<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi David,<div class="">Unfortunately NCBI does not always write their GFF the same way for all their species so a fix for a species could bring a bug for another species.</div><div class="">Could you please tell us which branch/last commit for your ensembl-pipeline and ensembl-io repositories?</div><div class=""><br class=""></div><div class="">Thanks</div><div class="">Thibaut</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 20 Sep 2016, at 13:26, Daniel Barrell <<a href="mailto:daniel.barrell@eaglegenomics.com" class="">daniel.barrell@eaglegenomics.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Odd, D. rerio should have also failed then if my suspicions were correct. Guess there must be something else going on here.<div class=""><br class=""></div><div class="">Dan</div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div style="font-size:12.8px" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" style="color:rgb(136,136,136)" class=""><font color="#888888" face="ITC Avant Garde Std Bk" class=""><b class=""><br class=""></b></font></div><div dir="ltr" style="color:rgb(136,136,136)" class=""><font color="#888888" face="ITC Avant Garde Std Bk" class=""><b class=""><br class=""></b></font></div><div dir="ltr" style="color:rgb(136,136,136)" class=""><font color="#888888" face="ITC Avant Garde Std Bk" class=""><b class=""><br class=""></b></font></div><div dir="ltr" style="color:rgb(136,136,136)" class=""><font color="#888888" face="ITC Avant Garde Std Bk" class=""><b class=""><br class=""></b></font></div><div dir="ltr" class=""><font color="#888888" face="ITC Avant Garde Std Bk" style="color:rgb(136,136,136)" class=""><b class="">Daniel Barrell</b></font><br class=""><div style="color:rgb(136,136,136)" class=""><small class=""><font face="ITC Avant Garde Std Bk" class="">Platform Specialist<br class=""></font></small><span id="cid:part1.01080901.03080600@eaglegenomics.com"><E_Email_Sig.jpg></span></div><div style="color:rgb(136,136,136)" class=""><b style="font-size:12.8px;color:rgb(102,102,102)" class="">eagle</b><span style="font-size:12.8px;color:rgb(102,102,102)" class="">discover Best of Show Winner at Bio-IT World 2016</span></div><div class=""><font color="#666666" class=""><br class=""></font><small style="color:rgb(136,136,136)" class=""><font face="ITC Avant Garde Std Bk" class=""><b class="">Eagle Genomics Ltd</b><br class="">T: <a value="+441223654481" style="color:rgb(17,85,204)" class="">+44 (0)1223 654481</a><br class=""><a href="http://www.eaglegenomics.com/" style="color:rgb(17,85,204)" target="_blank" class="">http://www.eaglegenomics.com</a> <br class=""><small class="">Disclaimer: <a href="http://www.eaglegenomics.com/about/privacy-statement/" style="color:rgb(17,85,204)" target="_blank" class="">http://www.eaglegenomics.com/about/privacy-statement/</a> </small></font></small><br class=""></div><div style="color:rgb(136,136,136)" class=""><small class=""><font face="ITC Avant Garde Std Bk" class=""><small class=""><br class=""></small></font></small></div><div class=""><div style="font-family:Helvetica;font-size:12px;word-wrap:break-word" class=""><a href="https://youtu.be/rPdgFTo0FZM" style="color:rgb(17,85,204);font-family:arial,sans-serif;font-size:12.8px" target="_blank" class="">https://youtu.be/rPdgFTo0FZM</a><span style="font-family:arial,sans-serif;font-size:12.8px" class=""> </span><br class=""></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br class=""><div class="gmail_quote">On 20 September 2016 at 12:14, Herzig, David <span dir="ltr" class=""><<a href="mailto:david.herzig@roche.com" target="_blank" class="">david.herzig@roche.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Hi Daniel<div class=""><br class=""></div><div class="">Thx for the feedback.</div><div class=""><br class=""></div><div class="">I was able to use it for:</div><div class="">- d rerio</div><div class="">- m musculus</div><div class="">- r norvegicus</div><div class=""><br class=""></div><div class="">regards,</div><div class="">David</div><div class=""><br class=""></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Sep 20, 2016 at 1:11 PM, Daniel Barrell <span dir="ltr" class=""><<a href="mailto:daniel.barrell@eaglegenomics.com" target="_blank" class="">daniel.barrell@eaglegenomics.