[maker-devel] Maker ignores evidence and just returns gffs with genome contigs

[Carson Holt]

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.

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.

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.

—Carson
 

> On Jul 24, 2018, at 10:30 AM, Ganote, Carrie L <cganote at iu.edu> wrote:
> 
> Running maker, I don't see anything in the gff except the names of the contigs and their lengths:
> 
> ##gff-version 3
> SczI0sq_2092%3%3D3122    .       contig  1       119548  .       .       .       ID=SczI0sq_2092%3%3D3122;Name=SczI0sq_2092%3%3D3122
> ###
> SczI0sq_842%3%3D1778     .       contig  1       4693    .       .       .       ID=SczI0sq_842%3B%3D1778;Name=SczI0sq_842%3%3D1778
> ###
> ...
> 
> In my opts file, I have:
> 
> #-----Genome (these are always required)
> genome=/projects/Reference/genome.chr.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= #EST/cDNA sequence file in fasta format from an alternate organism
> est_gff=/projects/Reference/Maker/EST_assembled.all.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=  #protein sequence file in fasta format (i.e. from mutiple oransisms)
> protein_gff=/projects/Reference/Maker/exonerate_withCC.gff3  #aligned protein homology evidence from an external GFF3 file
> 
> #-----Repeat Masking (leave values blank to skip repeat masking)
> model_org= #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= #SNAP HMM file
> gmhmm= #GeneMark HMM file
> augustus_species= #Augustus gene prediction species model
> fgenesh_par_file= #FGENESH parameter file
> pred_gff=/projects/Reference/Maker/augustus_output.reformated.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
> 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
> 
> It ran for ~3 hours and all contigs in the log file said FINISHED. No failures. Did I set something wrong?
> 
> -Carrie
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