<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="">If you look in the folder of the failed contig under the .../theVoid directory there will be a file called query.masked.fasta.<div class=""><br class=""></div><div class="">Copy that file somewhere. Then because maker gave you the command that failed, you can run it all by itself outside of MAKER</div><div class=""><br class=""></div><div class="">Example —> </div><div class="">/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off query.masked.fasta</div><div class=""><br class=""></div><div class="">If it still fails, you now have a test file and command you can send to Mario Stanke (<a href="mailto:mario.stanke@uni-greifswald.de" class="">mario.stanke@uni-greifswald.de</a>). He made Augustus. It may be a bug he has already fixed (current Augustus version is 3.3) or there may be something in the species file causing the error that he can point out.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 12, 2017, at 1:37 AM, Jan FABI <<a href="mailto:jan.nagel@fabi.up.ac.za" class="">jan.nagel@fabi.up.ac.za</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class="">Dear Maker team<br class=""><br class=""></div>I am experiencing a problem while running maker and cannot find a solution to it online. <br class=""><br class=""></div>I am running maker on a new genome, using BRAKER trained models for Augustus and GeneMark. This was successful and performed as expected, except for one contig where an error was encountered. <br class=""><br class=""></div>This error occurs during Augustus and seems to have something to do with intron models. I have made sure that the input fasta does not contain characters other than ATCGN or contains "windows"/non-UNIX carriage returns. <br class=""><br class=""></div>I include the relevant portion of the log below. Could you help me determine the cause of this error.<br class=""><br class=""><br class=""><br class="">setting up GFF3 output and fasta chunks<br class="">preparing ab-inits<br class="">running augustus.<br class="">#--------- command -------------#<br class="">Widget::augustus:<br class="">/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus --species=Np_2017_braker --UTR=off /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0 > /tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0.Np_2017_braker.augustus<br class="">#-------------------------------#<br class="">Sampling error in intron model. state=37 base=26570<br class=""><br class="">/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR<br class=""> Tried to sample from empty list.<br class=""><br class="">Sampling error in intron model. state=37 base=26570<br class=""><br class="">/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR<br class=""> Tried to sample from empty list.<br class=""><br class="">ERROR: Augustus failed<br class="">--> rank=NA, hostname=xxx-VirtualBox<br class="">ERROR: Failed while preparing ab-inits<br class="">ERROR: Chunk failed at level:0, tier_type:2<br class="">FAILED CONTIG:NODE_1040_length_26483_cov_27.125137<br class=""><br class="">ERROR: Chunk failed at level:4, tier_type:0<br class="">FAILED CONTIG:NODE_1040_length_26483_cov_27.125137 <br class=""><div class=""><div class=""><div class=""><div class=""><div class=""><br class="">-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><span class="">Regards <br class="">Jan Nagel<br class="">----------------------------------------------------------------------<br class="">PhD Genetics student<br class="">Department of Genetics<br class="">Forestry and Agricultural Biotechnology Institute (FABI) <br class="">FABI 1, Room 1-55<br class="">University of Pretoria<br class="">74 Lunnon Rd. Hillcrest<br class="">0002<br class="">Gauteng Province<br class="">South Africa<br class=""><br class="">Email : <a href="mailto:jan.nagel@fabi.up.ac.za" target="_blank" class="">jan.nagel@fabi.up.ac.za</a><br class=""><br class="">Website: <a href="http://www.fabinet.up.ac.za/index.php/people-profile?profile=961" target="_blank" class="">http://www.fabinet.up.ac.za/index.php/people-profile?profile=961</a></span></div></div>
</div></div></div></div></div></div>
<br class="">
<div style="font-family:Arial,Helvetica,sans-serif" class=""><span style="font-size:10.0pt;line-height:105%;font-family:"Segoe UI",sans-serif" class="">This message and attachments are subject to a disclaimer.<br class="">
Please refer to <a href="http://upnet.up.ac.za/services/it/documentation/docs/004167.pdf" target="_blank" class="">http://upnet.up.ac.za/<wbr class="">services/it/documentation/<wbr class="">docs/004167.pdf</a> </span><span style="font-size:10pt;line-height:105%;font-family:Tahoma,sans-serif" class="">for
full details.</span></div>_______________________________________________<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></div></body></html>