<wbr class="">com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Hi David,<div class=""><br class=""></div><div class="">Line <span style="font-size:12.8px" class="">1184334 is the last line of the GFF3 file and contains '###'. There used to be code to ignore lines like these:</span></div><div class=""><br class=""></div><div class=""><table style="width:1835.56px;table-layout:fixed;color:rgb(51,51,51);font-family:-apple-system,blinkmacsystemfont,"segoe ui",roboto,helvetica,arial,sans-serif,"apple color emoji","segoe ui emoji","segoe ui symbol";font-size:14px;line-height:21px" class=""><tbody class=""><tr class=""></tr><tr class=""><td style="padding:0px 10px;line-height:20px;vertical-align:top;background-color:rgb(234,255,234)" class=""><span style="overflow:visible;font-family:consolas,"liberation mono",menlo,courier,monospace;font-size:12px;word-wrap:break-word;white-space:pre-wrap" class="">+ <span style="color:rgb(167,29,93)" class="">next</span> <span style="color:rgb(167,29,93)" class="">if</span> <span class="">$line</span> =~ <span style="color:rgb(24,54,145)" class=""><span class="">/</span>^#<span class="">/</span></span>;</span></td></tr><tr class=""><td style="padding: 0px 10px; width: 43.3333px; min-width: 50px; font-family: consolas, 'liberation mono', menlo, courier, monospace; font-size: 12px; line-height: 20px; text-align: right; white-space: nowrap; vertical-align: top; border-style: solid; border-color: rgb(238, 238, 238); border-width: 0px 1px 0px 0px; background-color: rgb(250, 250, 250);" class=""></td></tr></tbody></table></div><div class=""><br class=""></div><div class="">When the script moved to use ensembl-io I think it may have lost this check, however I would expect ensembl-io to handle the '###'. Which species files worked? I checked on NCBI and other species (e.g. horse) would also fail in the same way.</div><div class=""><br class=""></div><div class="">Dan</div><div class=""><br class=""></div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div data-smartmail="gmail_signature" class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div style="font-size:12.8px" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" style="color:rgb(136,136,136)" class=""><font color="#888888" face="ITC Avant Garde Std Bk" class=""><b class=""><br class=""></b></font></div><div dir="ltr" style="color:rgb(136,136,136)" class=""><font color="#888888" face="ITC Avant Garde Std Bk" class=""><b class=""><br class=""></b></font></div><div dir="ltr" style="color:rgb(136,136,136)" class=""><font color="#888888" face="ITC Avant Garde Std Bk" class=""><b class=""><br class=""></b></font></div><div dir="ltr" style="color:rgb(136,136,136)" class=""><font color="#888888" face="ITC Avant Garde Std Bk" class=""><b class=""><br class=""></b></font></div><div dir="ltr" class=""><font color="#888888" face="ITC Avant Garde Std Bk" style="color:rgb(136,136,136)" class=""><b class="">Daniel Barrell</b></font><br class=""><div style="color:rgb(136,136,136)" class=""><small class=""><font face="ITC Avant Garde Std Bk" class="">Platform Specialist<br class=""></font></small><span id="cid:part1.01080901.03080600@eaglegenomics.com"><E_Email_Sig.jpg></span></div><div style="color:rgb(136,136,136)" class=""><b style="font-size:12.8px;color:rgb(102,102,102)" class="">eagle</b><span style="font-size:12.8px;color:rgb(102,102,102)" class="">discover Best of Show Winner at Bio-IT World 2016</span></div><div class=""><font color="#666666" class=""><br class=""></font><small style="color:rgb(136,136,136)" class=""><font face="ITC Avant Garde Std Bk" class=""><b class="">Eagle Genomics Ltd</b><br class="">T: <a value="+441223654481" style="color:rgb(17,85,204)" class="">+44 (0)1223 654481</a><br class=""><a href="http://www.eaglegenomics.com/" style="color:rgb(17,85,204)" target="_blank" class="">http://www.eaglegenomics.com</a> <br class=""><small class="">Disclaimer: <a href="http://www.eaglegenomics.com/about/privacy-statement/" style="color:rgb(17,85,204)" target="_blank" class="">http://www.eaglege<wbr class="">nomics.com/about/privacy-<wbr class="">statement/</a> </small></font></small><br class=""></div><div style="color:rgb(136,136,136)" class=""><small class=""><font face="ITC Avant Garde Std Bk" class=""><small class=""><br class=""></small></font></small></div><div class=""><div style="font-family:Helvetica;font-size:12px;word-wrap:break-word" class=""><a