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By using the site you are agreeing to this as outlined in our <a href="https://www.ebi.ac.uk/data-protection/ensembl/privacy-notice" rel=""> Privacy Policy </a> </div> </aside> </div> </div> </div> <div id="primary" class="content-area col-lg-9" itemprop="mainContentOfPage"> <div itemscope itemtype="http://schema.org/Article" id="content" class="site-content" role="main"> <article id="post-13907" class="post-13907 page type-page status-publish hentry"> <header class="entry-header"> <h1 class="entry-title" itemprop="name">Ensembl 106</h1> </header> <div class="entry-content" itemprop="articleBody"> <table class="table table-bordered"> <thead class="thead-light"> <tr> <th colspan="2">Known bugs in Ensembl</th> </tr> </thead> <tbody id="known_bugs_table"> <tr> <td colspan="2"> <h3>Data dumps for B. tabaci Uganda-1 directs to 404 error</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site, Mirrors</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 106</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>Download Fasta/Genes/GFF3 directs to 404. The reason this happens linked to naming change causing an issue for this species. Original name changed from sweetpotug to uganda-1.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>Navigate directly to the Ensembl Genomes FTP site: http://ftp.ensemblgenomes.org/pub/metazoa/release-53/</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Alignment of External Feature – unable to retrieve sequence from Uniprot/SwissProt</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site, Mirrors</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 102, Ensembl 103, Ensembl 104, Ensembl 105, Ensembl 106, Ensembl 107</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>Alignment of External Feature for ENST00000216181.11 MYH9-201 page is unable to retrieve the sequence from UniProt/SWISSProt.<p></p> <p>This is the link to the page ([https://dec2021.archive.ensembl.org/Homo_sapiens/Transcript/Similarity/Align?db=core;extdb=uniprot/swissprot;g=ENSG00000100345;r=22:36281280-36388010;sequence=P35579.240;t=ENST00000216181])</p> <p>The URL incorrectly contains the UniProt entry and its version (P35579.240), and this leads to the problem.</p> </td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>Manually remove the version number from the UniProt entry in the URL.<p></p> <p>E.g https://dec2021.archive.ensembl.org/Homo_sapiens/Transcript/Similarity/Align?db=core;extdb=uniprot/swissprot;g=ENSG00000100345;r=22:36281280-36388010;sequence=P35579.240;t=ENST00000216181</p> <p>becomes</p> <p>https://dec2021.archive.ensembl.org/Homo_sapiens/Transcript/Similarity/Align?db=core;extdb=uniprot/swissprot;g=ENSG00000100345;r=22:36281280-36388010;sequence=P35579;t=ENST00000216181</p> </td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Missing Protein Features for Beta Vulgaris in Plants BioMart</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 106</td> </tr> <tr> <td colspan="2"><strong>Description:</strong>BetaVulgaris species is missing some Protein Features in Biomart, data will be recovered and presented in our next release.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>Use archived version from previous release..</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Duplicate species in protists and fungi</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 105, Ensembl 106, Ensembl 107</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>hyaloperonospora_arabidopsidis (version 2) was accidentally loaded into fungi release 105 and incorporated into fungal compara. While some communities think of this as a fungus (e.g. FungiDB where we got the species from), in Ensembl it has traditionally been a protist.<p></p> <p>So we already have an older version in protists (version 1). To keep with how we have thought about this in Ensembl, it may be sensible to only have this species in protists.</p> <p>Data dumps, compara, search indices etc has made this really complex. Temporarily, the species has gone off Ensembl Protists. This will be reinstated in release 107. Until then, please use our archive sites for this data. Meanwhile, there is a newer version in Ensembl Fungi. We will remove this in release 108. After that point, this species will go back to existing only in Ensembl Protists.</p> </td> </tr> <tr> <td colspan="2"><strong>Workaround:</strong> No workaround.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Missing alias in meta table for Rat</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 105, Ensembl 106, Ensembl 107</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>The Rat DB for 105 is missing aliases for species name in the ‘meta’ table, compared to Release 104.<p></p> <p>Specifically, the record with meta.meta_key = ‘species.alias’ are the missing ones.</p> <p>As a result, the Perl API (Registry) can query the DB using the “species.production_name” only, which is “Rattus_norvegicus”.<br>Also, this must be an exact string match.</p> <p>Although not blocking an issue, it was customary to use aliases – e.g. “Rat”, “Rattus norvegicus” – to query the DB.</p> </td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>To identify the species, the string specified in meta table, having meta_key =  “species.production_name”, must be used.<p></p> <p>In the rat case, the string is “rattus_norvegicus” (without quotes).</p> </td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>UniProt Variants track out of date</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 106</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>Variant records in our human GRCh38 database have been updated with UniProt links from 2021/10/08 but this information has not been used to update the tracks seen in region views. The track shows variants present only in 2021/06/11, as seen in our previous release.<p></p> <p>The track will be updated in our next release, 107</p> </td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>No workaround.