Evidencemodeler

Introduction

Evidencemodeler is a software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/evidencemodeler

Home page: https://github.com/EVidenceModeler/EVidenceModeler

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster	Version(s)
ANVIL	1.1.1
BELL	1.1.1
GAUTSCHI	1.1.1
NEGISHI	1.1.1
SCHOLAR	1.1.1

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

Warning

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:

Anvil

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition 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
module biocontainers evidencemodeler

# Your evidencemodeler workflow...

Bell, Gautschi, or Negishi

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers evidencemodeler

# Your evidencemodeler workflow...

Gautschi-AI

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers evidencemodeler

# Your evidencemodeler workflow...

Gilbreth

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers evidencemodeler

# Your evidencemodeler workflow...

Scholar

#!/bin/bash
#SBATCH -A queue     # Queue 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
module biocontainers evidencemodeler

# Your evidencemodeler workflow...