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RAxML-NG#

RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree

RAxML-NG at NHPCC#

There are two ways to run RAxML-NG on Panthera cluster:

  • Interactive mode
  • Using subraxml command

Interactive mode#

First, create an interactive job to connect to one of the compute nodes: 

u111112@login1:~/wrkdir> srun -n 4 --mem=1G -p short -t 10 --pty /bin/bash
srun: job 57293 queued and waiting for resources
srun: job 57293 has been allocated resources
u111112@cn-12-1:~/wrkdir>

Then, you have to load the RAxML-NG module:

u111112@cn-12-1:~/wrkdir> ml RAxML-NG

Tip

In order to see all RAxML versions installed on Panthera you can type RAxML and press the Tab key twice. For more information on how to use modules, please visit this page.

Finally, you can use your software:

u111112@cn-12-1:~/wrkdir> your_software_command ...

Using subraxml command#

This is the fast and easiest method most users prefer to load and run RAxML-NG on the cluster. Simply on login node press subraxml command without any options to see it's help:

u111112@login1:~/wrkdir> subraxml
Create and submit job for RAxML and RAxML-NG

Usage: subraxml <INPUT> [OPTION]

        -n  <n1[:n2]>     Number of MPI and OpenMP processors.
        -N  <n3[:n4]>     Number of nodes and number of tasks per node. 
        -m  <mem>         Memory required for job (GB).
        -p  <part>        Partition name to submit the job. (use 'sinfo')
        -v  <ver>         Software version.
                             RAxML   : 8.2.12i, 8.2.12g, 8.2.12m Default: 8.2.12i
                             RAxML-NG: 1.2.1, 1.2.0, 1.0.2, 1.1.0 Default: 1.2.1
        -o  <opt>         Options for raxmlHPC or raxml-ng commands. 
        -j  <jobname>     Default: RAxML
        -t  <time>        run time of the job. Valid format: M, H:M:S, D-H, D-H:M
        -so <sopt>        Additional slurm options if needed.
        -no               Only write job file.
        -ng               Run RAxML-NG
        -h | --help       Print this message and exit.

 Example:   subraxml input.fas -n 8 -m 2 -o '-f a -x 423774 -p 423774 -N 1000 -m GTRGAMMAI -O' -t 1-0
 Example:   subraxml testDNA.fa -n 8 -m 2 -o '--model GTR+G' -ng -t 1-0