<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">The failure is internal to Augustus. Try updating Augustus to 3.3. If it still fails after that let me know. We will have to isolate the command and files used, so you can send it as a test dataset to the Augustus devlopers.<div class=""><br class=""></div><div class="">—Carson<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 20, 2018, at 8:47 AM, Aditi Rambani <<a href="mailto:ar834@cornell.edu" class="">ar834@cornell.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="caret-color: rgb(0, 0, 0); font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hello, </div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Maker successfully annotated the genome but keeps failing for one contig with error message attached below. Can you please help me troubleshoot this ? There is no issue with augustus for rest of the contigs. </div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Thank you</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Aditi </div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div class="">#--------- command -------------#</div><div class="">Widget::augustus:</div><div class="">~/augustus-3.2/bin/augustus --species=Cxxx --strand=forward --UTR=off --hintsfile=/tmp/maker_dSn0ps/0/71_0.26253049-26257472.Cxxx.auto_annotator.xdef.augustus --extrinsicCfgFile=/data/home/srs57/programs/augustus-3.2/config/extrinsic/extrinsic.MPE.cfg /tmp/maker_dSn0ps/0/71_0.26253049-26257472.Cxxx.auto_annotator.augustus.fasta > /tmp/maker_dSn0ps/0/71_0.26253049-26257472.Cxxx.auto_annotator.augustus</div><div class="">#-------------------------------#</div><div class="">Sampling error in intron model. state=14 base=4422</div><div class=""><br class=""></div><div class="">~/augustus-3.2/bin/augustus: ERROR</div><div class=""><span style="white-space: pre;" class=""></span>Tried to sample from empty list.</div><div class=""><br class=""></div><div class="">Sampling error in intron model. state=14 base=4422</div><div class=""><span style="font-size: 12pt;" class="">~/augustus-3.2/bin/augustus: ERROR</span><br class=""></div><div class=""><span style="white-space: pre;" class=""></span>Tried to sample from empty list.</div><div class=""><br class=""></div><div class="">ERROR: Augustus failed</div><div class="">--> rank=NA, hostname=xxx</div><div class="">ERROR: Failed while annotating transcripts</div><div class="">ERROR: Chunk failed at level:1, tier_type:4</div><div class="">FAILED CONTIG:Contigxxx</div><div class=""><br class=""></div><div class="">ERROR: Chunk failed at level:6, tier_type:0</div><div class="">FAILED CONTIG:<span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;" class="">Contigxxx</span></div><div class=""><br class=""></div><div class="">examining contents of the fasta file and run log</div></div></div></blockquote></div><br class=""></div></body></html>