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<div>Running maker, I don't see anything in the gff except the names of the contigs and their lengths:</div>
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<div>##gff-version 3</div>
<div>SczI0sq_2092%3%3D3122 . contig 1 119548 . . . ID=SczI0sq_2092%3%3D3122;Name=SczI0sq_2092%3%3D3122</div>
<div>###</div>
<div>SczI0sq_842%3%3D1778 . contig 1 4693 . . . ID=SczI0sq_842%3B%3D1778;Name=SczI0sq_842%3%3D1778</div>
<div>###</div>
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<div>...</div>
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<div>In my opts file, I have:</div>
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<div>#-----Genome (these are always required)</div>
<div><b>genome=/projects/Reference/genome.chr.fa #genome sequence (fasta file or fasta embeded in GFF3 file)</b></div>
<div>organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic</div>
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<div>#-----Re-annotation Using MAKER Derived GFF3</div>
<div>maker_gff= #MAKER derived GFF3 file</div>
<div>est_pass=0 #use ESTs in maker_gff: 1 = yes, 0 = no</div>
<div>altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no</div>
<div>protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no</div>
<div>rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no</div>
<div>model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no</div>
<div>pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no</div>
<div>other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no</div>
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<div>#-----EST Evidence (for best results provide a file for at least one)</div>
<div>est= #set of ESTs or assembled mRNA-seq in fasta format</div>
<div>altest= #EST/cDNA sequence file in fasta format from an alternate organism</div>
<div><b>est_gff=/projects/Reference/Maker/EST_assembled.all.gff #aligned ESTs or mRNA-seq from an external GFF3 file</b></div>
<div>altest_gff= #aligned ESTs from a closly relate species in GFF3 format</div>
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<div>#-----Protein Homology Evidence (for best results provide a file for at least one)</div>
<div>protein= #protein sequence file in fasta format (i.e. from mutiple oransisms)</div>
<div><b>protein_gff=/projects/Reference/Maker/exonerate_withCC.gff3 #aligned protein homology evidence from an external GFF3 file</b></div>
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<div>#-----Repeat Masking (leave values blank to skip repeat masking)</div>
<div>model_org= #select a model organism for RepBase masking in RepeatMasker</div>
<div>rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker</div>
<div>repeat_protein= #provide a fasta file of transposable element proteins for RepeatRunner</div>
<div>rm_gff= #pre-identified repeat elements from an external GFF3 file</div>
<div>prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no</div>
<div>softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)</div>
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<div>#-----Gene Prediction</div>
<div>snaphmm= #SNAP HMM file</div>
<div>gmhmm= #GeneMark HMM file</div>
<div>augustus_species= #Augustus gene prediction species model</div>
<div>fgenesh_par_file= #FGENESH parameter file</div>
<div><b>pred_gff=/projects/Reference/Maker/augustus_output.reformated.gff #ab-initio predictions from an external GFF3 file</b></div>
<div>model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)</div>
<div>est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no</div>
<div>protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no</div>
<div>trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no</div>
<div>snoscan_rrna= #rRNA file to have Snoscan find snoRNAs</div>
<div>unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no</div>
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<div>#-----Other Annotation Feature Types (features MAKER doesn't recognize)</div>
<div>other_gff= #extra features to pass-through to final MAKER generated GFF3 file</div>
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<div>#-----External Application Behavior Options</div>
<div>alt_peptide=C #amino acid used to replace non-standard amino acids in BLAST databases</div>
<div>cpus=1 #max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)</div>
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<div>#-----MAKER Behavior Options</div>
<div>max_dna_len=100000 #length for dividing up contigs into chunks (increases/decreases memory usage)</div>
<div>min_contig=1 #skip genome contigs below this length (under 10kb are often useless)</div>
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<div>pred_flank=200 #flank for extending evidence clusters sent to gene predictors</div>
<div>pred_stats=0 #report AED and QI statistics for all predictions as well as models</div>
<div>AED_threshold=1 #Maximum Annotation Edit Distance allowed (bound by 0 and 1)</div>
<div>min_protein=0 #require at least this many amino acids in predicted proteins</div>
<div>alt_splice=0 #Take extra steps to try and find alternative splicing, 1 = yes, 0 = no</div>
<div>always_complete=0 #extra steps to force start and stop codons, 1 = yes, 0 = no</div>
<div>map_forward=0 #map names and attributes forward from old GFF3 genes, 1 = yes, 0 = no</div>
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<div>keep_preds=0 #Concordance threshold to add unsupported gene prediction (bound by 0 and 1)</div>
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<div>split_hit=10000 #length for the splitting of hits (expected max intron size for evidence alignments)</div>
<div>single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no</div>
<div>single_length=250 #min length required for single exon ESTs if 'single_exon is enabled'</div>
<div>correct_est_fusion=0 #limits use of ESTs in annotation to avoid fusion genes</div>
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<div>tries=2 #number of times to try a contig if there is a failure for some reason</div>
<div>clean_try=0 #remove all data from previous run before retrying, 1 = yes, 0 = no</div>
<div>clean_up=0 #removes theVoid directory with individual analysis files, 1 = yes, 0 = no</div>
<div>TMP= #specify a directory other than the system default temporary directory for temporary files</div>
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<div>It ran for ~3 hours and all contigs in the log file said FINISHED. No failures. Did I set something wrong?</div>
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<div>-Carrie</div>
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