<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi David,<div class="">The problem is in the database. It appears that the last analysis in the analysis table, ‘goa_import’ is using the last analysis_id possible, 65535.</div><div class=""><br class=""></div><div class="">You will need to first change the analysis_id of this analysis, I have chosen 9000 but you can put a different value:</div><div class="">UPDATE analysis SET analysis_id = 9000 WHERE analysis_id = 65535; ALTER TABLE analysis AUTO_INCREMENT = 1; UPDATE analysis_description SET analysis_id = 9000 WHERE analysis_id = 65535; UPDATE object_xref SET analysis_id = 9000 WHERE analysis_id = 65535;</div><div class=""><br class=""></div><div class="">If you rerun the import script it should work fine.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Thibaut</div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On 10 Feb 2017, at 13:21, Herzig, David <<a href="mailto:david.herzig@roche.com" class="">david.herzig@roche.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Ensembl Team<div class=""><br class=""></div><div class="">I had an issue with loading the NCBI data (mus musculus) into release 87.</div><div class=""><br class=""></div><div class="">I have used the same process as for version 85 (where is works fine).</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">With version 85 I got the success output:</div><div class=""><div class="">------------------------------------------</div><div class="">46189 genes parsed</div><div class="">118972 transcripts parsed</div><div class="">1205181 exons parsed</div><div class="">23538 non coding genes parsed</div><div class="">0 Curated Genomic genes parsed</div><div class="">35 rRNA genes parsed</div><div class="">425 tRNA genes parsed</div><div class="">------------------------------------------</div><div class="">46189 genes stored</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">With the version 87 I got the following error:</div><div class=""><div class="">-------------------- EXCEPTION --------------------</div><div class="">MSG: Could not retrieve just stored analysis from database.</div><div class="">Possibly incorrect db permissions or missing analysis table</div><div class=""><br class=""></div><div class="">STACK Bio::EnsEMBL::DBSQL::AnalysisAdaptor::store /home/ensembl/release-87/ensembl/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm:425</div><div class="">STACK Bio::EnsEMBL::DBSQL::GeneAdaptor::store /home/ensembl/release-87/ensembl/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm:1264</div><div class="">STACK toplevel /home/ensembl/release-87/ensembl-pipeline/scripts/refseq_import/<a href="http://parse_ncbi_gff3.pl:986/" class="">parse_ncbi_gff3.pl:986</a></div><div class="">Date (localtime) = Fri Feb 10 13:18:53 2017</div><div class="">Ensembl API version = 87</div><div class="">---------------------------------------------------</div></div><div class=""><br class=""></div><div class="">I used the same GFF3 file: ref_GRCm38.p4_top_level.gff3.gz</div><div class="">For loading I used the script: ensembl-pipeline/scripts/refseq_import/<a href="http://parse_ncbi_gff3.pl/" class="">parse_ncbi_gff3.pl</a> (correct one for version 85 and 87 (if there is a difference))</div><div class=""><br class=""></div><div class="">For other species (e.g. r norvegicus) it is working fine.</div><div class=""><br class=""></div><div class="">Any ideas from your side?</div><div class=""><br class=""></div><div class="">regards,</div><div class="">David<br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><font face="tahoma, sans-serif" class="">David Herzig</font></div><div dir="ltr" class=""><font face="tahoma, sans-serif" class="">Scientific Application Developer<br class="">SIAD Solution Delivery & Architecture, pRED Informatics<br class="">Roche Pharma Research and Early Development<br class="">Roche Innovation Center Basel<br class=""><br class="">F. Hoffmann-La Roche Ltd<br class="">Grenzacherstrasse 124<br class="">4070 Basel<br class="">Switzerland<br class="">Phone +41 61 687 31 70</font><p style="font-family:arial;font-size:small" class=""><span lang="DE" style="font-family:imago" class=""><span style="font-family: arial, sans-serif; font-size: 10pt;" class=""><font face="tahoma, sans-serif" class="">Learn more about pRED Informatics at </font></span><a href="http://go.roche.com/pREDi" style="color:rgb(17,85,204);font-family:arial,sans-serif;font-size:13.3333px" target="_blank" class=""><span style="font-size:12.8px" class="">http://go.roche.com/</span><b style="font-size:12.8px" class="">pREDi</b></a><br class=""></span></p></div></div></div></div></div>
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