| Ensembl Compara FTP file issues | |
| Affects: Ensembl 111, 113, 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. | |
| Workaround: Please use the workarounds specified above, or use the latest version of Ensembl data suitable for your needs. | |
| 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. | |
| Incorrect Wallaby sequence in MAF files for both its LastZ alignments on Ensembl FTP | |
| Affects: Ensembl 100-115 | Fix version: Ensembl 116 |
| Description: Due to a sequence mismatch in cached genome sequence files, MAF files for both LastZ alignments involving Wallaby have some alignment blocks with runs of IUPAC ambiguity code ‘N’ instead of the correct genome sequence. In ‘hsap_grch38.v.neug_meug_1.0.lastz_net.tar.gz’, this affects 7 alignment blocks that cumulatively span over 1 kilobase of the Wallaby genome. In ‘mdom_asm229v1.v.neug_meug_1.0.lastz_net.tar.gz’, it affects 39 alignment blocks spanning just under 30 kilobases of the Wallaby genome. This issue will be fixed in release 116. | |
| Workaround: Affected sequence could be corrected using the sequence data in the Wallaby ‘toplevel’ genome sequence file at: (https://ftp.ensembl.org/pub/release-115/fasta/notamacropus_eugenii/dna/Notamacropus_eugenii.Meug_1.0.dna.toplevel.fa.gz). | |
| Split alignment block lines in pairwise genomic alignment MAF files | |
| Affects: Ensembl 100-115 | Fix version: Ensembl 116 |
| Description: Pairwise genomic alignment MAF files available via the Ensembl FTP site have a comment in their alignment block (“a”) lines, preventing them from being parsed by some bionformatics software. This issue will be fixed in release 116. | |
| Workaround: An example script is available, which may be used to preprocess affected LastZ MAF files so that they can be parsed more easily: https://github.com/Ensembl/ensembl-compara/blob/release/116/scripts/examples/drop_maf_gab_ids.py | |
| Avena sativa cv. OT3098 homoeologues misclassified as paralogues | |
| Affects: Ensembl 109, 110, 111, 112, 113, 114, 115, Ensembl Genomes | Fix version: Ensembl 116 |
| When first made available in Ensembl Plants 109, Avena sativa cultivar OT3098 was loaded into Plants Compara databases without subgenome component information. As a result, homologues that would otherwise be classified as homoeologues will have been annotated as paralogues. | |
| Workaround: No current workaround | |
| Large number of ancient paralogies for Triticum aestivum Kariega in a Wheat cultivar supertree | |
| Affects: Ensembl 113, 114, 115 | Fix versions: Ensembl 116 |
| 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. | |
| Some core statistics missing for human in Biomart 115 | |
| Affects: 115, BioMart | Fix version: Ensembl 116 |
| Some core statistics were not built for human in the latest Biomart build, such as %GC content. These will be reprocessed and produced for the Ensembl 116 release. | |
| Workaround: Use a recent Ensembl archive to export statistics such as %GC content for human. | |
| Mosquito Anopheles melas (Mosquito, CM1001059_A) – sequences not available in Biomart | |
| Affects: 115, Ensembl Genomes, BioMart | Fix version: N/A |
| Gene info for Anopheles melas (Mosquito, CM1001059_A) was included in the latest Biomart build in error. Sequences and other data will not be available via Biomart for this species. Sequence info is accessible via the browser and FTP sites. | |
| Workaround: No current workaround | |
| Missing Gene Ontology pages on Gene-based displays | |
| Affects: Ensembl 114, 115, Ensembl Genomes, BioMart | Fix version: Ensembl 116 |
| 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. | |
| Gene Ontology and Phenotype VEP plugins are non-functional for Plants and Metazoa | |
| Affects: Ensembl 114, 115, Ensembl Genomes, BioMart | Fix version: N/A |
| Description: Due to issues affecting the Phenotypes and Gene Ontology VEP plugins, these not functional for plant and metazoan species. | |
| Workaround: There is currently no workaround. Avoid enabling these plugins to prevent VEP jobs failing. | |
| Missing orthologue projections for Drosophila virilis | |
| Affects: Live Site | Fix version: Ensembl 116 |
| Description: Drosophila virilis assembly and annotation has been updated in e115 but are missing orthologue projections. | |
| Workaround: Users can access this information from the latest archive. Archive of release 59 of EnsemblMetazoa: eg59-metazoa.ensembl.org (May 2024) | |
| Some Vertebrates and Plants LastZ alignments have conflicting reference metadata | |
| Affects: Live Site | Fix version: Ensembl 116 |