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Broken Cactus HAL alignment on the web for Brugia malayi</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site, Mirrors</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 105, Ensembl 106, Ensembl 107</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>For {_}Brugia malayi{_}, the Cactus HAL alignment in the *”Example region”* throws the following error:<br>{code:java}AJAX error – Runtime Error in component “EnsEMBL::Web::Component::Location::Compara_AlignSliceBottom [content]”<p></p> <p>The issue does not affect the whole _Brugia malayi_ genome. There are regions in _Brugia malayi_ for which the display works.</p> </td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>No workaround</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Missing Gene names attributes in Zea_mays GTF/GFF Files</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 104, Ensembl 105, Ensembl 106</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>Annotation attribute  gene_name  are missing  for Zea_mays GTF/GFF3 Files.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>Previous versions Release 103 /50 of maize contains gene name attributes in gtf/gff3 .<br>Alternatively, the ID History convertor can be used to map stable ids from current release to previous release (<a class="external-link" href="http://plants.ensembl.org/Oryza_sativa/Tools/IDMapper)" target="_blank" rel="nofollow noopener">http://plants.ensembl.org/Oryza_sativa/Tools/IDMapper)</a> to get the gene names.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Arabidopsis names have ” in their symbol</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 104, Ensembl 105, Ensembl 106</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>We’ve discovered a small number of genes in Arabidopsis with ” in their symbols:<p></p> <p>Gene: B”BETA (AT5G28850)[https://plants.ensembl.org/Arabidopsis_thaliana/Gene/Summary?g=AT5G28850;r=5:10876788-10881485;t=AT5G28850.1;db=core]</p> <p>Gene: U2B” (AT2G30260) [https://plants.ensembl.org/Arabidopsis_thaliana/Gene/Summary?g=AT2G30260;r=2:12905345-12907665;t=AT2G30260.1;db=core]</p> <p>which causes issues with searching for these gene symbols.</p> </td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>No workaround.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Missing Pig microarray data</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 106</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>New regulatory tracks were added to sus scrofa in Release 106. However, microarray probeset information (oligo probes) was not added in the process. This means that microarray and oligo probe mapping is missing from Release 106 in the genome browser and BioMart.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>Microarray and oligo probe information can be accessed using the archive sites or the 105 release of BioMart.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Corrupted conservation scores in Compara MySQL dump file</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 106</td> </tr> <tr> <td colspan="2"><strong><strong>Description: </strong></strong>During the Ensembl Compara 106 production process, data corruption occurred in the MySQL BLOB columns used to store the ‘expected_score’ and ‘diff_score’ in the Compara ‘conservation_score’ table.<p></p> <p>This corruption was identified during the course of Compara MySQL data dumps, and the Compara release database ‘conservation_score’ table was restored from a backup containing the correct data.</p> <p>However, the fix was not applied to the conservation-score MySQL dump file at the following location:</p> <p>https://ftp.ensembl.org/pub/release-106/mysql/ensembl_compara_106/conservation_score.txt.gz</p> <p>As a result, while a query against ‘ensembl_compara_106’ on the Ensembl public MySQL server will return correct conservation-score data, the same query applied to a locally installed ‘ensembl_compara_106’ database may encounter an error or return invalid conservation-score data.</p> <p>Because the issue was fixed in the ‘ensembl_compara_106’ release database, it will not affect Ensembl Compara 107 or later.</p> </td> </tr> <tr> <td colspan="2"><strong><strong>Workaround: </strong></strong>The Ensembl 105 ‘conservation_score’ MySQL dump file  (http://ftp.ensembl.org/pub/release-105/mysql/ensembl_compara_105/conservation_score.txt.gz) can be used as a drop-in replacement for the 106 version for the species sets ‘amniotes’, ‘mammals’, ‘pig_breeds’ and ‘sauropsids’, because there were no changes in the conservation-score data for these species sets between Ensembl 105 and 106.<p></p> <p>Unfortunately, there is no equivalent workaround for the ‘fish’ species set, because its alignment and associated conservation scores were updated in Ensembl 106. It is safe to have the Ensembl 105 fish conservation scores in a Compara 106 database, as their database IDs don’t overlap with those of the Ensembl 106 fish alignments. But they will be taking up space in the ‘conservation_score’ table. If this is a problem, the 105 fish conservation scores can be removed by deleting rows from the ‘conservation_score’ table where they have a ‘genomic_align_block_id’ between 19720000000001 and 19729999999999 (inclusive).</p> </td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Malfunctioning search for Hyaloperonospora arabidopsidis in 106</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 106, Ensembl 107</td> </tr> <tr> <td colspan="2"> <p><strong><strong>Description: </strong></strong>Users may find that doing a search for <em>Hyaloperonospora arabidopsidis</em> on our sites returns it as a Fungi. However, please note that this species has now being placed back in Ensembl Protists. The link to this species in Ensembl Protists is: (http://protists.ensembl.org/Hyaloperonospora_arabidopsidis)</p> </td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>The link to this species in Ensembl Protists is: (http://protists.ensembl.org/Hyaloperonospora_arabidopsidis)</td> </tr> </tbody> </table> <p></p> </div> </article> </div> <footer class="site-info" itemscope itemtype="http://schema.org/WPFooter"> <a href="http://wordpress.org/" title="Semantic Personal Publishing Platform">Proudly powered by WordPress</a>. 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