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hoffmangroup / segway

Application for semi-automated genomic annotation.
http://segway.hoffmanlab.org/
GNU General Public License v2.0
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Default queue submitting along side specified queue from native specification (--cluster-opt) #57

Open EricR86 opened 8 years ago

EricR86 commented 8 years ago

Original report (BitBucket issue) by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

Currently on an SGE (only?) system jobs are submitted to a default queue alongside the specified queue when using --cluster-opt.

Specifically when specifying a queue with: --cluster-opt="-q labqueue"

When inspecting the job itself you see it submitted to the following queues: "default,labqueue"

EricR86 commented 8 years ago

Original comment by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

The current workaround for this is to remove user permissions from the default queue but this is not particularly a good solution.

EricR86 commented 8 years ago

Original comment by Michael Hoffman (Bitbucket: hoffman, GitHub: michaelmhoffman).

For example, in our case the default request at /$SGE_ROOT/$SGE_CELL/common/sge_request, has -q all.q. You may need to ask for help on how to override instead of append to this list on a Grid Engine mailing list.

Another workaround might be to use the qalter command to change jobs after they're queued periodically.