| Ensembl Compara FTP file issues | |
| Affects: Ensembl 111, 112, 113, 114, 115 | Fix version: N/A |
| Description: Tunicate alignment file ‘cint_kh.v.csav_csav2.0.lastz_net.tar.gz’ is absent from the Vertebrates FTP site in releases 111, 113 and 115. It can be accessed from the FTP site of the most recent even-numbered Ensembl release. Amniota constrained elements file ‘gerp_constrained_elements.catagonus_wagneri.bb’ is missing from the Ensembl Vertebrates FTP site releases 111-113. Constrained elements for this species can be found at: https://ftp.ensembl.org/pub/release-114/bed/ensembl-compara/60_amniotes.gerp_constrained_element/ In Ensembl releases 112-114, genome-specific homology TSV files for 5 genomes in collection cores were not stored within a directory named for the collection core database housing data for that genome. Instead, each affected homology TSV was written to a directory named for the given genome, and placed alongside other genome directories. | |
| Workaround: Please use the workarounds specified above, or use the latest version of Ensembl data suitable for your needs. | |
Sheep Texel FTP data | |
| Affects: Live site, 113 FTP | Expected fix: Ensembl 114, Ensembl 115 |
| Description: There is an issue affecting the species page for sheep Texel where links to the FTP data are incorrectly linking to files for Ovis_aries_rambouillet. Sheep Texel files are currently unavailable on the 113 FTP site. We are looking into the issues with sheep FTP files on 113. We expect fixes to both species pages and FTP file bases in our upcoming releases. | |
| Workaround: Please use the 112 archive page for Texel to access FTP files. | |
| LastZ MAF archives of a few wheat cultivars missing from Ensembl Plants FTP site | |
| Affects: Ensembl 106-115 | Fix version: Ensembl 116 |
| In the set of Ensembl releases from 106 to 115 (inclusive), a small number of Wheat cultivar LastZ MAF files have been missing due to clashing file names. MAF archive files for LastZ alignments of T. aestivum Chinese Spring respectively against wheat cultivars Landmark and Lancer both had name ‘taes_iwgsc.v.tala_pgsbv2.1.lastz_net.tar.gz’. As a result, T. aestivum Lancer MAF archives were missing since release 111, and prior to that release, no LastZ MAF archives were present for either of these two genomes. MAF archive files for LastZ alignments of T. aestivum Chinese Spring respectively against wheat cultivars Mace and Mattis both had name ‘taes_iwgsc.v.tama_pgsbv2.1.lastz_net.tar.gz’. As a result, T. aestivum Mattis MAF archives were missing since release 113. | |
| Workaround: MAF files will be regenerated in release 116 for all four affected LastZ alignment datasets. | |
Missing Gene Ontology pages on Gene-based displays | |
| Affects: Live site, Ensembl Genomes, BioMart | Expected fix: Ensembl 115 |
| Description: Gene Ontology (GO) related pages on the Gene-based display tabs are unavailable. The following pages are unavailable on the live site: GO: Cellular component GO: Biological Process GO: Molecular function Please make use of the Ensembl archive sites to access these gene-based display pages. This also affects Ensembl Genome sites and Biomart, please use the latest archive where possible. | |
| Workaround: Please use the latest Ensembl archive site to access these pages. | |
Getting the wrong species alias for Ovis aries (Sheep) Texel | |
| Affects: Live site | Expected fix: Ensembl 114 |
| Description: In ensembl-vep we expect to get the species latin name using the aliases through the Bio::EnsEMBL::Registry::get_alias() function – https://github.com/Ensembl/ensembl-vep/blob/eb55c2293637c34a0f80dfca88c439e77dd52def/modules/Bio/EnsEMBL/VEP/BaseRunner.pm#L143 It is an old code but intuitively the idea is to able to run VEP using “–species sheep”. The scientific name which should be returned as ovis_aries would then be used to get proper database or cache files. If “–species ovis_aries” is used (which is the case for web VEP) get_alias() should return ovis_aries.In e113, using “–species ovis_aries” is returning “ovis_aries_rambouillet”.Affected VEP areas: | |
| Workaround: Please use data from the Ensembl 112 archive. | |
Incorrect source project label for regulation data in cow | |
| Affects: Live site | Expected fix: Ensembl 114 |
| Description: Source data for cow e.g. [https://rc.ensembl.org/Bos_taurus/Regulation/Evidence?db=funcgen;fdb=funcgen;r=9:96621727-96624008;rf=ENSBTAR9_93FCH2] incorrectly lists ENCODE instead of FAANG. | |
| Workaround: There is currently no workaround, however, this bug is not known to affect downstream analyses. | |
“Genotype: frequency (count)” does not match “Allele: frequency (count)” | |
| Affects: Live site | Expected fix: Ensembl 114 |
| Description: We observed the mismatch allele and genotype frequencies for a population on the variant genotype page. Allele frequency looks good however genotype frequency does not match with the allele frequency. | |
| Workaround: The table for sample genotypes also looks okay. | |
Motif widget only shows human data | |
| Affects: Live Site | Expected fix: Ensembl 114 |
| Description: The Motif widget only shows human data, even if it is accessed from other species’ pages. | |
| Workaround: There is currently no workaround. | |
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| Affects: Live site, Ensembl 100, Ensembl 101, Ensembl 102, Ensembl 103, Ensembl 104, Ensembl 105, Ensembl 106, Ensembl 107, Ensembl 108, Ensembl 109, Ensembl 110, Ensembl 111, Ensembl 112 | Expected fix: Ensembl 114 |
