<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Sorry for the slow reply. Your e-mail was marked as spam for some reason by the e-mail list software, and I only review the spam folder on the list server every few weeks.<div class=""><br class=""></div><div class="">You provided est_gff and protein_gff. Those files are either malformated, or the contig names in the fasta and the names in the GFF3 you provided (column 2) do not match.</div><div class=""><br class=""></div><div class="">I also see lots of URI escape sequences (preceeded with % in GFF3) SczI0sq_2092%3%3D3122, so you may be using basd characters in the fasta IDs that are then being escaped.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""> <br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 24, 2018, at 10:30 AM, Ganote, Carrie L <<a href="mailto:cganote@iu.edu" class="">cganote@iu.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div class="">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 class="">##gff-version 3</div>
<div class="">SczI0sq_2092%3%3D3122 . contig 1 119548 . . . ID=SczI0sq_2092%3%3D3122;Name=SczI0sq_2092%3%3D3122</div>
<div class="">###</div>
<div class="">SczI0sq_842%3%3D1778 . contig 1 4693 . . . ID=SczI0sq_842%3B%3D1778;Name=SczI0sq_842%3%3D1778</div>
<div class="">###</div>
</div>
<div class="">...</div>
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<div class="">In my opts file, I have:</div>
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<div class="">#-----Genome (these are always required)</div>
<div class=""><b class="">genome=/projects/Reference/genome.chr.fa #genome sequence (fasta file or fasta embeded in GFF3 file)</b></div>
<div class="">organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic</div>
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</div>
<div class="">#-----Re-annotation Using MAKER Derived GFF3</div>
<div class="">maker_gff= #MAKER derived GFF3 file</div>
<div class="">est_pass=0 #use ESTs in maker_gff: 1 = yes, 0 = no</div>
<div class="">altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no</div>
<div class="">protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no</div>
<div class="">rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no</div>
<div class="">model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no</div>
<div class="">pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no</div>
<div class="">other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no</div>
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</div>
<div class="">#-----EST Evidence (for best results provide a file for at least one)</div>
<div class="">est= #set of ESTs or assembled mRNA-seq in fasta format</div>
<div class="">altest= #EST/cDNA sequence file in fasta format from an alternate organism</div>
<div class=""><b class="">est_gff=/projects/Reference/Maker/EST_assembled.all.gff #aligned ESTs or mRNA-seq from an external GFF3 file</b></div>
<div class="">altest_gff= #aligned ESTs from a closly relate species in GFF3 format</div>
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</div>
<div class="">#-----Protein Homology Evidence (for best results provide a file for at least one)</div>
<div class="">protein= #protein sequence file in fasta format (i.e. from mutiple oransisms)</div>
<div class=""><b class="">protein_gff=/projects/Reference/Maker/exonerate_withCC.gff3 #aligned protein homology evidence from an external GFF3 file</b></div>
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</div>
<div class="">#-----Repeat Masking (leave values blank to skip repeat masking)</div>
<div class="">model_org= #select a model organism for RepBase masking in RepeatMasker</div>
<div class="">rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker</div>
<div class="">repeat_protein= #provide a fasta file of transposable element proteins for RepeatRunner</div>
<div class="">rm_gff= #pre-identified repeat elements from an external GFF3 file</div>
<div class="">prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no</div>
<div class="">softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)</div>
</div>
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<div class="">
<div class="">#-----Gene Prediction</div>
<div class="">snaphmm= #SNAP HMM file</div>
<div class="">gmhmm= #GeneMark HMM file</div>
<div class="">augustus_species= #Augustus gene prediction species model</div>
<div class="">fgenesh_par_file= #FGENESH parameter file</div>
<div class=""><b class="">pred_gff=/projects/Reference/Maker/augustus_output.reformated.gff #ab-initio predictions from an external GFF3 file</b></div>
<div class="">model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)</div>
<div class="">est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no</div>
<div class="">protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no</div>
<div class="">trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no</div>
<div class="">snoscan_rrna= #rRNA file to have Snoscan find snoRNAs</div>
<div class="">unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no</div>
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</div>
<div class="">#-----Other Annotation Feature Types (features MAKER doesn't recognize)</div>
<div class="">other_gff= #extra features to pass-through to final MAKER generated GFF3 file</div>
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</div>
<div class="">#-----External Application Behavior Options</div>
<div class="">alt_peptide=C #amino acid used to replace non-standard amino acids in BLAST databases</div>
<div class="">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>
<div class="">#-----MAKER Behavior Options</div>
<div class="">max_dna_len=100000 #length for dividing up contigs into chunks (increases/decreases memory usage)</div>
<div class="">min_contig=1 #skip genome contigs below this length (under 10kb are often useless)</div>
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</div>
<div class="">pred_flank=200 #flank for extending evidence clusters sent to gene predictors</div>
<div class="">pred_stats=0 #report AED and QI statistics for all predictions as well as models</div>
<div class="">AED_threshold=1 #Maximum Annotation Edit Distance allowed (bound by 0 and 1)</div>
<div class="">min_protein=0 #require at least this many amino acids in predicted proteins</div>
<div class="">alt_splice=0 #Take extra steps to try and find alternative splicing, 1 = yes, 0 = no</div>
<div class="">always_complete=0 #extra steps to force start and stop codons, 1 = yes, 0 = no</div>
<div class="">map_forward=0 #map names and attributes forward from old GFF3 genes, 1 = yes, 0 = no</div>
</div>
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<div class="">keep_preds=0 #Concordance threshold to add unsupported gene prediction (bound by 0 and 1)</div>
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<div class="">split_hit=10000 #length for the splitting of hits (expected max intron size for evidence alignments)</div>
<div class="">single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no</div>
<div class="">single_length=250 #min length required for single exon ESTs if 'single_exon is enabled'</div>
<div class="">correct_est_fusion=0 #limits use of ESTs in annotation to avoid fusion genes</div>
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<div class="">tries=2 #number of times to try a contig if there is a failure for some reason</div>
<div class="">clean_try=0 #remove all data from previous run before retrying, 1 = yes, 0 = no</div>
<div class="">clean_up=0 #removes theVoid directory with individual analysis files, 1 = yes, 0 = no</div>
<div class="">TMP= #specify a directory other than the system default temporary directory for temporary files</div>
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<div class="">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 class="">-Carrie</div>
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