JSON formatted files missing on the FTP site

We experienced problems generating the content of the JSON dumps for our FTP site, leading to many files missing from the ftp://ftp.ensembl.org/pub/current_json directory. All Ensembl and Ensembl Genomes divisions have been affected, please refer to the attached file for the complete list of affected species.

This will be fixed in upcoming Ensembl release. Meanwhile, please use the JSON files from previous release, which can be found in our archives: http://apr2020.archive.ensembl.org/index.html

Incorrect display ids/labels captured for UCSC external references in mouse

Ensembl identifiers (ENS ids) are displayed as UCSC external references for mouse.

The linking out to UCSC website works correctly.

Truncated GVF and VCF files for some non-vertebrate species

The GVF and VCF files that we make available on the FTP site, which store variation data, were inadvertently truncated for all fungi, metazoa, and protist species. This affects Ensembl Genomes releases 47 and 48.

The affected GVF and VCF files have been fixed and are now available in the respective FTP directories.

Missing RefSeq data in homo_sapiens otherfeatures 101

This will also affect VEP queries using the RefSeq transcript set.

This will be fixed in Ensembl 103.

Missing BioMart datasets for Sorghum bicolor and apple

Wrong figures in the block-size distribution of EPO alignments

Missing GOC scores for polyploids

Polyploid species only have Gene Order Conservation (GOC) scores computed for one of their sub-genomes.

The issue will be fixed in the Ensembl 102. In the meantime, you can retrieve the complete data for the species available in the release 99 from our archives.

No GOC scores for homoeologues

Gene Order Conservation scores have not been computed for homoeologues.

You can retrieve Gene Order Conservation scores for homoeologues listed in the Ensembl 99 from our archives.

Long-read tracks missing for blue whale and vaquita

Long-read transcriptomic data was used to annotate the blue whale and vaquita genomes, but the tracks are not currently available to view.

Tracks will be available in Ensembl 102.

rfam_genes have wrong strand when loaded with ensembl-genomeloader

The https://github.com/Ensembl/ensembl-genomeloader (GL) is used to load non-vertebrate genomes and their annotations from the ENA. It is also used to annotate non-coding genes matching RFAM HMMs, but in some cases the assigned strand is the template strand. This affects some microbial and plant genomes loaded with the GL.

We will remove the rfam_genes from the affected genomes and run the RNA features pipeline instead.

Missing gene trees for vault RNAs

Due to an issue with the biotype group in the core databases, vault RNAs were not correctly parsed by our pipelines.  As we had to reuse the Ensembl 100 data, the gene IDs from the release 100 are used in the current release. Since these vaultRNA genes have disappeared, the pipeline removed the associated gene tree(s) and homologies.

The ncRNA trees are being reused from Ensembl 100, so the archive will still hold the correct data.

GRCh38 – COSMIC insertion coordinates off by +1

For GRCh38 Ensembl 100, Ensembl 101: 2.63 % (256,099 / 9,729,777) COSMIC variation are affected.

http://jan2020.archive.ensembl.org/index.html

For GRCh38, Ensembl 99 contained 10,067,510 COSMIC variation data with 251,353 being insertions.

GRCh37 – COSMIC insertion coordinates off by +1

For GRCh37 Ensembl 100, Ensembl 101: 2.66 % (253,428 / 9,511,409) COSMIC variation is affected.

http://ftp.ensembl.org/pub/grch37/release-99/variation/

This contained 4,478,854 COSMIC mutations, compared to 9,511,409 in the current database.

Gene trees missing ncRNA genes for all 101 species

Due to issues with the ncRNA gene trees pipeline, we were unable to make the required updates this release. We will be reusing the data from Ensembl 100 and, therefore, all ncRNA trees will be missing the newest species.

None.

Links to INSDC protein cross-references do not work for sugar beet

Links to INSDC protein records lead to pages on the ENA site with no records.
For example, the “INSDC protein ID” link for a beet transcript is KMS96696.1, which displays no information.
The “[align]” link next to the accession does not produce results either, for the same reason.

Protein records are available at NCBI, using the pattern “https://www.ncbi.nlm.nih.gov/protein/<ID>”, e.g. https://www.ncbi.nlm.nih.gov/protein/KMS96696.

Incorrect links to SGD website for Saccharomyces cerevisiae

There has been a change in the syntax on how SGD is accessed. The current release displays outdated malformed links that do not work.

You can fix the broken link by changing:
http://db.yeastgenome.org/cgi-bin/locus.pl?locus=###ID###
to:
https://www.yeastgenome.org/locus/###ID###

Incorrect links to KEGG for some plant and microbe species

Links to KEGG for some microbe and plant species are malformed and do not work.

For example, in the General Identifiers page of a beet transcript, the KEGG link for 00052+2.4.1.22 goes to https://www.genome.jp/dbget-bin/www_bget?path:00052+2.4.1.22, rather than https://www.genome.jp/kegg-bin/show_pathway?map00052+2.4.1.22.

The workaround is to manually edit the url to the correct format.

Compara documentation on Ensembl Genomes sites is outdated

The documentation about comparative genomics on Ensembl Genomes sites is outdated. The “Gene Tree (?)” help link on tree pages, such as http://plants.ensembl.org/Arabidopsis_thaliana/Gene/Compara_Tree?g=AT3G52430;r=3:19431095-19434450;t=AT3G52430.1, takes you to http://plants.ensembl.org/Help/View?id=137 and http://plants.ensembl.org/info/genome/compara/homology_method.html , which should be updated to describe the HMM-based classification of sequences. Also the section on dNdS should be removed.

No workaround.

Drosophila melanogaster RNA gene cross-reference links do not work

Rfam and miRBase cross-reference links do not work, because they use the FlyBase ID instead of the RNA gene.

Search for the Rfam or miRBase ID on the respective websites.

Gene trees missing human ncRNA genes

Due to missing RFAM cross-references, a number of human ncRNA genes have not been clustered correctly and are, therefore, missing from gene trees and homology predictions.

No workaround. Use Ensembl release 98 if possible.

Drosophilidae cores imported from the FlyBase have stop codon missing from their CDSs

Drosophilidae cores imported from FlyBase have missing stop codon in their CDS.
No proteins and their domains are affected.

There since since 2017-08.

No workaround. The species core will be reimported from FlyBase in a future release.

Missing data in mouse for 3D Protein Viewer

They are missing from the ‘Protein Summary’ view on our transcript pages.

These data are also used to drive our interactive views showing variants on 3D PDB models. The  ‘3D Protein Model’ views on the variant page and transcript pages currently return no data

Views of novel variants on 3D structures are also missing in the VEP web interface.

GRCh37 REST VEP – Conservation Parameter