Dear Galaxy community, I am trying to configure a local instance of galaxy on our SGE cluster. I have some problems to configure jobs, this is my job_conf.xml:
<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is
configured by default (if there is no explicit config). -->
<job_conf>
<plugins>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
<plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
</plugins>
<destinations default="local">
<destination id="local" runner="local"/>
<destination id="big_jobs" runner="drmaa">
<param id="nativeSpecification">-P cassava -R y -pe snodes 40</param>
</destination>
</destinations>
<tools>
<tool id="metaspades" destination="big_jobs" />
</tools>
</job_conf>
When I try to run metaspades, the jobs remain in the Unfinished jobs within galaxy and I cannot see them in the queue (qstat). Did I miss something in my configurations ?
This is the message in the terminal (access via ssh -C -L 8081:localhost:8081):
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "lib/galaxy/queue_worker.py", line 131, in send_task
self.connection.drain_events(timeout=timeout)
File "/media/vol2/home/galaxy/galaxy/.venv/lib/python3.6/site-packages/kombu/connection.py", line 323, in drain_events
return self.transport.drain_events(self.connection, **kwargs)
File "/media/vol2/home/galaxy/galaxy/.venv/lib/python3.6/site-packages/kombu/transport/virtual/base.py", line 966, in drain_events
raise socket.timeout()
socket.timeout
127.0.0.1 - - [14/Apr/2020:15:21:36 +0200] "GET /admin/jobs_control?job_lock=true HTTP/1.1" 200 - "http://127.0.0.1:8081/admin/jobs" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/80.0.3987.149 Safari/537.36"
[pid: 60177|app: 0|req: 427/436] 127.0.0.1 () {44 vars in 875 bytes} [Tue Apr 14 15:21:36 2020] GET /admin/jobs_control?job_lock=true => generated 18 bytes in 10955 msecs (HTTP/1.1 200) 2 headers in 95 bytes (1 switches on core 0)
127.0.0.1 - - [14/Apr/2020:15:22:53 +0200] "GET /admin/job_info?jobid=8 HTTP/1.1" 200 - "http://127.0.0.1:8081/admin/jobs" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/80.0.3987.149 Safari/537.36"
[pid: 60177|app: 0|req: 428/437] 127.0.0.1 () {46 vars in 986 bytes} [Tue Apr 14 15:22:53 2020] GET /admin/job_info?jobid=8 => generated 6644 bytes in 307 msecs (HTTP/1.1 200) 2 headers in 88 bytes (1 switches on core 3)