Ensembl 110 – Ensembl Blog

Broken page in human example self-alignment synteny
Affects: Live site, Ensembl 100, Ensembl 101, Ensembl 102, Ensembl 103, Ensembl 104, Ensembl 105, Ensembl 106, Ensembl 107, Ensembl 108, Ensembl 109	Expected fix: Ensembl 111
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: select * from meta where meta_key like '%assembly.default%'; +---------+------------+------------------+-------------------------------+ \| meta_id \| species_id \| meta_key \| meta_value \| +---------+------------+------------------+-------------------------------+ \| 29 \| 1 \| assembly.default \| ASM15428v1_ \| \| 48 \| 2 \| assembly.default \| ASM23678v2_ \| \| 67 \| 3 \| assembly.default \| gacin33v1.0_ \| \| 86 \| 4 \| assembly.default \| ASM100588v2_ \| \| 105 \| 5 \| assembly.default \| ASM18825v1_ \| \| 124 \| 6 \| assembly.default \| ASM103947v1_ \| \| 143 \| 7 \| assembly.default \| ASM17335v1_ \| Therefore, most files will have an extra underscore at the end of the file. Here are some examples for annotation files: Acetivibrio_thermocellus_jcm_21531_gca_000521465.ASM52146v1_.57.gff3.gz Acetivibrio_thermocellus_jcm_21531_gca_000521465.ASM52146v1_.57.gtf.gz
Workaround: Please use Ensembl Bacteria archives.

VEP Missing data for Bacteria
Affects: Live site	Expected fix: Ensembl 111
Description: With our fresh load of newly annotated Bacteria species, we were unable to compute the VEP related dataset for a subset of species: actinomyces_naeslundii_gca_002860635 actinomyces_urogenitalis_gca_002861525 actinotignum_timonense_gca_002860725 aerococcus_christensenii_gca_002861505 bifidobacterium_longum_gca_002861445 brevibacterium_ravenspurgense_gca_002861415 corynebacterium_amycolatum_gca_002861405 corynebacterium_aurimucosum_gca_002861385 corynebacterium_coyleae_gca_002861345 corynebacterium_coyleae_gca_002861365 corynebacterium_riegelii_gca_002861325 corynebacterium_tuscaniense_gca_002884935 fusobacterium_nucleatum_gca_002884895 gardnerella_vaginalis_gca_0028611 gardnerella_vaginalis_gca_002861145 gardnerella_vaginalis_gca_002861885 gardnerella_vaginalis_gca_002861905 gardnerella_vaginalis_gca_002861925 gardnerella_vaginalis_gca_002862005 gardnerella_vaginalis_gca_002884775 kocuria_rhizophila_gca_002861865 lactobacillus_crispatus_gca_002861805 lactobacillus_crispatus_gca_002861815 limosilactobacillus_pontis_gca_002940945 micrococcus_luteus_gca_002863375 micrococcus_luteus_gca_002884675 moraxella_osloensis_gca_002863315 neisseria_perflava_gca_002863305 neisseria_sicca_gca_002863285 oligella_urethralis_gca_002884655 prevotella_buccalis_gca_002884635 rothia_mucilaginosa_gca_002861015 staphylococcus_pettenkoferi_gca_002884615 staphylococcus_sp_umb0328_gca_002940975 streptococcus_macedonicus_gca_002860805 streptococcus_mitis_gca_002860825 streptococcus_mitis_gca_002860865 streptococcus_oralis_subsp_dentisani_gca_002860885 streptococcus_oralis_subsp_dentisani_gca_002860905 streptococcus_parasanguinis_gca_002860845 streptococcus_salivarius_gca_002860765 streptococcus_salivarius_gca_002860785 winkia_neuii_gca_002860625 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: aplysia_californica_gca000002075v2 ascaris_suum brugia_malayi caenorhabditis_brenneri caenorhabditis_briggsae caenorhabditis_japonica caenorhabditis_remanei capitella_teleta centruroides_sculpturatus_gca000671375v2 crassostrea_virginica_gca002022765v4 dermacentor_andersoni_gca023375885v2rs dermatophagoides_pteronyssinus_gca001901225v2 diabrotica_virgifera_gca917563875v2rs haemaphysalis_longicornis_gca013339765v1 hymenolepis_microstoma mercenaria_mercenaria_gca014805675v2 necator_americanus octopus_sinensis_gca006345805v1 onchocerca_volvulus parasteatoda_tepidariorum_gca000365465v3 pomacea_canaliculata_gca003073045v1 pristionchus_pacificus rhipicephalus_sanguineus_gca013339695v1 schistosoma_haematobium_gca000699445v2rs stegodyphus_dumicola_gca010614865v2rs stegodyphus_mimosarum strongyloides_ratti tetranychus_urticae trichinella_spiralis trichuris_muris
Workaround: Please use Ensembl archives.

Missing mitochondria ‘sequence_location’ attribute
Affects: Live site	Expected fix: Ensembl 112
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.
Workaround: Please use Ensembl archives prior to release 109.

Amino-acid substitution model used with cDNA alignment in 11 Wheat cultivar gene trees

Affects: Ensembl 110, Ensembl 111, Ensembl 112

Fix versions: Ensembl 113

Description:

Due to a software bug, the WAG amino-acid substitution model was used with a cDNA alignment to infer 11 Wheat cultivar gene trees in Ensembl Plants release 106.

This issue was fixed in release 113 with the recomputation of Wheat cultivar gene trees.

