Ensembl 110

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.