consequence in an upcoming release. | |
| Workaround: No current workaround. | |
| RESOLVED: BLAST databases not available for 69 genomes | |
| Affects: Partial releases | Expected fix: within two releases |
| Description: Due to errors in processing, BLAST database files are unavailable for 69 genomes. BLAST jobs submitted against these genomes will fail to start. The list of affected genomes is available below. | |
| Workaround: No current workaround. | |
| RESOLVED: Variant track view not displaying when zoomed in | |
| Affects: Ensembl Beta | Expected fix: Within next two beta releases |
| Description: Variation tracks turn blank when zoomed into a gene via the genome browser app. This has been observed in T2T-CHM13. | |
| Workaround: No current workaround. | |
| RESOLVED: Norway Rat – Rattus norvegicus – mRatBN7.2 currently unavailable | |
| Affects: Ensembl Beta | Expected fix: within the next two releases |
| Description: The Rattus norvegicus mRatBN7.2 genome on beta.ensembl.org is currently unavailable due a fault in the release process for this species. | |
| Workaround: No current workaround. Please make use of other Rattus norvegicus genomes where applicable to your needs. | |
| RESOLVED: Outdated regulatory annotation tracks for human and mouse | |
| Affects: Ensembl Beta | Expected fix: within the next two releases |
| Description: The regulatory annotation tracks for human and mouse are showing data from an older release (March 2023) than the release version of Ensembl beta. The counts shown for regulatory features match the latest release, and hence these counts are incorrect. | |
| Workaround: No current workaround on beta. Up to date regulation tracks are available via ensembl.org and ensemblgenomes.org/ | |
| RESOLVED: Incorrect counts on popular species display | |
| Affects: Ensembl Beta | Expected fix: within next two releases |
| Description: The counts displayed within the black bubbles on the popular species grid of the https://beta.ensembl.org/species-selector page may not accurately represent the total count of genomes available for that species available in https://beta.ensembl.org | |
| Workaround: No current workaround. Please use the species search bar to search across all species in https://beta.ensembl.org | |
| RESOLVED: Incorrect URLs from annotation provider links | |
| Affects: Ensembl Beta | Expected fix: Within the next two releases |
| Description: Annotation provider links on the species homepage are formed of broken URLs.Example: Human T2T-CHM13v2.0 species homepageFor more information on our gene annotation process, please see Ensembl Help and documentation | |
| Workaround: No workaround | |