[maker-devel] Stalling on re-annotation

[Bradley Colquitt]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150420/e279b7da/attachment-0002.html>