Purdue University

Commands

• evidence_modeler.pl
• BPbtab.pl
• EVMLite.pl
• EVM_to_GFF3.pl
• convert_EVM_outputs_to_GFF3.pl
• create_weights_file.pl
• execute_EVM_commands.pl
• extract_complete_proteins.pl
• gff3_file_to_proteins.pl
• gff3_gene_prediction_file_validator.pl
• gff_range_retriever.pl
• partition_EVM_inputs.pl
• recombine_EVM_partial_outputs.pl
• summarize_btab_tophits.pl
• write_EVM_commands.pl

Module

You can load the modules by:

module load biocontainers
module load evidencemodeler

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Evidencemodeler on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=evidencemodeler
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers evidencemodeler


evidence_modeler.pl --genome genome.fasta \
                   --weights weights.txt \
                   --gene_predictions gene_predictions.gff3 \
                   --protein_alignments protein_alignments.gff3 \
                   --transcript_alignments transcript_alignments.gff3 \
                 > evm.out