Question: PBS script not able to locate the tool
0
gravatar for MAPK
20 months ago by
MAPK1.5k
United States
MAPK1.5k wrote:

I need your help with this PBS script below. I am trying to run this command raxmlHPC-PTHREADS -T $PBS_NP -m PROTGAMMAAUTO -s test_mpkk.fas -p 12345 -n T-AUTO. I have raxmlHPC-PTHREADS tool in my directory /home/standard-RAxML-master. I have setup the path to this tool in bash enviroment and typed source ~/.bashrc (also in the script) before running the job, but it is not finding the tool. Could you please check my pbs script and let me know what's the issue. Thanks for your help .

#!/bin/bash
#PBS -N Raxml
#PBS -l nodes=1:ppn=12
#PBS -l walltime=30:00:00
#PBS -j oe

###Return to the directory where you run the job
cd $PBS_O_WORKDIR
start=`date +%s`

source ~/.bashrc
raxmlHPC-PTHREADS -T $PBS_NP -m PROTGAMMAAUTO -s test_mpkk.fas -p 12345 -n T-AUTO 

end=`date +%s`
echo 'Start: '$start
echo 'End: '$end
runtime=$((end-start))
echo 'Runtime: '$runtime
pbs • 614 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by MAPK1.5k

Some clusters are setup in such a way that /home directories may not be available on execution nodes. Have you looked into that possibility?

ADD REPLYlink written 20 months ago by genomax78k

Try providing absolute path to the tool. This always happens with our cluster.

ADD REPLYlink written 20 months ago by venu6.3k
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