Description: On the stats page on the vertebrates site, the example for human self-alignment synteny leads to a broken page.
Workaround:
There is currently no workaround.
Missing TSV dumped files in Ensembl Genomes FTP sites
Affects: Live site, Ensembl 108, Ensembl 109
Expected fix: Ensembl 111
Description: Some TSV dumped FTP files were either missing or partially generated since release 108.
Workaround:
Use FTP files from previous releases.
Inaccurate information provided by the ID History Converter for human and mouse
Affects: Live site, Mirrors, Ensembl 109
Expected fix: Ensembl 111
Description: A bug affects the process feeding data into the ID History Converter, resulting in missing information about stableID-related events, such as retirement or changes in general. This affects human and mouse.
Workaround:
The Gene History page on the website should provide enough information to reconstruct the history of the missing / retired stable IDs. However, the procedure may require navigating through the archived web sites.
Broken murinae gene tree view for three supertrees
Affects: Live site, Ensembl 107, Ensembl 108, Ensembl 109
Expected fix: Ensembl 111
Description: For members trees of three murinae collection supertrees (mur_PTHR24062, mur_PTHR26452, mur_PTHR26453) the strains Gene tree view is broken (e.g. ENSMUSG00000051591)
Workaround:
There is currently no workaround.
Alternate loci no longer constructed into full chromosomes within sequence marts
Affects: Live site
Expected fix: Ensembl 111
Description: Within previous releases we constructed full artificial chromosomes for each alternate loci of GRCH38 for use within the sequence mart. These sequences are being released as scaffolds for this release. No data will be lost and the human related sequences are reduced by 95%.
Workaround:
There is currently no workaround.
All assembly default values within Ensembl Bacteria end with an underscore
Affects: Live site
Expected fix: Ensembl 111
Description: In Ensembl Bacteria, all assembly default values end with an underscore. For example:
Therefore those annotations won’t be available for VEP computation this release.
Workaround:
Please use Ensembl Bacteria archives.
Three gene families missing CAFE analysis
Affects: Live site
Expected fix: Ensembl 111
Description: Three gene trees (ENSGT01100000263574, ENSGT01100000263548, ENSGT01100000263507) will not have a CAFE analysis.
Workaround:
Please use Ensembl archives to retrieve the three gene trees.
Assembly name not matching its source data for metazoan species
Affects: Live site
Expected fix: Ensembl 111
Description: We detected a bug in our code that omitted the existing assembly name from some genomes we imported and failed back to use the GCA accession instead.
Workaround:
There is currently no workaround.
Biomart joint query timeout
Affects: Live site
Expected fix: Ensembl 111
Description: Joint queries on BioMart (i.e. adding additional datasets to an existing query) result in the following error:
There was a problem with the request.
Workaround:
Please create separate BioMart queries.
Inactive homology links for about half of Protostomes species
Affects: Live site
Expected fix: Ensembl 111
Description: For about half of the Protostomes metazoa species the orthology and paralogy links are inactive from the gene summary page (example). The affected species are:
Description: Mitochondrial DNA sequences from 12 species (list species) were mistakenly processed as nuclear DNA sequences which then affected pairwise and multiple genome alignments, and consequently syntenies for vertebrate and metazoan genomes involved.
Workaround:
Please use Ensembl archives.
Missing data in ontology database
Affects: Live site, APIs, Ensembl 109
Expected fix: Ensembl 111
Description: Some data is missing in the ontology database. This will be fixed in the upcoming Ensembl release.