qsub command not found

If you see a qsub: command not found or qconf: not found or qstat: command not found error in your smrtpipe.log file, this indicates that the Job Managment system (In this case SGE) may not be configured properly. Specifically, the smrtanalysis user does not have the qsub or any q-commands defined in its path.

To fix this problem for the smrtanalysis user, you must define the SGE_ROOT and SGE_CELL variables in the user's .bashrc file. Execute the following lines (including quotations) to add the relevant lines in the ~smrtanalysis/.bashrc file:

echo "export SGE_ROOT=<root_name>
export SGE_CELL=<cell_name>
source $SGE_ROOT/$SGE_CELL/common/settings.sh" >> ~smrtanalysis/.bashrc

Where <root_name> is usually /usr/share/gridengine in CentOS, or /var/lib/gridengine in Ubuntu, and <cell_name> is usually default if you installed SGE using yum or apt (recommended).

To fix this problem more universally and for all users, you can add the following lines to the SEYMOUR_HOME/etc/setup.sh file:

export SGE_ROOT=<root_name>
export SGE_CELL=<cell_name>

CONFIG_FILES=(
  ${SEYMOUR_HOME}/analysis/etc/setup.sh
  ${SEYMOUR_HOME}/common/etc/setup.sh
  "${SGE_ROOT}/${SGE_CELL}/common/settings.sh"  <-- add this line without the quotes to the CONFIG_FILES definition
)