<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="">Hi Brad,<div class=""><br class=""></div><div class="">The issue is probably either a formatting issue with this the new_data.gff3 file, or an extreme amount of data in that file overlapping the contig. If you think it might be a formatting issue I could take a look. You can upload the GFF3 and other run files here —> <a href="http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi" class="">http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi</a></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Apr 19, 2015, at 7:12 PM, Bradley Colquitt <<a href="mailto:bradley.colquitt@gmail.com" class="">bradley.colquitt@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello MAKER team,<div class=""><br class=""></div><div class="">I've run into an issue while updating a previous run using new data. The programs hangs (48 hours running) and consumes at lot of RAM (20GB) while processing a particular scaffold (a relatively small one, 200kb, with 24 transcript models). While running using MPI, a similar hang occurs on a few other scaffolds of around the same length (scaffolds 590-620) </div><div class=""><br class=""></div><div class="">MAKER version: 2.31.8</div><div class="">est_gff generated using HISAT/StringTie</div><div class=""><br class=""></div><div class="">Maker_opts.ctl file: </div><div class=""><div class="">#-----Genome (these are always required)</div><div class="">genome=genome.fa </div><div class="">organism_type=eukaryotic </div><div class=""><br class=""></div><div class="">#-----Re-annotation Using MAKER Derived GFF3</div><div class="">maker_gff=</div><div class="">est_pass=0 </div><div class="">altest_pass=1</div><div class="">protein_pass=1 </div><div class="">rm_pass=1 </div><div class="">model_pass=1 </div><div class="">pred_pass=1 </div><div class="">other_pass=0 </div><div class=""><br class=""></div><div class="">#-----EST Evidence (for best results provide a file for at least one)</div><div class="">est= </div><div class="">altest= organism</div><div class="">est_gff=new_data.gff3</div><div class="">altest_gff= </div><div class=""><br class=""></div><div class="">#-----Protein Homology Evidence (for best results provide a file for at least one)</div><div class="">protein= </div><div class="">protein_gff= </div><div class="">#-----Repeat Masking (leave values blank to skip repeat masking)</div><div class="">model_org= </div><div class="">rmlib= </div><div class="">repeat_protein= </div><div class="">rm_gff= </div><div class="">prok_rm=0 </div><div class="">softmask=1 </div><div class=""><br class=""></div><div class="">#-----Gene Prediction</div><div class="">snaphmm= </div><div class="">gmhmm=</div><div class="">augustus_species= </div><div class="">fgenesh_par_file= </div><div class="">pred_gff=previous_maker.gff</div><div class="">model_gff= </div><div class="">est2genome=0 </div><div class="">protein2genome=0 </div><div class="">trna=0</div><div class="">snoscan_rrna= </div><div class="">unmask=0 </div><div class=""><br class=""></div><div class="">#-----Other Annotation Feature Types (features MAKER doesn't recognize)</div><div class="">other_gff=</div><div class=""><br class=""></div><div class="">#-----External Application Behavior Options</div><div class="">alt_peptide=C </div><div class="">cpus=1 </div><div class=""><br class=""></div><div class="">#-----MAKER Behavior Options</div><div class="">max_dna_len=1000000</div><div class="">min_contig=1000 </div><div class=""><br class=""></div><div class="">pred_flank=200 </div><div class="">pred_stats=1 </div><div class="">AED_threshold=1 </div><div class="">min_protein=0 </div><div class="">alt_splice=0 </div><div class="">always_complete=0</div><div class="">map_forward=1 </div><div class="">keep_preds=1 </div><div class=""><br class=""></div><div class="">split_hit=10000</div><div class="">single_exon=1</div><div class="">single_length=250</div><div class="">correct_est_fusion=0 </div><div class=""><br class=""></div><div class="">tries=2</div><div class="">clean_try=0 </div><div class="">clean_up=0</div><div class="">TMP=/media/data/maker/tmp </div></div><div class=""><br class=""></div><div class="">Any help would be greatly appreciated. Thanks.</div><div class="">Brad Colquitt</div></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></body></html>