Maker protocols Pmajor

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This page describes the various rounds of Maker-based annotations for the Parus major (Great Tit) genome.

Round 1

Rationale

For this round no P. major-based ESTs were available. Zebrafinch (T. guttata) is the closest relative for which a reasonably complete gene-model set is available. As a first pass, it was decided to let gene predictions be driven by ab-inititio predictions rather than by Zebrafinch EST.

Invoking maker script

Do not forget to load the maker module: <source lang='bash'> module load maker/2.28 </source>

script submitted by SLURM (sbatch command): <source lang='bash'>

  1. !/bin/bash
  2. SBATCH --time=48000
  3. SBATCH --nodes=1
  4. SBATCH --ntasks=16
  5. SBATCH --output=output_%j.txt
  6. SBATCH --error=error_output_%j.txt
  7. SBATCH --job-name=test_maker
  8. SBATCH --partition=ABGC_Research
  9. SBATCH --mail-type=ALL
  10. SBATCH --mail-user=hendrik-jan.megens@wur.nl

maker </source>

Maker settings

content of maker_opts.ctl

#-----Genome (these are always required)
 genome=Pam.fa #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= #MAKER derived GFF3 file
 est_pass=0 #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=0 #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= #set of ESTs or assembled mRNA-seq in fasta format
 altest= Taeniopygia_guttata.taeGut3.2.4.74.cdna.all.fa #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= Taeniopygia_guttata.taeGut3.2.4.74.pep.all.fa #protein sequence file in fasta format (i.e. from mutiple oransisms)
 protein_gff=  #aligned protein homology evidence from an external GFF3 file
 
 #-----Repeat Masking (leave values blank to skip repeat masking)
 model_org=Metazoa #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= /cm/shared/apps/WUR/ABGC/snap/snap-2013-11-29/HMM/mam54.hmm #SNAP HMM file
 gmhmm= #GeneMark HMM file
 augustus_species= chicken #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)
 est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
 protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
 unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no
 
 #-----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=16 #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=0 #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=0 #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)
 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=1 #remove all data from previous run before retrying, 1 = yes, 0 = no
 clean_up=1 #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

content of maker_exe.ctl

 #-----Location of Executables Used by MAKER/EVALUATOR
 makeblastdb=/cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/makeblastdb #location of NCBI+ makeblastdb executable
 blastn=/cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/blastn #location of NCBI+ blastn executable
 blastx=/cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/blastx #location of NCBI+ blastx executable
 tblastx=/cm/shared/apps/WUR/ABGC/blast/ncbi-blast-2.2.28+/bin/tblastx #location of NCBI+ tblastx executable
 formatdb= #location of NCBI formatdb executable
 blastall= #location of NCBI blastall executable
 xdformat= #location of WUBLAST xdformat executable
 blasta= #location of WUBLAST blasta executable
 RepeatMasker=/cm/shared/apps/WUR/ABGC/RepeatMasker/RepeatMasker-4-0-3/RepeatMasker #location of RepeatMasker executable
 exonerate=/cm/shared/apps/WUR/ABGC/exonerate/exonerate-2.2.0-x86_64/bin/exonerate #location of exonerate executable
 
 #-----Ab-initio Gene Prediction Algorithms
 snap=/cm/shared/apps/WUR/ABGC/snap/snap-2013-11-29/snap #location of snap executable
 gmhmme3= #location of eukaryotic genemark executable
 gmhmmp= #location of prokaryotic genemark executable
 augustus=/cm/shared/apps/WUR/ABGC/augustus/augustus.2.7/src/augustus #location of augustus executable
 fgenesh= #location of fgenesh executable
 
 #-----Other Algorithms
 probuild= #location of probuild executable (required for genemark)

contents of maker_bopts.ctl

 #-----BLAST and Exonerate Statistics Thresholds
 blast_type=ncbi+ #set to 'ncbi+', 'ncbi' or 'wublast'
 
 pcov_blastn=0.8 #Blastn Percent Coverage Threhold EST-Genome Alignments
 pid_blastn=0.85 #Blastn Percent Identity Threshold EST-Genome Aligments
 eval_blastn=1e-10 #Blastn eval cutoff
 bit_blastn=40 #Blastn bit cutoff
 depth_blastn=0 #Blastn depth cutoff (0 to disable cutoff)
 
 pcov_blastx=0.5 #Blastx Percent Coverage Threhold Protein-Genome Alignments
 pid_blastx=0.4 #Blastx Percent Identity Threshold Protein-Genome Aligments
 eval_blastx=1e-06 #Blastx eval cutoff
 bit_blastx=30 #Blastx bit cutoff
 depth_blastx=0 #Blastx depth cutoff (0 to disable cutoff)
 
 pcov_tblastx=0.8 #tBlastx Percent Coverage Threhold alt-EST-Genome Alignments
 pid_tblastx=0.85 #tBlastx Percent Identity Threshold alt-EST-Genome Aligments
 eval_tblastx=1e-10 #tBlastx eval cutoff
 bit_tblastx=40 #tBlastx bit cutoff
 depth_tblastx=0 #tBlastx depth cutoff (0 to disable cutoff)
 
 pcov_rm_blastx=0.5 #Blastx Percent Coverage Threhold For Transposable Element Masking
 pid_rm_blastx=0.4 #Blastx Percent Identity Threshold For Transposbale Element Masking
 eval_rm_blastx=1e-06 #Blastx eval cutoff for transposable element masking
 bit_rm_blastx=30 #Blastx bit cutoff for transposable element masking
 
 ep_score_limit=20 #Exonerate protein percent of maximal score threshold
 en_score_limit=20 #Exonerate nucleotide percent of maximal score threshold

See also

Maker pipeline as installed on Anunna

External links

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