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Add doNotRun='true' to the run section of your BEAST XML file.
Start an interactive session with enough memory to start the BEAST job: qrsh -pe mthread 8
In the interactive session, load the BEAST module and start the execution of your XML file. In the -threads option, specify the number of SNAPP steps you specific in your XML (in the example it is 48)
Code Block
language bash
module load bio/beast beast -threads 48 your_file.xml

This creates 48 step directories and a run<number>.sh script for each one. You can submit a separate job for each of the bash scripts. A sample job file (beast_step_run.job) and a bash script to submit the jobs are below.

Code Block

language	bash
title	beast_step_run.job

# /bin/sh
# ----------------Parameters---------------------- #
#$ -S /bin/sh
#$ -q lThM.q
#$ -l mres=16G,h_data=16G,h_vmem=16G,himem
#$ -cwd
#$ -j y
#$ -N beast_step_run
#$ -o beast_step_run.log
#
# ----------------Modules------------------------- #
module load bioinformatics/beast
#
# ----------------Your Commands------------------- #
#
echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME
echo + NSLOTS = $NSLOTS

#
if [ -z $1 ]; then
  echo "Give the run number as an argument: e.g. qsub beast_step_run.job 0"
  exit 1
fi

source ./run${1}.sh
#
echo = `date` job $JOB_NAME done

Code Block

language	bash
title	submit.sou

for x in $(seq 0 47); do
  qsub -o run${x}.log beast_step_run.job ${x}
done

Change the seq command to match the range of steps. Shown here is for 48 steps which are numbered run0.sh to run47.sh

Submit the steps as separate cluster jobs with: source submit.sou

When all the jobs are complete, run the PathSampleAnalyser to get the final output. In the below example, the output is redirected to the file pathsampler.out . You should of course adjust the arguments (like alpha and burnInPercentage to suite your analysis.

Code Block

language	bash
title	PathSampleAnalyser

qrsh -pe mthread 8
module load bio/beast
javaapplauncher beast.inference.PathSampleAnalyser -nrOfSteps 48 -alpha 0.3 path_run1 25-rootdir /path/to/your/runs -burnInPercentage 25 >pathsampler.out 2>&1

You can see all the PathSampleAnalyser arguments with: applauncher PathSampleAnalyser -help

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