Stopping Celera Assembler jobs - pb-dyim/SMRT-Analysis GitHub Wiki

Celera Assembler SGE jobs cannot be stopped by using the smrtpipe --kill command in the SMRT Pipe job directory. This is because during the Celera Assembler workflow, some jobs are submitted to SGE by SMRT Pipe (such as jobs submitted by the SFilter module) and others are submitted by Celera Assembler (such as overlapper jobs.) Celera Assembler-submitted jobs typically have names that end with _asm or _celera.

Monitor and possibly terminate Celera Assembler-submitted jobs manually by using the qstat and qdel commands:

#Look for assembler jobs run by smrtanalysis in ``my_queue``:

qstat -U smrtanalysis -q my_queue | grep _asm
3637705 0.00000 rCA_asm    smrtanalysis      qw    09/10/2012 09:26:53

#Manually delete the job:

qdel 3637705