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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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How to run nextdenovo on a set of cloud service with SGE? #77

Closed AntetokounmJie closed 3 years ago

AntetokounmJie commented 3 years ago

Question or Expected behavior Hi sir i wanna run nextdenovo on a cloud service and i set the parameter in my run.cfg like this to run the test file:

job_type = sge cluster_options = -l vf={vf} -pe smp {cpu} -S {bash} -w n sge_queue = "the node name given by the cloud service company"

The first split job is good to submit and excute, but the second step`s align jobs just stuck there. when i type qstat , then the state always show as "qw". how can solve this?

Operating system LSB Version: :core-4.1-amd64:core-4.1-noarch Distributor ID: CentOS Description: CentOS Linux release 7.5.1804 (Core) Release: 7.5.1804 Codename: Core

GCC gcc version 4.8.5 20150623 (Red Hat 4.8.5-39) (GCC)

Python Python 3.7.3

NextDenovo nextDenovo v2.3.0

Additional context (Optional) None

AntetokounmJie commented 3 years ago

besides ,if i type "qhost -q", i will got several nodes. but i just wanna use one of them to excute my jobs. so how can i custom my run.cfg file. thanks a lot :)

moold commented 3 years ago

The qw state means your jobs are queued and waiting, you can use qstat -j PID to check. For NextDenovo, see here to instlal drmaa, and then set job_type = sge is ok, you also can adjust cluster_options to meet your requirement. If you still have problems, you need to ask your system administrator for help, which is usually caused by incorrect SGE system configuration.