<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 error is being thrown by snap itself. Perhaps there is an issue with the genome.hmm file. Did you generate the file immediately previously to this run? Perhaps you can redo that process, and review any errors that come up during training.<div class=""><br class=""></div><div class="">Some details on training SNAP from the wiki —> <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018#Training_ab_initio_Gene_Predictors" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018#Training_ab_initio_Gene_Predictors</a></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 4, 2019, at 4:46 PM, Paul Sheridan <<a href="mailto:paul@tupac.bio" class="">paul@tupac.bio</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class="">Dear MAKER Team,</div><div class=""><br class=""></div><div class="">I am running MAKER 2.31.10 a 32 core instance. My first pass completed successfully. However, my second pass using SNAP and Augustus trained ab initio gene predictions failed. Here is some example output which illustrates the problem:</div><div class=""><br class=""></div><div class="">MAKER WARNING: Changes in control files make re-use of all old data impossible</div><div class="">All old files will be erased before continuing</div><div class="">processing all repeats</div><div class="">doing repeat masking</div><div class="">doing repeat masking</div><div class="">#---------------------------------------------------------------------</div><div class="">Now starting the contig!!</div><div class="">SeqID: scf7180000008677_pilon_pilon</div><div class="">Length: 49996</div><div class="">#---------------------------------------------------------------------</div><div class=""><br class=""></div><div class="">doing repeat masking</div><div class="">preparing ab-inits</div><div class="">running snap.</div><div class="">#--------- command -------------#</div><div class="">Widget::snap:</div><div class="">/usr/bin/snap /root/tuna-round-2/genome.maker.output/snap/round1/genome.hmm /tmp/maker_8RuX8Z/scf718</div><div class="">0000006915_pilon_pilon.abinit_masked.0 > /tmp/maker_8RuX8Z/scf7180000006915_pilon_pilon.abinit_maske</div><div class="">d.0.genome%2Ehmm.snap</div><div class="">#-------------------------------#</div><div class="">setting up GFF3 output and fasta chunks</div><div class="">processing all repeats</div><div class="">doing repeat masking</div><div class="">in cluster::shadow_cluster...</div><div class="">...finished clustering.</div><div class="">error: unknown command "/root/tuna-round-2/genome.maker.output/snap/round1/genome.hmm", see 'snap help'</div><div class="">ERROR: Snap failed</div><div class="">--> rank=21, hostname=localhost</div><div class="">ERROR: Failed while preparing ab-inits</div><div class="">ERROR: Chunk failed at level:0, tier_type:2</div><div class="">FAILED CONTIG:scf7180000007575_pilon_pilon</div><div class=""><br class=""></div><div class="">I confirmed that the path to genome.hmm is correct. In addition, run.log contains the following kind of output:</div><div class=""><br class=""></div><div class="">STARTED<span style="white-space:pre" class=""> </span>genome.maker.output/genome_datastore/00/6E/scf7180000008677_pilon_pilon//theVoid.scf7180000008677_pilon_pilon/scf7180000008677_pilon_pilon.abinit_m</div><div class="">asked.0.genome%2Ehmm.snap<span style="white-space:pre" class=""> </span></div><div class="">DIED<span style="white-space:pre" class=""> </span>RANK<span style="white-space:pre" class=""> </span>30:4:0:0</div><div class="">DIED<span style="white-space:pre" class=""> </span>COUNT<span style="white-space:pre" class=""> </span>2</div><div class="">DIED<span style="white-space:pre" class=""> </span>RANK<span style="white-space:pre" class=""> </span>30</div><div class="">DIED<span style="white-space:pre" class=""> </span>COUNT<span style="white-space:pre" class=""> </span>2</div><div class=""><br class=""></div><div class="">How can I resolve this issue?</div><div class=""><br class=""></div><div class="">Also, is the warning about it being impossible to use the old data to be expected?</div><div class=""><br class=""></div><div class="">Attached files:</div><div class="">- maker_otps1.ctl: first pass control file </div><div class="">- maker_opts2.ctl: second pass control file </div><div class="">- run.log: log file for an example contig</div><div class=""><br class=""></div><div class="">Thanks in Advance,</div><div class=""><br class=""></div><div class="">Paul Sheridan</div><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class="">CSO at Tupac Bio<div class=""><a href="mailto:paul@tupac.bio" class="">Email: paul@tupac.bio</a></div><div class="">Homepage: <a href="http://www.paulsheridan.net/" target="_blank" class="">www.paulsheridan.net</a></div><div class="">Mobile: +81 80 7889 0859</div></div></div></div></div>
<span id="cid:f_ju38b9m41"><maker_opts2.ctl></span><span id="cid:f_ju38b9lm0"><run.log></span><span id="cid:f_ju38b9mr2"><maker_opts1.ctl></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></body></html>