Run RAxML on the Cluster¶
- RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees.
- This guide will cover how to run RAxML on the Cluster.
- This is the link to the RAxML Manual
- To run RAxML, you can specify the follwing with the associated flags passed into
- -m : Model of Binary (Morphological), Nucleotide, Multi-State, or Amino Acid Substitution.
- -p : Specify a random number seed for the parsimony inferences. This allows you to reproduce your results and helps debug the program.
- -s : Specify the name of the alignment data file in PHYLIP format.
- -# : Specify the number of alternative runs on distinct starting trees
- -n : Specifies the name of the output file.
- You can find more information and more flags by running
raxmlHPC -hafter loading the requried modules on the Cluster.
Walkthrough: Run RAxML on the Cluster¶
- This walkthrough will cover how to run an ML search on binary data in a PHYLIP file.
- The example used in this walkthough plus many more can be found here.
binary.phycan be found here
- PBS Script can be found here
- You can transfer the files to your account on the cluster to follow along. The file transfer guide may be helpful.
Part 1: The PBS Script¶
#PBS -N raxmlTest #PBS -A [Account] #PBS -l nodes=1:ppn=2 #PBS -l pmem=2gb #PBS -l walltime=3:00 #PBS -q inferno #PBS -j oe #PBS -o raxmlTest.out cd $PBS_O_WORKDIR module load gcc/4.9.0 module load openmpi/1.8 module load raxml/8.0.19 raxmlHPC -m BINGAMMA -p 12345 -s binary.phy -# 20 -n T5
#PBSdirectives are standard, requesting just 3 minutes of walltime and 1 node with 2 cores. More on
#PBSdirectives can be found in the PBS guide
$PBS_O_WORKDIRis a variable that represents the directory you submit the PBS script from. Make sure the files you want to use are in the same directory you put the PBS script.
- Output Files will also show up in this dir as well
module load raxml/8.0.19loads the 8.0.19 version of RAxML. To see what versions of a software are available, run
module avail [Software], and load the one you want. The other modules are dependencies that must be loaded before RAxML is loaded.
raxmlHPC -m BINGAMMA -p 12345 -s binary.phy -# 20 -n T5will have RAxML carry out 20 ML searches on 20 randomized stepwise addition parsimony trees.
Part 2: Submit Job and Check Status¶
- Make sure you're in the dir that contains the
PBSScript as well as the
- Submit as normal, with
qsub <pbs script name>. In this case
- Check job status with
qstat -t 22182721, replacing the number with the job id returned after running qsub
- You can delete the job with
qdel 22182721, again replacing the number with the jobid returned after running qsub
Part 3: Collecting Results¶
- In the directory where you submitted the
PBSscript, you should see a
raxmlTest.outfile which contains the results of the job, 20
RAxML_info.T5file, and a
cator open the file in a text editor to take a look.
raxmlTest.outshould look like this.
- All output files can be found here.
- After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
- Congratulations! You successfully ran RAxML on the cluster.