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Hello,
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<div class="">I previously used Maker to annotate two different fungal genomes that were created using Illumina sequences only. For these genomes, I had over 11,000 genes predicted. </div>
<div class="">I recently obtained PacBio sequences for the same genomes, so I created two hybrid assemblies. Both assemblies were very familiar in length and completed number of orthologs to the Illumina only assembly, but had much fewer, but longer contigs. </div>
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<div class="">I re-ran Maker using the settings below. For one of my genomes, I got around 11,000 genes predicted again, as expected. However, for the other genome, I am continuously getting ~4,400 predicted genes. </div>
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<div class="">I am asking for help as to how I can determine why I keep getting fewer predicted genes for only one of my genomes, even though I ran them the same?</div>
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<div class="">Thanks,</div>
<div class="">Morgan S. </div>
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<div class="">maker_opts.log</div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----Genome (these are always required)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">genome=/work/Geomicrobiology/msobol/IODP_329_SPG/1368D2H1/repeatmasker/unicycler/1368D_unicycler_contigs.fasta.masked #genome sequence (fasta file or$</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----Re-annotation Using MAKER Derived GFF3</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">maker_gff=/work/Geomicrobiology/msobol/IODP_329_SPG/1368D2H1/maker/1368D_2H1_contigs.fasta.maker.output/1368D_2H1_contigs.fasta.all.gff #MAKER derive$</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">est_pass=0 #use ESTs in maker_gff: 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">altest_pass=1 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">protein_pass=1 #use protein alignments in maker_gff: 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----EST Evidence (for best results provide a file for at least one)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">est= #set of ESTs or assembled mRNA-seq in fasta format</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">altest= #EST/cDNA sequence file in fasta format from an alternate organism</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">est_gff= #aligned ESTs or mRNA-seq from an external GFF3 file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">altest_gff= #aligned ESTs from a closly relate species in GFF3 format</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----Protein Homology Evidence (for best results provide a file for at least one)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">protein=/work/Geomicrobiology/msobol/IODP_329_SPG/uniprot_sprot.fasta #protein sequence file in fasta format (i.e. from mutiple oransisms)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">protein_gff= #aligned protein homology evidence from an external GFF3 file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----Repeat Masking (leave values blank to skip repeat masking)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">model_org= #select a model organism for RepBase masking in RepeatMasker</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">repeat_protein= #provide a fasta file of transposable element proteins for RepeatRunner</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">rm_gff= #pre-identified repeat elements from an external GFF3 file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">softmask=0 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----Gene Prediction</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">snaphmm= #SNAP HMM file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">gmhmm=/home/msobol/genemark/68D_2/output/gmhmm.mod #GeneMark HMM file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">augustus_species=1368D_uni #Augustus gene prediction species model</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">fgenesh_par_file= #FGENESH parameter file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">pred_gff= #ab-initio predictions from an external GFF3 file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">protein2genome=1 #infer predictions from protein homology, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">snoscan_rrna= #rRNA file to have Snoscan find snoRNAs</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----Other Annotation Feature Types (features MAKER doesn't recognize)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">other_gff= #extra features to pass-through to final MAKER generated GFF3 file</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----External Application Behavior Options</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">alt_peptide=C #amino acid used to replace non-standard amino acids in BLAST databases</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">cpus=1 #max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">#-----MAKER Behavior Options</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">max_dna_len=100000 #length for dividing up contigs into chunks (increases/decreases memory usage)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">min_contig=1 #skip genome contigs below this length (under 10kb are often useless)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">pred_flank=200 #flank for extending evidence clusters sent to gene predictors</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">pred_stats=1 #report AED and QI statistics for all predictions as well as models</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">AED_threshold=1 #Maximum Annotation Edit Distance allowed (bound by 0 and 1)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">min_protein=0 #require at least this many amino acids in predicted proteins</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">alt_splice=0 #Take extra steps to try and find alternative splicing, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">always_complete=0 #extra steps to force start and stop codons, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">map_forward=0 #map names and attributes forward from old GFF3 genes, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">keep_preds=1 #Concordance threshold to add unsupported gene prediction (bound by 0 and 1)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">split_hit=10000 #length for the splitting of hits (expected max intron size for evidence alignments)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">single_exon=1 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">single_length=250 #min length required for single exon ESTs if 'single_exon is enabled'</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">correct_est_fusion=0 #limits use of ESTs in annotation to avoid fusion genes</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">tries=2 #number of times to try a contig if there is a failure for some reason</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">clean_try=0 #remove all data from previous run before retrying, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">clean_up=0 #removes theVoid directory with individual analysis files, 1 = yes, 0 = no</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">TMP= #specify a directory other than the system default temporary directory for temporary files</span></div>
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