3.0.8 Pipeline for predicting genes with GeneMark-EX and AUGUSTUS with RNA-Seq and/or proteins Mario Stanke, Alexandre Lomsadze, Katharina J. Hoff, Tomas Bruna, Lars Gabriel, and Mark Borodovsky Stanke, M., Diekhans, M., Baertsch, R. and Haussler, D. (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics, doi: 10.1093/bioinformatics/btn013. Protein Prediction braker3_access scheduler_regmem 3 scheduler.conf perl !$more_memory perl "node_exclusive=0\\n" . "mem=30G\\n" . "nodes=1\\n" . "threads_per_process=8\\n" scheduler_himem 3 scheduler.conf perl $more_memory perl "node_exclusive=0\\n" . "mem=60G\\n" . "nodes=1\\n" . "threads_per_process=8\\n" invoke_wrapper perl "braker3_expanse" 1 invoke_wrapperb perl " braker.pl" 2 input_genome Sequence File perl "--genome=genome.fa" genome.fa 3 num_threads perl "--threads 8" 4 runtime 1 scheduler.conf Maximum Hours to Run (up to 168 hours) 0.5 The maximum hours to run must be less than 168 perl $runtime > 168.0 The maximum hours to run must be greater than 0.05 perl $runtime < 0.05 perl "runhours=$value\\n" The job will run on 16 processors as configured. If it runs for the entire configured time, it will consume 16 x $runtime cpu hours perl defined $nucleotid_db Estimate the maximum time your job will need to run. We recommend testimg initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. select_inputfile My data is RNAseq file input_protfile Protein Sequence File perl !$select_inputfile perl "--prot_seq=prot.fa" prot.fa Please select your protein sequence file perl !$select_inputfile && !defined $input_protfile 3 input_rnaseqfile RNAseq File perl $select_inputfile perl "--bam=/mnt/rnaseq.bam" rnaseq.bam Please select your RNAseq file perl $select_inputfile && !defined $input_rnaseqfile 3 specify_speciesname Specify your species name perl (defined $value)? " --species=$value":"" Species name. Existing species will not be overwritten. Uses Sp_1 etc., if no species is assigned- 4 specify_workingdir Specify a working directory perl defined $value ? "--workingdir=/mnt/" : "" 4 ouput_gff3 Output in GFF3 format instead of GTF perl ($value)? "--gff3":"" 10 more_memory I need more memory all_results *