Iqtree2

Introduction

IQ-TREE is an efficient phylogenomic software by maximum likelihood.

For more information, please check:

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

Home page: http://www.iqtree.org

Note

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

Versions

Cluster	Version(s)
ANVIL	2.2.2.6, 2.2.2.9
BELL	2.2.2.6, 2.2.2.9
GAUTSCHI	2.2.2.6, 2.2.2.9
NEGISHI	2.2.2.6, 2.2.2.9
SCHOLAR	2.2.2.6, 2.2.2.9

Commands

• iqtree2

Module

You can load the modules by:

module load biocontainers
module load iqtree2

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 iqtree2 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=iqtree2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers iqtree2

# Your iqtree2 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=iqtree2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers iqtree2

# Your iqtree2 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=iqtree2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers iqtree2

# Your iqtree2 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=iqtree2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers iqtree2

# Your iqtree2 workflow...

Scholar

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=iqtree2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers iqtree2

# Your iqtree2 workflow...