[maker-devel] Maker not producing expected output
Carson Holt
carsonhh at gmail.com
Sat Oct 17 14:24:42 MDT 2015
You will only get fasta files for the contig when there are gene models present on that contig. The only ab initio predictor you provided parameters for is GeneMark, and apparently it did not predict any genes for the contig in question. If it did you would have at least a fasta files in the output that contained all predictions made by GeneMark. MAKER doesn’t make gene models, rather it provides hints to other gene predictors based on the evidence alignments and then promotes and polishes the models they make. If they produce no models, then you will get no results.
You can try adding additional gene predictors like SNAP (incase GeneMark just isn’t performing well), or you can check the length of your contig (contigs shorter than about 10kb rarely produce any results - they are too short to be annotatable). Try looking at the results from one of the larger contigs, or use fasta_merge to gather all results from all contigs.
—Carson
> On Oct 16, 2015, at 10:10 PM, Kevin Kocot <kmkocot at gmail.com> wrote:
>
> Hello,
>
> I've run Maker on a draft invertebrate genome and it seemed to finish successfully. However, many of the expected output files were not produced. If I go to, for example, XX_datastore/00/0C/scaffold-334630/, all I see is:
>
> theVoid.scaffold-334630
> run.log
> scaffold-334630.gff
>
> In particular, I'm looking for the transcripts and proteins fasta files. I'm sure I have a configuration setting incorrect or one of the dependencies not correctly installed, but I can't figure out what the problem is. Any thoughts on how I can resolve this issue and generate these files? Ideally I would love to be able to generate these files without having to run the whole pipeline again. Details on my configuration settings and the contents of the run.log file from my example above are pasted below.
>
> Thank you,
> Kevin
>
> -----
> run.log from the example folder above looks like this:
> -----
> SHARED_ID d574e9ca9b0019a9fe147ccb9db3588b
> CTL_OPTIONS maker_gff
> CTL_OPTIONS other_gff
> CTL_OPTIONS est test-transcriptome.fa
> CTL_OPTIONS est_reads
> CTL_OPTIONS altest KK273.fa
> CTL_OPTIONS est_gff
> CTL_OPTIONS altest_gff
> CTL_OPTIONS protein test-AA.fa
> CTL_OPTIONS protein_gff
> CTL_OPTIONS model_org all
> CTL_OPTIONS repeat_protein te_proteins.fasta
> CTL_OPTIONS rmlib
> CTL_OPTIONS rm_gff
> CTL_OPTIONS organism_type eukaryotic
> CTL_OPTIONS predictor est2genome,genemark,protein2genome
> CTL_OPTIONS est2genome 1
> CTL_OPTIONS altest2genome 0
> CTL_OPTIONS snaphmm
> CTL_OPTIONS gmhmm output/gmhmm.mod
> CTL_OPTIONS augustus_species
> CTL_OPTIONS fgenesh_par_file
> CTL_OPTIONS model_gff
> CTL_OPTIONS pred_gff
> CTL_OPTIONS max_dna_len 100000
> CTL_OPTIONS split_hit 10000
> CTL_OPTIONS pred_flank 200
> CTL_OPTIONS pred_stats 0
> CTL_OPTIONS min_protein 0
> CTL_OPTIONS AED_threshold 1
> CTL_OPTIONS single_exon 0
> CTL_OPTIONS single_length 250
> CTL_OPTIONS keep_preds 0
> CTL_OPTIONS map_forward 0
> CTL_OPTIONS est_forward 0
> CTL_OPTIONS correct_est_fusion 0
> CTL_OPTIONS alt_splice 0
> CTL_OPTIONS always_complete 0
> CTL_OPTIONS alt_peptide C
> CTL_OPTIONS evaluate 0
> CTL_OPTIONS blast_type ncbi+
> CTL_OPTIONS softmask 1
> CTL_OPTIONS pcov_blastn 0.8
> CTL_OPTIONS pid_blastn 0.85
> CTL_OPTIONS eval_blastn 1e-10
> CTL_OPTIONS bit_blastn 40
> CTL_OPTIONS depth_blastn 0
> CTL_OPTIONS pcov_rm_blastx 0.5
> CTL_OPTIONS pid_rm_blastx 0.4
> CTL_OPTIONS eval_rm_blastx 1e-06
> CTL_OPTIONS bit_rm_blastx 30
> CTL_OPTIONS pcov_blastx 0.5
> CTL_OPTIONS pid_blastx 0.4
> CTL_OPTIONS depth_blastx 0
> CTL_OPTIONS eval_blastx 1e-06
> CTL_OPTIONS bit_blastx 30
> CTL_OPTIONS pcov_tblastx 0.8
> CTL_OPTIONS pid_tblastx 0.85
> CTL_OPTIONS eval_tblastx 1e-10
