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