[maker-devel] Stalling on re-annotation

[Carson Holt]

Hi Brad,

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 —> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi <http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi>

—Carson



> On Apr 19, 2015, at 7:12 PM, Bradley Colquitt <bradley.colquitt at gmail.com> wrote:
> 
> Hello MAKER team,
> 
> 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) 
> 
> MAKER version: 2.31.8
> est_gff generated using HISAT/StringTie
> 
> Maker_opts.ctl file: 
> #-----Genome (these are always required)
> genome=genome.fa 
> organism_type=eukaryotic 
> 
> #-----Re-annotation Using MAKER Derived GFF3
> maker_gff=
> est_pass=0 
> altest_pass=1
> protein_pass=1 
> rm_pass=1 
> model_pass=1 
> pred_pass=1 
> other_pass=0 
> 
> #-----EST Evidence (for best results provide a file for at least one)
> est= 
> altest= organism
> est_gff=new_data.gff3
> altest_gff= 
> 
> #-----Protein Homology Evidence (for best results provide a file for at least one)
> protein=  
> protein_gff= 
> #-----Repeat Masking (leave values blank to skip repeat masking)
> model_org= 
> rmlib= 
> repeat_protein= 
> rm_gff= 
> prok_rm=0 
> softmask=1 
> 
> #-----Gene Prediction
> snaphmm= 
> gmhmm=
> augustus_species= 
> fgenesh_par_file= 
> pred_gff=previous_maker.gff
> model_gff= 
> est2genome=0 
> protein2genome=0 
> trna=0
> snoscan_rrna= 
> unmask=0 
> 
> #-----Other Annotation Feature Types (features MAKER doesn't recognize)
> other_gff=
> 
> #-----External Application Behavior Options
> alt_peptide=C 
> cpus=1 
> 
> #-----MAKER Behavior Options
> max_dna_len=1000000
> min_contig=1000 
> 
> pred_flank=200 
> pred_stats=1 
> AED_threshold=1 
> min_protein=0 
> alt_splice=0 
> always_complete=0
> map_forward=1 
> keep_preds=1 
> 
> split_hit=10000
> single_exon=1
> single_length=250
> correct_est_fusion=0 
> 
> tries=2
> clean_try=0 
> clean_up=0
> TMP=/media/data/maker/tmp 
> 
> Any help would be greatly appreciated. Thanks.
> Brad Colquitt
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