> CTL_OPTIONS bit_tblastx 40
> CTL_OPTIONS depth_tblastx 0
> CTL_OPTIONS ep_score_limit 20
> CTL_OPTIONS en_score_limit 20
> CTL_OPTIONS enable_fathom 0
> CTL_OPTIONS unmask 0
> CTL_OPTIONS model_pass 0
> CTL_OPTIONS est_pass 0
> CTL_OPTIONS altest_pass 0
> CTL_OPTIONS protein_pass 0
> CTL_OPTIONS rm_pass 0
> CTL_OPTIONS other_pass 0
> CTL_OPTIONS pred_pass 0
> CTL_OPTIONS run genemark
> LOGCHILD /media/kmkocot/Sclerite/genome_projects/test/Ray_2_assembly/MAKER/test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/run.log.child.0
> LOGCHILD /media/kmkocot/Sclerite/genome_projects/test/Ray_2_assembly/MAKER/test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/run.log.child.0
> LOGCHILD /media/kmkocot/Sclerite/genome_projects/test/Ray_2_assembly/MAKER/test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/run.log.child.0
> STARTED test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/scaffold-334630.abinit_nomask.0.gmhmm%2Emod.genemark
> FINISHED test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/scaffold-334630.abinit_nomask.0.gmhmm%2Emod.genemark
> STARTED test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/scaffold-334630.0.pred.raw.section
> FINISHED test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/scaffold-334630.0.pred.raw.section
> LOGCHILD /media/kmkocot/Sclerite/genome_projects/test/Ray_2_assembly/MAKER/test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/run.log.child.0
> LOGCHILD /media/kmkocot/Sclerite/genome_projects/test/Ray_2_assembly/MAKER/test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/run.log.child.0
> LOGCHILD /media/kmkocot/Sclerite/genome_projects/test/Ray_2_assembly/MAKER/test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/run.log.child.0
> STARTED test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/scaffold-334630.0.final.section
> FINISHED test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/scaffold-334630.0.final.section
> LOGCHILD /media/kmkocot/Sclerite/genome_projects/test/Ray_2_assembly/MAKER/test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/run.log.child.0
> LOGCHILD /media/kmkocot/Sclerite/genome_projects/test/Ray_2_assembly/MAKER/test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/run.log.child.0
> LOGCHILD /media/kmkocot/Sclerite/genome_projects/test/Ray_2_assembly/MAKER/test_scaffolds_annotated_as_metazoan_by_MG-RAST.maker.output/test_scaffolds_annotated_as_metazoan_by_MG-RAST_datastore/00/0C/scaffold-334630//theVoid.scaffold-334630/run.log.child.0
>
> -----
> maker_opts
> -----
> #-----Genome (these are always required)
> genome=/media/kmkocot/Sclerite/genome_projects/test/Ray_2_assembly/MAKER/test_scaffolds_annotated_as_metazoan_by_MG-RAST.fas #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=/media/kmkocot/Sclerite/genome_projects/test/Ray_2_assembly/MAKER/test-transcriptome.fa #set of ESTs or assembled mRNA-seq in fasta format
> altest=/media/kmkocot/Sclerite/genome_projects/test/Ray_2_assembly/MAKER/KK273.fa #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=/media/kmkocot/Sclerite/genome_projects/test/Ray_2_assembly/MAKER/test-AA.fa #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= #provide an organism specific repeat library in fasta format for RepeatMasker
> repeat_protein=/usr/local/bin/maker/data/te_proteins.fasta #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=/media/kmkocot/Sclerite/genome_projects/test/Ray_2_assembly/MAKER/output/gmhmm.mod #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
>
> --
> Kevin M. Kocot, Ph.D.
> NSF International Postdoctoral Research Fellow
> Degnan Lab
> The University of Queensland
> School of Biological Sciences
> 325 Goddard Building 8
> St. Lucia, QLD 4072
> Australia
> Ph: +61 0402 488 430
>
>
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