[maker-devel] Maker Issue re-annotating

Tue Feb 11 09:12:23 MST 2020

Good morning,

I'm trying to de novo annotate a genome with ~100,000 scaffolds and a
scaffold N50 of 189,900 using Maker. I've been able to use MPICH to
parallelize the first round of <aker, and it will finish in ~2 weeks.
However, I'm trying to improve the annotation using SNAP and when I do so
every scaffold fails. I'm wondering if you could give me any advice or tell
me what I might be doing wrong?

Here are the parameters used in the maker_opts.ctl file-

#-----Genome (these are always required)

genome=blackbear_DNAzoo.FINAL.fasta #genome sequence (fasta file or fasta
embeded in GFF3 file)

organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic

#-----Re-annotation Using MAKER Derived GFF3

maker_gff=blackbear_DNAzoo.FINAL.all.gff #MAKER derived GFF3 file

est_pass=1 #use ESTs in maker_gff: 1 = yes, 0 = no

altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no

protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no

rm_pass=1 #use repeats in maker_gff: 1 = yes, 0 = no

model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no

pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no

other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no

#-----EST Evidence (for best results provide a file for at least one)

est=Ursus_maritimus.UrsMar_1.0.cdna.all.fa #set of ESTs or assembled
mRNA-seq in fasta format

altest= #EST/cDNA sequence file in fasta format from an alternate organism

est_gff= #aligned ESTs or mRNA-seq from an external GFF3 file

altest_gff= #aligned ESTs from a closly relate species in GFF3 format

#-----Protein Homology Evidence (for best results provide a file for at
least one)

protein=Ursus_maritimus.UrsMar_1.0.pep.all.fa  #protein sequence file in
fasta format (i.e. from mutiple organisms)

protein_gff=  #aligned protein homology evidence from an external GFF3 file

#-----Repeat Masking (leave values blank to skip repeat masking)

model_org=all #select a model organism for RepBase masking in RepeatMasker

rmlib= #provide an organism specific repeat library in fasta format for
RepeatMasker

repeat_protein= #provide a fasta file of transposable element proteins for
RepeatRunner

rm_gff= #pre-identified repeat elements from an external GFF3 file

prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change
this), 1 = yes, 0 = no

softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg
and dust filtering)

#-----Gene Prediction

snaphmm=blackbear.hmm #SNAP HMM file

gmhmm= #GeneMark HMM file

augustus_species= #Augustus gene prediction species model

fgenesh_par_file= #FGENESH parameter file

pred_gff= #ab-initio predictions from an external GFF3 file

model_gff= #annotated gene models from an external GFF3 file (annotation
pass-through)

run_evm=0 #run EvidenceModeler, 1 = yes, 0 = no

est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no

protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no

trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no

snoscan_rrna= #rRNA file to have Snoscan find snoRNAs

snoscan_meth= #-O-methylation site fileto have Snoscan find snoRNAs

unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 =
yes, 0 = no

allow_overlap=0 #allowed gene overlap fraction (value from 0 to 1, blank
for default)

#-----Other Annotation Feature Types (features MAKER doesn't recognize)

other_gff= #extra features to pass-through to final MAKER generated GFF3
file

#-----External Application Behavior Options

alt_peptide=C #amino acid used to replace non-standard amino acids in BLAST
databases

cpus=1 #max number of cpus to use in BLAST and RepeatMasker (not for MPI,
leave 1 when using MPI)

#-----MAKER Behavior Options

max_dna_len=100000 #length for dividing up contigs into chunks
(increases/decreases memory usage)

min_contig=1 #skip genome contigs below this length (under 10kb are often
useless)

pred_flank=200 #flank for extending evidence clusters sent to gene
predictors

pred_stats=1 #report AED and QI statistics for all predictions as well as
models

AED_threshold=1 #Maximum Annotation Edit Distance allowed (bound by 0 and 1)

min_protein=0 #require at least this many amino acids in predicted proteins

alt_splice=0 #Take extra steps to try and find alternative splicing, 1 =
yes, 0 = no

always_complete=0 #extra steps to force start and stop codons, 1 = yes, 0 =
no

map_forward=0 #map names and attributes forward from old GFF3 genes, 1 =
yes, 0 = no

keep_preds=1 #Concordance threshold to add unsupported gene prediction
(bound by 0 and 1)

split_hit=10000 #length for the splitting of hits (expected max intron size
for evidence alignments)

min_intron=20 #minimum intron length (used for alignment polishing)

single_exon=0 #consider single exon EST evidence when generating
annotations, 1 = yes, 0 = no

single_length=250 #min length required for single exon ESTs if 'single_exon
is enabled'

correct_est_fusion=0 #limits use of ESTs in annotation to avoid fusion genes

tries=2 #number of times to try a contig if there is a failure for some
reason

clean_try=0 #remove all data from previous run before retrying, 1 = yes, 0
= no

clean_up=0 #removes theVoid directory with individual analysis files, 1 =
yes, 0 = no

TMP= #specify a directory other than the system default temporary directory
for temporary files

Thanks,
-- 
Megan Ramaker, PhD
Postdoctoral Trainee
HudsonAlpha Institute for Biotechnology
601 Genome Way
Huntsville, AL 35806
478-284-6723
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