[maker-devel] Stalling on re-annotation

[Bradley Colquitt]

Thanks Carson, file was just uploaded in my account bradley.colquitt. I
should note that the GFF3 file was created by converting from GTF using
gffread.

On Thu, Apr 23, 2015 at 9:02 AM Carson Holt <carsonhh at gmail.com> wrote:

> 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
>
> —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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>
>
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