<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On May 1, 2018, at 10:16 AM, Kapeel Chougule <<a href="mailto:kapeelc@gmail.com" class="">kapeelc@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi,<div class=""><br class=""></div><div class="">I am using MAKER v3 to update community annotation with new RNA-seq evidence data. Part of my problem is that MAKER shows below error when repeat masking. I have attached the community annotation gff, maker log and maker_opts.ctl for your reference. I searched for this error in the maker-dev google group and found some <a href="https://groups.google.com/forum/#!topic/maker-devel/651ka80F3s4" class="">hints</a> to update BLAST to 2.7, rmblast to 2.6 and reconfigure RepeatMasker which I did but it still fails with the error. Any help appreciated.</div><div class=""><br class=""></div><div style="margin: 0in 0in 0.0001pt; font-size: inherit; font-family: Cambria;" class="">deleted:0 hits<span class=""></span></div><div style="margin: 0in 0in 0.0001pt; font-size: inherit; font-family: Cambria;" class="">collecting blastx repeatmasking<span class=""></span></div><div style="margin: 0in 0in 0.0001pt; font-size: inherit; font-family: Cambria;" class="">processing all repeats<span class=""></span></div><div style="margin: 0in 0in 0.0001pt; font-size: inherit; font-family: Cambria;" class="">in cluster::shadow_cluster...<span class=""></span></div><div style="margin: 0in 0in 0.0001pt; font-size: inherit; font-family: Cambria;" class="">Died at /mnt/grid/ware/hpc/home/data/mcampbel/applications/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.<span class=""></span></div><div style="margin: 0in 0in 0.0001pt; font-size: inherit; font-family: Cambria;" class="">--> rank=1, hostname=<a href="http://bnbcompute15.blacknblue.cshl.edu/" class="">bnbcompute15.blacknblue.cshl.edu</a><span class=""></span></div><div style="margin: 0in 0in 0.0001pt; font-size: inherit; font-family: Cambria;" class="">ERROR: Failed while processing all repeats<span class=""></span></div><div style="margin: 0in 0in 0.0001pt; font-size: inherit; font-family: Cambria;" class="">ERROR: Chunk failed at level:3, tier_type:1<span class=""></span></div><div style="margin: 0in 0in 0.0001pt; font-size: inherit; font-family: Cambria;" class="">FAILED CONTIG:Chr06<span class=""></span></div><p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: inherit; font-family: Cambria;"><span class=""> </span></p><div style="margin: 0in 0in 0.0001pt; font-size: inherit; font-family: Cambria;" class="">ERROR: Chunk failed at level:2, tier_type:0<span class=""></span></div><p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: inherit; font-family: Cambria;"><span class=""></span></p><div class=""><span style="font-family: Cambria; font-size: inherit;" class="">FAILED CONTIG:Chr06</span></div><div class=""><br class=""></div><div class=""> </div><div class=""><div class="">Thanks</div><div class=""><br class=""></div><div class="">Kapeel</div>-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><font face="'courier new', monospace" class=""><b class=""><div class=""><br class=""></div><div class="">Kapeel Chougule<br class=""></div>Computational Scientist<font face="'courier new', monospace" class=""> Developer II<br class=""></font></b></font><font face="'courier new', monospace" class=""><b class=""><font face="'courier new', monospace" class="">One Bungtown Road Cold Spring Harbor, NY 11724<br class=""><font face="'courier new', monospace" class=""><a href="http://www.warelab.org/" target="_blank" class="">http://www.warelab.org/</a></font><br class=""><br class=""></font></b></font></div></div></div>
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<span id="cid:DDA7DD8D-E9C9-4628-B51D-D3EB1870FBB7@localdomain"><Chr06.gff></span><span id="cid:73DB8CD3-096D-4327-8F2D-3715885545B6@localdomain"><maker_opts.ctl></span><span id="cid:00CA23D4-91DC-4E64-A406-C2E7F4C57A0B@localdomain"><maker.run.log></span>_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></blockquote></div><br class=""><div class=""><br class=""></div></body></html>