Applications/iqtree

Application Details

• Description: Allows maximum likelihood analysis of large phylogenetic data. IQ-TREE explores the tree space efficiently and often achieves higher likelihoods than RAxML and PhyML. Other key features of IQ-TREE are (i) a very fast model selection procedure including partition scheme finding, (ii) partitioned analysis for phylogenomic data, (iii) ultrafast bootstrap approximation, (iv) implementation of several branch tests and (v) tree topology tests. W-IQ-TREE an intuitive and user-friendly web interface and server for IQ-TREE is also available.
• Version: MPI 1.4.4
• Licence: Open source

usage

Interactive

While logged into viper login node: you could find the example file used in this path /home/ViperAdmin/software/source/iqtree/iqtree-mpi-1.4.4-Linux/example.phy copy it to the location where you would like to run the below steps

[username@login01 ~]$ interactive
salloc: Granted job allocation 296769
Job ID 296769 connecting to c170, please wait...
Last login: Wed Jan 25 09:10:51 2017 from 10.254.5.246
[username@c170 ~]$ module add openmpi/gcc/1.10.2
[username@c170 ~]$ mpirun  /trinity/clustervision/CentOS/7/apps/iqtree/1.4.4/openmpi-1.10.2/gcc-4.9.3/bin/iqtree-mpi -s example.phy
 

Batch Session

Below is how to submit the same example using our scheduler slurm. please replace /home/USERNAME/PATH/OF/DIR with the path of the directory where you copied the example.phy file or to the file that you want to use.

#!/bin/bash
#SBATCH -J IQtree_example   # Job name, you can change it to whatever you want
#SBATCH -o %N.%j.out        # Standard output will be written here
#SBATCH -e %N.%j.err        # Standard error will be written here
#SBATCH -n 14               # number of cores
#SBATCH -N 1                # Number of nodes
#SBATCH -p highmem          # Slurm partition, where you want the job to be queued
#SBATCH --exclusive         # Request exclusive access to a node (all 28 cores, 128GB of RAM)

module add openmpi/gcc/1.10.2
cd /home/USERNAME/PATH/OF/DIR
mpirun  /trinity/clustervision/CentOS/7/apps/iqtree/1.4.4/openmpi-1.10.2/gcc-4.9.3/bin/iqtree-mpi -s example.phy

Then the next step is to submit the above script to slurm for example if you name the above text file iqtree.sh

[user@login01 ~]$ sbatch iqtree.sh
Submitted batch job 409671

Next Steps

• http://www.iqtree.org/doc/

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