Closed tangerzhang closed 6 years ago
You can try
[General]
pwatcher_type = fs_based
job_type = sge
The default might work for you.
But if you know how to submit jobs to your PBS, you can specify that explicitly, something like:
[job.defaults]
submit = job_queue = qsub -S /bin/bash -V -q myqueue \
-N ${JOB_NAME} \
-o "${JOB_STDOUT}" \
-e "${JOB_STDERR}" \
-pe smp ${NPROC} \
"${JOB_SCRIPT}"
kill = qdel ${JOB_NAME}
[General]
pwatcher_type = fs_based
job_type = pbs
Or as simpler, "blocking" calls, with -W block=true
:
[job.defaults]
submit = job_queue = qsub -S /bin/bash -W block=true -V -q myqueue \
-N ${JOB_NAME} \
-o "${JOB_STDOUT}" \
-e "${JOB_STDERR}" \
-pe smp ${NPROC} \
"${JOB_SCRIPT}"
[General]
pwatcher_type = blocking
Feel free to update the PBS section here:
hi everyone,
Could someone please provide me some insights for allocating times in the test.cfg to run in PBS cluster. My esitmated genome size is 1.1GB and I have raw reads coverage of 70x. I selected 30x seed read coverage.
Thank you in advance,
AJ
The time for each job is controlled by the block size. Smaller blocks => more but quicker jobs.
Hi, I used the config file (attached below) you suggested in PBS system. But FALCON only works locally, not submit any job to PBS grid. Any suggestion? Thanks!