| Description: Due to a configuration consistency issue, some LastZ alignments have the same genome configured as both a ‘reference_genome’ and ‘non_reference_genome’. Eleven alignment datasets are affected: eight in Ensembl Plants and three in Ensembl Vertebrates. This issue has resulted in these alignments being dumped to the Ensembl FTP with the reference genome switched. For example, the LastZ alignment represented by ‘oana_mornana1.p.v1.v.mdom_asm229v1.lastz_net.tar.gz’ in release 114 is represented by ‘mdom_asm229v1.v.oana_mornana1.p.v1.lastz_net.tar.gz’ in release 115. Statistics pages of affected pairwise alignments refer to the same genome as both reference and non-reference. Furthermore, Compara Perl API method ‘MethodLinkSpeciesSet::find_pairwise_reference’ may return incorrect results for affected pairwise alignment MLSSes. The affected Ensembl Plants datasets are: Oryza nivara vs Oryza sativa Japonica Group (MLSS ID: 9262) Oryza barthii vs Oryza sativa Japonica Group (MLSS ID: 9269) Oryza punctata vs Oryza sativa Japonica (MLSS ID: 9275) Oryza glumipatula vs Oryza sativa Japonica Group (MLSS ID: 9280) Oryza meridionalis vs Oryza sativa Japonica Group (MLSS ID: 9434) Oryza longistaminata vs Oryza sativa Japonica Group (MLSS ID: 9442) Triticum aestivum vs Oryza sativa Japonica Group (MLSS ID: 9631) Triticum dicoccoides vs Triticum aestivum (MLSS ID: 9811) The affected Ensembl Vertebrates datasets are: Lamprey vs Ciona intestinalis (MLSS ID: 798) Zebrafish vs Japanese medaka (MLSS ID: 1285) Platypus vs Opossum (MLSS ID: 1819) | |
| Workaround: All affected Plants alignments are available in the Ensembl Plants archive of May 2024. Affected Vertebrates alignments can be accessed via the Ensembl release 114 archive. | |
| Three contributing ncRNA trees not used in TreeBeST inference | |
| Affects: Live Site | Fix version: Ensembl 116 |
| Description:
Due to a pipeline synchronisation issue, three ncRNA trees were inferred by TreeBeST before all contributing trees were ready, and as a result those contributing trees were not used when inferring the final gene tree. * The phylogeny inferred by PhyML using a genomic alignment (‘pg_it_phyml’) did not contribute to the inference of the gene tree with stable_id ‘RF00929’. * The phylogeny inferred by FastTree using a genomic alignment (‘ftga_it_nj’) did not contribute to the inference of the gene tree containing Mouse gene Gm22811 (ENSMUSG00000088093). * The phylogeny inferred by RAxML using the S16 model (‘ss_it_s16’) did not contribute to the inference of the gene tree containing Abingdon island giant tortoise gene ENSCABG00000006715. We aim to fix this issue in release 116. | |
| Workaround: For the first two gene trees listed, we recommend accessing their counterparts in the release 114 Ensembl archive.
For Abingdon island giant tortoise gene ENSCABG00000006715, the most recent available alternative gene tree can be accessed from the Ensembl release 96 database or FTP dumps. | |
| Missing GO annotations for 29 plant species | |
| Affects: Live Site | Fix version: Ensembl 1116 |
| Description: Due to a faulty pipeline, GO annotations are missing for 29 plant species as below: Actinidia chinensisAegilops umbellulata Amborella trichopoda Ananas comosus Arabidopsis lyrata Arabis alpina Cajanus cajan Cannabis sativa (female) Capsicum annuum Chara braunii Chenopodium quinoa Citrus clementina Coffea canephora Corchorus capsularis Cucumis melo Cucumis sativus Cynara cardunculus Daucus carota Eragrostis curvula Eucalyptus grandis Eutrema salsugineum Glycine soja Gossypium raimondii Juglans regia Lupinus angustifolius Prunus avium Prunus dulcis Setaria viridis Solanum tuberosum RH89-039-16 | |
| Workaround: Users can access the GO annotations if a species is available in the archives. There is no other workaround at the moment. Archive sites: Archive of release 59 of EnsemblPlants: eg59-plants.ensembl.org (May 2024) Archive of release 56 of EnsemblPlants: eg56-plants.ensembl.org (Feb 2023) Archive of release 52 of EnsemblPlants: eg52-plants.ensembl.org (Dec 2021) Archive of release 49 of EnsemblPlants: eg49-plants.ensembl.org (Dec 2020) Archive of release 45 of EnsemblPlants: eg45-plants.ensembl.org (Sep 2019) | |
| Amino-acid substitution model used with cDNA alignment in 59 Rice cultivar gene trees | |
| Affects: Ensembl 112, 113, 114, 115, Ensembl Genomes | Fix version: Ensembl 116 |
| Due to a software bug, the WAG amino-acid substitution model was used with a cDNA alignment to infer 59 Rice cultivar gene trees in Ensembl Plants release 112. The 59 affected gene trees are listed below. We urge users to exercise caution when interpreting these gene trees or their associated homologies. | |
| Workaround: There is currently no workaround. | |