Difference between revisions of "Applications/iqtree"
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==Application Details== | ==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 | + | *Version: MPI 1.4.4 |
| − | *Licence: | + | *Licence: Open source |
==usage== | ==usage== | ||
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Last login: Wed Jan 25 09:10:51 2017 from 10.254.5.246 | 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 ~]$ module add openmpi/gcc/1.10.2 | ||
| − | [username@c170 ~]$ /trinity/clustervision/CentOS/7/apps/ | + | [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 |
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</pre> | </pre> | ||
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Below is how to submit the same example using our scheduler slurm. | Below is how to submit the same example using our scheduler slurm. | ||
| − | please replace /home/USERNAME/PATH/OF/DIR | + | 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. |
<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;"> | <pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;"> | ||
#!/bin/bash | #!/bin/bash | ||
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#SBATCH --exclusive # Request exclusive access to a node (all 28 cores, 128GB of RAM) | #SBATCH --exclusive # Request exclusive access to a node (all 28 cores, 128GB of RAM) | ||
| − | module | + | module add openmpi/gcc/1.10.2 |
cd /home/USERNAME/PATH/OF/DIR | cd /home/USERNAME/PATH/OF/DIR | ||
| − | /trinity/clustervision/CentOS/7/apps/ | + | mpirun /trinity/clustervision/CentOS/7/apps/iqtree/1.4.4/openmpi-1.10.2/gcc-4.9.3/bin/iqtree-mpi -s example.phy |
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</pre> | </pre> | ||
Then the next step is to submit the above script to slurm | Then the next step is to submit the above script to slurm | ||
| − | for example if you name the above text file | + | for example if you name the above text file iqtree.sh |
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| − | [user@login01 ~]$ sbatch | + | [user@login01 ~]$ sbatch iqtree.sh |
Submitted batch job 409671 | Submitted batch job 409671 | ||
</pre> | </pre> | ||
| − | == | + | ==Next Steps== |
* http://www.iqtree.org/doc/ | * http://www.iqtree.org/doc/ | ||
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Latest revision as of 10:48, 16 November 2022
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