In order to test that, I've just downloaded a new galaxy-central and
configured it to submit jobs in our SGE cluster. Same problem. The job
starts and finishes, but galaxy keeps informing it's still running.
I've also attached the job_conf.xml file.
Need help, please!
-Adhemar
galaxy.jobs.runners ERROR 2013-10-08 15:29:16,721 Unhandled exception
checking active jobs
Traceback (most recent call last):
File
"/opt/bioinformatics/share/galaxy20131008/lib/galaxy/jobs/runners/__init__.py",
line 362, in monitor
self.check_watched_items()
File
"/opt/bioinformatics/share/galaxy20131008/lib/galaxy/jobs/runners/drmaa.py",
line 217, in check_watched_items
log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag,
external_job_id, e.__class__.name, e )
AttributeError: type object 'InvalidJobException' has no attribute 'name'
<?xml version="1.0"?>
<job_conf>
<plugins workers="10">
<!-- <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="10"/> -->
<plugin id="sge" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="10"/>
</plugins>
<handlers default="handlers">
<handler id="main"/>
<handler id="handler0" tags="handlers"/>
<handler id="handler1" tags="handlers"/>
<handler id="handler2" tags="handlers"/>
<handler id="handler3" tags="handlers"/>
<handler id="handler4" tags="handlers"/>
<handler id="handler5" tags="handlers"/>
<handler id="handler6" tags="handlers"/>
<handler id="handler7" tags="handlers"/>
<handler id="handler8" tags="handlers"/>
<handler id="handler9" tags="handlers"/>
</handlers>
<destinations default="sge_cluster">
<!--
<destination id="local" runner="local"/>
-->
<destination id="sge_cluster" runner="sge" tags="longjobs">
<param id="nativeSpecification">-V -q galaxy.q</param>
</destination>
</destinations>
</job_conf>
2013/10/8 Adhemar <azn...@gmail.com>
> Hi,
> After the last update I'm getting the following error.
> The job is submitted to SGE e executed, but galaxy doesn't get the result
> and keeps showing the job is executing (yellow box).
> Any clues?
> Thanks,
> Adhemar
>
>
>
> galaxy.jobs.runners ERROR 2013-10-08 13:01:18,488 Unhandled exception
> checking active jobs
> Traceback (most recent call last):
> File
> "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/jobs/runners/__init__.py",
> line 362, in monitor
> self.check_watched_items()
> File
> "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/jobs/runners/drmaa.py",
> line 217, in check_watched_items
> log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag,
> external_job_id, e.__class__.name, e )
> AttributeError: type object 'InvalidJobException' has no attribute 'name'
>
>
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