| Description: An alignment artefact has been detected in ncRNA homology and gene-tree alignments (e.g. [ENSBTAG00000045380|http://may2024.archive.ensembl.org/Bos_taurus/Gene/Compara_Tree?collapse=none;db=core;g=ENSBTAG00000045380]). In affected cases, the alignment sequence is generated from an unflanked ncRNA sequence and a CIGAR line of a flanked genomic alignment. This may result in the original sequence being followed by a sequence of ‘N’ ambiguity symbols, or in some cases, in an alignment composed entirely of ‘N’ ambiguity symbols. As of Ensembl 112, this issue affected 193,110 ncRNA genes and 31,987 trees. Ensembl 113 saw us take our first steps to mitigate this issue, as a result it affects 75,360 genes and 8,805 trees in that release. | |
| Workaround: There is currently no workaround. | |
Age-of-Base file lacks data for chromosomes 1 to 7 | |
| Affects: Live site, Ensembl 111, Ensembl 112 | Expected fix: Ensembl 114 |
| Description: Due to a pipeline synchronisation issue, the Age-of-Base data file generated in Ensembl release 111 lacks data for chromosomes 1 through 7. | |
| Workaround: For chromosomes 1-7, we recommend to access the Age-of-Base resource via the Ensembl 110 archive site. | |
C-terminal ‘X’ missing from some Compara protein member sequences | |
| Affects: Live site, Ensembl 112 | Expected fix: Ensembl 114 |
| Description: For some protein sequences whose CDS ends with a partial codon (e.g. ENSAPOG00000012172), the C-terminal ‘X’ which can be found in the translation in the core database was found to be absent from the sequence of the corresponding member in the Compara database. As of release 113, this issue affects 1,928 proteins in Vertebrates, 160 in Plants, 60 in Pan Compara, and 3 in Metazoa. We aim to correct 95% of affected protein sequences in Ensembl release 114. The remaining affected protein sequences — in Aegilops_tauschii, Oryza brachyantha, Oryza rufipogon and Triticum_dicoccoides — will be fixed when we next update the protein trees for these species. | |
| Workaround: There is currently no workaround. | |
Large number of ancient paralogies for Triticum aestivum Kariega in a Wheat cultivar supertree | |
| Affects: Live site | Expected fix: Ensembl 116 |
| Description: During preparation of Wheat cultivar protein trees for Ensembl release 113, it became apparent that supertree PTHR11439_SF127 has approximately 40,000 genes in Triticum aestivum cultivar Kariega. Generation of the 261 million ancient paralogies between these genes took two weeks, and it would not have been possible to include them in Ensembl Plants 113 without delaying the release. We aim to mitigate this issue in Ensembl Plants release 116, by making the proteins in the Wheat cultivars PTHR11439_SF127 supertree available via the gene families web view. | |
| Workaround: A cross-section of relevant ancient paralogies was loaded during production, involving genes in other subtrees of the Wheat cultivars PTHR11439 supertree, which have stable IDs TraesKAR6A01G0279700, TraesKAR7B01G0056390, TraesKAR7B01G0463280 and TraesKAR1D01G0304830. Due to the large number of paralogies involved, these may be slow to load on the Ensembl Plants website, though it is possible to access them via the Ensembl REST API and Compara Perl API. | |
Issues affecting Cactus alignments | |
| Affects: Live site | Expected fix: Timeline currently unknown |
| Description: Long loading times were observed during testing of several Cactus alignments, so the following measures were adopted to mitigate this. Cactus alignments accessed via the API are filtered to remove shorter alignment blocks. This may cause Cactus alignments to appear sparse when viewed at larger scales, so please view Cactus alignments at the smallest scale that allows for viewing the feature(s) of interest. In the image alignment view, gene tracks are switched off by default for all but the current genome. In addition, alternative gene model tracks are switched off by default in the 16-Wheat Cactus alignment. Please switch on gene tracks as needed using the configuration bar at the top of the alignment view. Because the 16-Wheat Cactus alignment was loaded separately for each component (A, B and D) and non-polyploid genomes were included in alignments for all three components, particularly long loading times were observed when viewing this alignment from non-polyploid genomes, so the Wheat Cactus has been removed from the alignment selection dropdown menu for non-polyploid genomes on the Ensembl Plants website. Their alignments can be viewed from the perspective of polyploid genomes. In an issue unrelated to loading time, the 16-Wheat Cactus alignment has in effect 3 species trees — one per genome component — so this alignment has a single dummy species tree to facilitate access to the alignment, which is hidden from view on the Ensembl Plants website. The full Wheat Cactus species tree can be accessed via the Compara API or from the Plants species-tree location on the Ensembl Genomes FTP site: http://ftp.ensemblgenomes.org/pub/release-60/plants/compara/species_trees/16_wheat_Cactus_default.nh We aim to address these issues more comprehensively in Ensembl 114 and subsequent releases. | |
| Workaround: There is currently no workaround. | |
Incorrect allele and genotype frequency in Watkins Collection | |
| Affects: Ensembl Plants 60 | Expected fix: Ensembl Plants 61 |
| Description: Approximately 1% of the wheat variants that were loaded from the Watkins Collection has an incorrect allele and genotype frequency. This results from sample overlap between the Axiom and the Watkins Collection. | |
| Workaround: There is currently no workaround. | |