href="https://youtu.be/rPdgFTo0FZM" style="color:rgb(17,85,204);font-family:arial,sans-serif;font-size:12.8px" target="_blank" class="">https://youtu.be/rPdgFTo0FZM</a><span style="font-family:arial,sans-serif;font-size:12.8px" class=""> </span><br class=""></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br class=""><div class="gmail_quote"><div class=""><div class="">On 20 September 2016 at 11:16, Herzig, David <span dir="ltr" class=""><<a href="mailto:david.herzig@roche.com" target="_blank" class="">david.herzig@roche.com</a>></span> wrote:<br class=""></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class=""><div class=""><div dir="ltr" class="">Hi Ensembl Users<div class=""><br class=""></div><div class="">I have setup the ensembl environment for several species. Everything is ok.</div><div class="">After that I imported data from NCBI by using the <a href="http://parse_ncbi_gff3.pl/" target="_blank" class="">parse_ncbi_gff3.pl</a> script. Works fine for almost all species. But for the specie sus scrofa I have the following issue:</div><div class=""><br class=""></div><div class="">I downloaded the file from NCBI:</div><div class="">/<a href="http://ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/GFF/ref_Sscrofa10.2_top_level.gff3" target="_blank" class="">ftp.ncbi.nlm.nih.gov/genomes/<wbr class="">Sus_scrofa/GFF/ref_Sscrofa10.2<wbr class="">_top_level.gff3</a><br class=""></div><div class=""><br class=""></div><div class="">I used the <a href="http://parse_ncbi_gff3.pl/" target="_blank" class="">parse_ncbi_gff3.pl</a> script to import it.</div><div class=""><br class=""></div><div class="">The process starts successfully but after a while I get the following error message and the process stops:</div><div class=""><br class=""></div><div class="">Can't call method "phase" on an undefined value at /home/ensembl/release-85/ensem<wbr class="">bl-pipeline/scripts/refseq_imp<wbr class="">ort/<a href="http://parse_ncbi_gff3.pl/" target="_blank" class="">parse_ncbi_gff3.pl</a> line 882, <__ANONIO__> line 1184334.<br class=""></div><div class=""><br class=""></div><div class="">Any ideas?</div><div class=""><br class=""></div><div class="">regards,</div><div class="">David</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">-- <br class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><p style="font-family:arial;font-size:small" class=""><span style="font-family:imago" class="">David Herzig<br class="">Scientist, pRED Informatics<br class="">Roche Pharma Research and Early Development</span></p><p style="font-family:arial;font-size:small" class=""><span style="font-family:imago" class="">Roche Innovation Center Basel</span></p><p style="font-family:arial;font-size:small" class=""><span lang="DE" style="font-family:imago" class="">F. Hoffmann-La Roche Ltd<br class="">Grenzacherstrasse 124<br class="">4070 Basel<br class="">Switzerland<br class="">Phone <a href="tel:%2B41%2061%20687%2031%2070" value="+41616873170" target="_blank" class="">+41 61 687 31 70</a></span></p><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>
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<br class=""></blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div data-smartmail="gmail_signature" class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><p style="font-family:arial;font-size:small" class=""><span style="font-family:Imago" class="">David Herzig<br class="">Scientist, pRED Informatics<br class="">Roche Pharma Research and Early Development</span></p><p style="font-family:arial;font-size:small" class=""><span style="font-family:Imago" class="">Roche Innovation Center Basel</span></p><p style="font-family:arial;font-size:small" class=""><span lang="DE" style="font-family:Imago" class="">F. Hoffmann-La Roche Ltd<br class="">Grenzacherstrasse 124<br class="">4070 Basel<br class="">Switzerland<br class="">Phone <a href="tel:%2B41%2061%20687%2031%2070" value="+41616873170" target="_blank" class="">+41 61 687 31 70</a></span></p><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:13.3333339691162px" target="_blank" class=""><span style="font-size:12.8000001907349px" class="">http://go.roche.com/</span><b style="font-size:12.8000001907349px" class="">pREDi</b></a><br class=""></span></p></div></div></div></div>
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