#-----Genome (these are always required) genome=/gscratch/srlab/sam/data/P_generosa/genomes/Pgenerosa_v074.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= /gscratch/srlab/sam/data/P_generosa/transcriptomes/ctenidia/Trinity.fasta, /gscratch/srlab/sam/data/P_generosa/transcriptomes/gonad/Trinity.fasta, /gscratch/srlab/sam/data/P_generosa/transcriptomes/heart/Trinity.fasta, /gscratch/srlab/sam/data/P_generosa/transcriptomes/larvae/EPI99/Trinity.fasta, /gscratch/srlab/sam/data/P_generosa/transcriptomes/juvenile/EPI115/Trinity.fasta, /gscratch/srlab/sam/data/P_generosa/transcriptomes/juvenile/EPI116/Trinity.fasta, /gscratch/srlab/sam/data/P_generosa/transcriptomes/juvenile/EPI123/Trinity.fasta, /gscratch/srlab/sam/data/P_generosa/transcriptomes/juvenile/EPI124/Trinity.fasta #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= /gscratch/srlab/sam/data/C_gigas/gigas_ncbi_protein/GCA_000297895.1_oyster_v9_protein.faa, /gscratch/srlab/sam/data/P_generosa/proteomes/20180827_trinity_geoduck.fasta.transdecoder.pep, /gscratch/srlab/sam/data/P_generosa/proteomes/ctenidia/Trinity.fasta.transdecoder.pep, /gscratch/srlab/sam/data/P_generosa/proteomes/gonad/Trinity.fasta.transdecoder.pep, /gscratch/srlab/sam/data/P_generosa/proteomes/heart/Trinity.fasta.transdecoder.pep, /gscratch/srlab/sam/data/P_generosa/proteomes/juvenile/EPI115/Trinity.fasta.transdecoder.pep, /gscratch/srlab/sam/data/P_generosa/proteomes/juvenile/EPI116/Trinity.fasta.transdecoder.pep, /gscratch/srlab/sam/data/P_generosa/proteomes/juvenile/EPI123/Trinity.fasta.transdecoder.pep, /gscratch/srlab/sam/data/P_generosa/proteomes/juvenile/EPI124/Trinity.fasta.transdecoder.pep, /gscratch/srlab/sam/data/P_generosa/proteomes/larvae/EPI99/Trinity.fasta.transdecoder.pep, /gscratch/srlab/sam/data/C_virginica/virginica_ncbi_protein/GCF_002022765.2_C_virginica-3.0_protein.faa #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=all #select a model organism for RepBase masking in RepeatMasker rmlib=/gscratch/srlab/sam/data/P_generosa/repeats/Pgenerosa_v074-families.fa #provide an organism specific repeat library in fasta format for RepeatMasker repeat_protein=/gscratch/srlab/programs/maker-2.31.10/data/te_proteins.fasta #provide a fasta file of transposable element proteins for RepeatRunner rm_gff=/gscratch/srlab/sam/data/P_generosa/repeats/Pgenerosa_v074.fa.out.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= #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) est2genome=1 #infer gene predictions directly from ESTs, 1 = yes, 0 = no protein2genome=1 #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 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=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=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=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