RAxML-Teaching: Difference between revisions
No edit summary |
No edit summary |
||
| Line 40: | Line 40: | ||
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=RAxML.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=RAxML.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=RAxML.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
| Line 59: | Line 60: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ml RAxML/8.2.11-foss-2016b-mpi-sse3 | ml RAxML/8.2.11-foss-2016b-mpi-sse3 | ||
raxmlHPC-PTHREADS-AVX -help | |||
</pre> | </pre> | ||
Revision as of 13:07, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
8.2.11
Author / Distributor
Description
"RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." More details are at RAxML
Running Program
The last version of this application is at /usr/local/apps/eb/RAxML/8.2.11-foss-2016b-mpi-sse3
To use this version, please load the module with
ml RAxML/8.2.11-foss-2016b-mpi-sse3
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_RAxML
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=RAxML.%j.out
#SBATCH --error=RAxML.%j.err
cd $SLURM_SUBMIT_DIR
ml RAxML/8.2.11-foss-2016b-mpi-sse3
raxmlHPC-PTHREADS-AVX [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml RAxML/8.2.11-foss-2016b-mpi-sse3 raxmlHPC-PTHREADS-AVX -help
Installation
Source code is obtained from RAxML
System
64-bit Linux