The 11 affected gene trees are listed below. We urge users to exercise caution when interpreting these gene trees or their associated homologies.

gene_tree_root_id
2006351471
2006351484
2006351490
2006351498
2006351508
2006351525
2006351530
2006529290
2006529300
2006529304
2006529312

Workaround: There is currently no workaround.

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.

Cactus guide tree branch length overestimation
Affects: Ensembl 110, 111, 112, 113, 114, 115, Ensembl Genomes	Fix version: won’t fix
We have discovered that the branch lengths of the guide trees used for several cactus-whole genome alignments were substantially overestimated. This was due to a bug in the component of our BUSCO-based species tree pipeline which estimates the branch lengths based on fourfold degenerate sites. The bug did not affect the topology of the guide tree, and it has effectively been fixed in the latest version of the BUSCO-based species-tree pipeline by changing the software used to produce back-translated codon alignments. This issue is unlikely to have affected the quality of the whole-genome alignments; however, the branch lengths of the guide trees stored in the HAL files of the affected alignments should not be used for downstream analyses, such as inference of conservation scores and constrained elements. The issue should not affect the inference of constrained elements using PhyloP as implemented in the HAL package, as the protocol includes the re-estimation of neutral rates. The issue likely affected the branch lengths stored in the following HAL files: https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Actinopterygii_123-way_20221206.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Aqua-faang_38-way_20220303.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Coleoptera_36-way_20230217.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Crustacea_16-way-20230217.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Lepidoptera_218-way_20230215.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Percomorpha_38-way_202203.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Pigs_27-way_20230220.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Rice_27-way_202208.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Rodent_7-way_20221018.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Wheat_37-way_20221206.hal https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/Aves-59-way_20230814.hal https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/Drosophila-40-way_20230928.hal https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/Fowl-10-way_20240131.hal https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/Mammals-100-way_20230606.hal
Workaround: The branch lengths of the guide tree must be re-estimated before downstream analyses, for example, by using the halPhyloPTrain.py script from the HAL package.

Cactus guide tree branch length overestimation
Affects: Ensembl 110, 111, 112, 113, 114, 115, Ensembl Genomes	Fix version: won’t fix
We have discovered that the branch lengths of the guide trees used for several cactus-whole genome alignments were substantially overestimated. This was due to a bug in the component of our BUSCO-based species tree pipeline which estimates the branch lengths based on fourfold degenerate sites. The bug did not affect the topology of the guide tree, and it has effectively been fixed in the latest version of the BUSCO-based species-tree pipeline by changing the software used to produce back-translated codon alignments. This issue is unlikely to have affected the quality of the whole-genome alignments; however, the branch lengths of the guide trees stored in the HAL files of the affected alignments should not be used for downstream analyses, such as inference of conservation scores and constrained elements. The issue should not affect the inference of constrained elements using PhyloP as implemented in the HAL package, as the protocol includes the re-estimation of neutral rates. The issue likely affected the branch lengths stored in the following HAL files: https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Actinopterygii_123-way_20221206.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Aqua-faang_38-way_20220303.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Coleoptera_36-way_20230217.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Crustacea_16-way-20230217.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Lepidoptera_218-way_20230215.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Percomorpha_38-way_202203.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Pigs_27-way_20230220.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Rice_27-way_202208.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Rodent_7-way_20221018.hal https://ftp.ensembl.org/pub/rapid-release/data_files/multi/hal_files/Wheat_37-way_20221206.hal https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/Aves-59-way_20230814.hal https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/Drosophila-40-way_20230928.hal https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/Fowl-10-way_20240131.hal https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/Mammals-100-way_20230606.hal
Workaround: The branch lengths of the guide tree must be re-estimated before downstream analyses, for example, by using the halPhyloPTrain.py script from the HAL package.

Extraneous default plants homology TSV file
Affects: Ensembl 110	Fix version: won’t fix
An error during Ensembl release 110 resulted in generation of two default plants homology TSV files: a compressed file (‘Compara.110.protein_default.homologies.tsv.gz’) containing the default protein-tree homologies from Ensembl release 110, and an uncompressed file (‘Compara.110.protein_default.homologies.tsv’) containing protein-tree homologies from Ensembl release 109. We advise not to use the uncompressed file ‘Compara.110.protein_default.homologies.tsv’ at https://ftp.ensemblgenomes.ebi.ac.uk/pub/release-57/plants/tsv/ensembl-compara/homologies/ and if you have used these homologies in your analyses, we advise you to interpret them with caution.
Workaround: For the full set of Ensembl release 110 default protein-tree homologies, use the compressed file at: https://ftp.ensemblgenomes.ebi.ac.uk/pub/release-57/plants/tsv/ensembl-compara/homologies/Compara.110.protein_default.homologies.tsv.gz

Broken page in human example self-alignment synteny

Missing TSV dumped files in Ensembl Genomes FTP sites

Inaccurate information provided by the ID History Converter for human and mouse

Broken murinae gene tree view for three supertrees

Alternate loci no longer constructed into full chromosomes within sequence marts

All assembly default values within Ensembl Bacteria end with an underscore

VEP Missing data for Bacteria

Three gene families missing CAFE analysis

Assembly name not matching its source data for metazoan species

Biomart joint query timeout

Inactive homology links for about half of Protostomes species

Missing mitochondria ‘sequence_location’ attribute

Missing data in ontology database

Amino-acid substitution model used with cDNA alignment in 11 Wheat cultivar gene trees