<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="">First try using Augustu v3.3.3 or the live version from GitHub (<a href="https://github.com/Gaius-Augustus/Augustus" class="">https://github.com/Gaius-Augustus/Augustus</a>). You can specify the other augustus version in maker_exe.ctl. You can use ctl+z to pause the run right when MAKER reaches the specified augustus call. Or after trying the newer agusuts version, you can upload everything from the run to <a href="https://github.com/Gaius-Augustus/Augustus" class="">https://github.com/Gaius-Augustus/Augustus</a> and I can try to extract the files for you.<div class=""><br class=""></div><div class="">Or if you are adventurous you can run in the perl debugger.</div><div class=""><br class=""></div><div class="">#start debugger</div><div class="">perl -dS maker</div><div class=""><br class=""></div><div class="">#continue to augustus calls</div><div class="">DB<1> c Widget::augustus::run</div><div class=""><br class=""></div><div class="">#continue to augustus failure (right before dieing)</div><div class="">DB<2> c 282</div><div class=""><br class=""></div><div class="">At this point just copy the command as files still exist</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 2, 2020, at 2:54 AM, Lior Glick <<a href="mailto:liorglic@mail.tau.ac.il" class="">liorglic@mail.tau.ac.il</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="rtl" class=""><div style="" dir="ltr" class="">Hello,</div><div style="" dir="ltr" class="">I am using MAKER2 with Augustus 3.2.2. I keep getting an error message when annotating a specific contig. The relevant section of the MAKER stderr looks like this:</div><div style="" dir="ltr" class=""><br class=""></div><div style="" dir="ltr" class=""><font face="monospace" class="">Widget::augustus:<br class="">/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus --species=arabidopsis --strand=backward --UTR=off --hintsfile=/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.xdef.augustus --extrinsicCfgFile=/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/config/extrinsic/extrinsic.MPE.cfg /home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus.fasta > /home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus<br class="">#-------------------------------#<br class="">Sampling error in intron model. state=37 base=2391<br class=""><br class="">/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus: ERROR<br class=""> Tried to sample from empty list.<br class=""><br class="">Sampling error in intron model. state=37 base=2391<br class=""><br class="">/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus: ERROR<br class=""> Tried to sample from empty list.<br class=""><br class="">ERROR: Augustus failed<br class="">--> rank=NA, hostname=compute-0-301.power5<br class="">ERROR: Failed while annotating transcripts<br class="">ERROR: Chunk failed at level:1, tier_type:4<br class="">FAILED CONTIG:chunk08<br class=""><br class="">ERROR: Chunk failed at level:6, tier_type:0<br class="">FAILED CONTIG:chunk08<br class=""><br class="">examining contents of the fasta file and run log<br class=""><br class=""><br class=""><br class="">--Next Contig--<br class=""><br class="">Processing run.log file...<br class="">MAKER WARNING: The file chunk.maker.output/chunk_datastore/76/17/chunk08//theVoid.chunk08/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus<br class="">did not finish on the last run and must be erased<br class=""><br class=""><br class="">Maker is now finished!!!</font><br class=""></div><div style="" dir="ltr" class=""><br class=""></div><div style="" dir="ltr" class="">I found <a href="https://groups.google.com/g/maker-devel/c/WBD_GEvELDE" class="">this thread</a> with a similar error but slightly different augustus command. The suggestion there was to isolate the augustus command. This sounds like good advice, but most of the inputs to the command are stored in a temporary location and are deleted at the end of the MAKER run. Is there any way to restore them?</div><div style="" dir="ltr" class="">Alternatively, are there any known solutions/explanations to this error? All I could find was <a href="https://bioinf.uni-greifswald.de/bioinf/forum/viewtopic.php?f=4&t=150" class="">this thread</a> from the Augustus forum, but it doesn't seem to provide much help.</div><div style="" dir="ltr" class="">Would appreciate any ideas/workarounds.</div><div style="" dir="ltr" class="">Thanks!</div><div style="" dir="ltr" class=""><br class=""></div></div>
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