Failed to generate job destination
Hi, anyone has seen the following bug in Galaxy November release? galaxy.jobs.handler ERROR 2013-11-15 00:07:41,008 Failed to generate job destination Traceback (most recent call last): File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 311, in __check_if_ready_to_run self.job_wrappers[job.id].job_destination File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 620, in job_destination return self.job_runner_mapper.get_job_destination(self.params) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py", line 163, in get_job_destination self.__cache_job_destination( params ) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py", line 148, in __cache_job_destination raw_job_destination = self.job_wrapper.tool.get_job_destination( params ) AttributeError: 'NoneType' object has no attribute 'get_job_destination' Thanks, Bjoern
Hey Bjoern, Can you post your job_conf.xml or send it to galaxy-bugs@bx.psu.edu if it has something sensitive in it, alternatively your runner urls if you are still using the older format for specifying these things? Is this for every job or just certain tools? -John On Thu, Nov 14, 2013 at 5:14 PM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Hi,
anyone has seen the following bug in Galaxy November release?
galaxy.jobs.handler ERROR 2013-11-15 00:07:41,008 Failed to generate job destination Traceback (most recent call last): File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 311, in __check_if_ready_to_run self.job_wrappers[job.id].job_destination File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 620, in job_destination return self.job_runner_mapper.get_job_destination(self.params) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py", line 163, in get_job_destination self.__cache_job_destination( params ) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py", line 148, in __cache_job_destination raw_job_destination = self.job_wrapper.tool.get_job_destination( params ) AttributeError: 'NoneType' object has no attribute 'get_job_destination'
Thanks, Bjoern
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Hi John, please find attached my jobs_conf.xml file. I was not able to find any systematic in that error. It seems to happen not so often. Thanks, Bjoern
Hey Bjoern,
Can you post your job_conf.xml or send it to galaxy-bugs@bx.psu.edu if it has something sensitive in it, alternatively your runner urls if you are still using the older format for specifying these things? Is this for every job or just certain tools?
-John
On Thu, Nov 14, 2013 at 5:14 PM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Hi,
anyone has seen the following bug in Galaxy November release?
galaxy.jobs.handler ERROR 2013-11-15 00:07:41,008 Failed to generate job destination Traceback (most recent call last): File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 311, in __check_if_ready_to_run self.job_wrappers[job.id].job_destination File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 620, in job_destination return self.job_runner_mapper.get_job_destination(self.params) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py", line 163, in get_job_destination self.__cache_job_destination( params ) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py", line 148, in __cache_job_destination raw_job_destination = self.job_wrapper.tool.get_job_destination( params ) AttributeError: 'NoneType' object has no attribute 'get_job_destination'
Thanks, Bjoern
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It looks like you have tools with no matching id in toolbox.tools_by_id. Given the complexity of your job_conf.xml I assume you are using multiple Galaxy processes? Have you installed stuff from the tool shed or migrated tools and not restarted all Galaxy processes, or did you try to restart processes but when failed to shutdown? I assume tool shed installed tools are only available to the web process that installed them, so the handler process must be restarted. If restarting it doesn't work, I have attached a patch with added logging that might help. -John On Thu, Nov 14, 2013 at 5:59 PM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Hi John,
please find attached my jobs_conf.xml file. I was not able to find any systematic in that error. It seems to happen not so often.
Thanks, Bjoern
Hey Bjoern,
Can you post your job_conf.xml or send it to galaxy-bugs@bx.psu.edu if it has something sensitive in it, alternatively your runner urls if you are still using the older format for specifying these things? Is this for every job or just certain tools?
-John
On Thu, Nov 14, 2013 at 5:14 PM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Hi,
anyone has seen the following bug in Galaxy November release?
galaxy.jobs.handler ERROR 2013-11-15 00:07:41,008 Failed to generate job destination Traceback (most recent call last): File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 311, in __check_if_ready_to_run self.job_wrappers[job.id].job_destination File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 620, in job_destination return self.job_runner_mapper.get_job_destination(self.params) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py", line 163, in get_job_destination self.__cache_job_destination( params ) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py", line 148, in __cache_job_destination raw_job_destination = self.job_wrapper.tool.get_job_destination( params ) AttributeError: 'NoneType' object has no attribute 'get_job_destination'
Thanks, Bjoern
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participants (2)
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Björn Grüning -
John Chilton