<div dir="ltr"><div dir="ltr"><div dir="ltr">Hi Carson,<div><br></div><div>Indeed, I did generate the hmm file immediately previously to my second run. I redid the process by following these commands from the link you supplied:</div><div><br></div><div><div>mkdir snap</div><div>cd snap</div><div>gff3_merge -d /root/tuna-round-2/genome.maker.output/genome_master_datastore_index.log</div><div>maker2zff genome.all.gff</div><div>fathom -categorize 1000 genome.ann genome.dna</div><div>fathom -export 1000 -plus uni.ann uni.dna</div><div>forge export.ann export.dna</div><div><a href="http://hmm-assembler.pl">hmm-assembler.pl</a> genome . > ../genome1.hmm</div></div><div><br></div><div>I didn't find any errors generated by Snap during training. But when I reran MAKER, I got errors of this variety:</div><div><br></div><div><div>processing all repeats</div><div>processing all repeats</div><div>error: unknown command "/root/tuna-round-2/genome.maker.output/genome1.hmm", see 'snap help'</div><div>error: unknown command "/root/tuna-round-2/genome.maker.output/genome1.hmm", see 'snap help'</div><div>preparing masked sequence</div><div>processing all repeats</div><div>collecting blastx repeatmasking</div><div>preparing masked sequence</div><div>collecting blastx repeatmasking</div><div>collecting blastx repeatmasking</div><div>processing all repeats</div><div>processing all repeats</div><div>processing all repeats</div><div>processing all repeats</div><div>preparing masked sequence</div><div>collecting blastx repeatmasking</div><div>ERROR: Snap failed</div><div>--> rank=21, hostname=localhost</div><div>ERROR: Failed while preparing ab-inits</div><div>ERROR: Chunk failed at level:0, tier_type:2</div><div>FAILED CONTIG:scf7180000008536_pilon_pilon</div><div><br></div><div>ERROR: Snap failed</div><div>--> rank=5, hostname=localhost</div><div>ERROR: Failed while preparing ab-inits</div><div>ERROR: Chunk failed at level:0, tier_type:2</div><div>FAILED CONTIG:scf7180000008522_pilon_pilon</div><div><br></div><div>ERROR: Chunk failed at level:4, tier_type:0</div><div>FAILED CONTIG:scf7180000008536_pilon_pilon</div><div><br></div><div>preparing masked sequence</div><div>ERROR: Chunk failed at level:4, tier_type:0</div><div>FAILED CONTIG:scf7180000008522_pilon_pilon</div></div><div><br></div><div>Do you have any other suggestions?</div><div><br></div><div>Thanks in Advance,</div><div><br></div><div>Paul</div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Apr 7, 2019 at 6:00 AM Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">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><br></div><div>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" target="_blank">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><br></div><div>—Carson</div><div><br><div><br><blockquote type="cite"><div>On Apr 4, 2019, at 4:46 PM, Paul Sheridan <<a href="mailto:paul@tupac.bio" target="_blank">paul@tupac.bio</a>> wrote:</div><br class="gmail-m_5306265726991931013Apple-interchange-newline"><div><div dir="ltr"><div dir="ltr"><div>Dear MAKER Team,</div><div><br></div><div>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><br></div><div>MAKER WARNING: Changes in control files make re-use of all old data impossible</div><div>All old files will be erased before continuing</div><div>processing all repeats</div><div>doing repeat masking</div><div>doing repeat masking</div><div>#---------------------------------------------------------------------</div><div>Now starting the contig!!</div><div>SeqID: scf7180000008677_pilon_pilon</div><div>Length: 49996</div><div>#---------------------------------------------------------------------</div><div><br></div><div>doing repeat masking</div><div>preparing ab-inits</div><div>running snap.</div><div>#--------- command -------------#</div><div>Widget::snap:</div><div>/usr/bin/snap /root/tuna-round-2/genome.maker.output/snap/round1/genome.hmm /tmp/maker_8RuX8Z/scf718</div><div>0000006915_pilon_pilon.abinit_masked.0 > /tmp/maker_8RuX8Z/scf7180000006915_pilon_pilon.abinit_maske</div><div>d.0.genome%2Ehmm.snap</div><div>#-------------------------------#</div><div>setting up GFF3 output and fasta chunks</div><div>processing all repeats</div><div>doing repeat masking</div><div>in cluster::shadow_cluster...</div><div>...finished clustering.</div><div>error: unknown command "/root/tuna-round-2/genome.maker.output/snap/round1/genome.hmm", see 'snap help'</div><div>ERROR: Snap failed</div><div>--> rank=21, hostname=localhost</div><div>ERROR: Failed while preparing ab-inits</div><div>ERROR: Chunk failed at level:0, tier_type:2</div><div>FAILED CONTIG:scf7180000007575_pilon_pilon</div><div><br></div><div>I confirmed that the path to genome.hmm is correct. In addition, run.log contains the following kind of output:</div><div><br></div><div>STARTED<span style="white-space:pre-wrap"> </span>genome.maker.output/genome_datastore/00/6E/scf7180000008677_pilon_pilon//theVoid.scf7180000008677_pilon_pilon/scf7180000008677_pilon_pilon.abinit_m</div><div>asked.0.genome%2Ehmm.snap<span style="white-space:pre-wrap"> </span></div><div>DIED<span style="white-space:pre-wrap"> </span>RANK<span style="white-space:pre-wrap"> </span>30:4:0:0</div><div>DIED<span style="white-space:pre-wrap"> </span>COUNT<span style="white-space:pre-wrap"> </span>2</div><div>DIED<span style="white-space:pre-wrap"> </span>RANK<span style="white-space:pre-wrap"> </span>30</div><div>DIED<span style="white-space:pre-wrap"> </span>COUNT<span style="white-space:pre-wrap"> </span>2</div><div><br></div><div>How can I resolve this issue?</div><div><br></div><div>Also, is the warning about it being impossible to use the old data to be expected?</div><div><br></div><div>Attached files:</div><div>- maker_otps1.ctl: first pass control file </div><div>- maker_opts2.ctl: second pass control file </div><div>- run.log: log file for an example contig</div><div><br></div><div>Thanks in Advance,</div><div><br></div><div>Paul Sheridan</div><div><br></div>-- <br><div dir="ltr" class="gmail-m_5306265726991931013gmail_signature"><div dir="ltr">CSO at Tupac Bio<div><a href="mailto:paul@tupac.bio" target="_blank">Email: paul@tupac.bio</a></div><div>Homepage: <a href="http://www.paulsheridan.net/" target="_blank">www.paulsheridan.net</a></div><div>Mobile: +81 80 7889 0859</div></div></div></div></div>
<span id="gmail-m_5306265726991931013cid:f_ju38b9m41"><maker_opts2.ctl></span><span id="gmail-m_5306265726991931013cid:f_ju38b9lm0"><run.log></span><span id="gmail-m_5306265726991931013cid:f_ju38b9mr2"><maker_opts1.ctl></span>_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><br><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br></div></blockquote></div><br></div></div></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr">CSO at Tupac Bio<div>Email: paul@tupac.bio</div><div>Homepage: <a href="http://www.paulsheridan.net" target="_blank">www.paulsheridan.net</a></div><div>Mobile: +81 80 7889 0859</div></div></div>