Manager assigns job but it never reaches the handler
Hi all! When user tried to run Phantom Peak, the job was assigned to a handler by the manager but it keeps hanging. No messages appear on the handler.log file. As an admin I can use the tool successfully with no abnormal behavior. When the user deleted the job, the following message appeared on the handler.log galaxy.jobs.handler DEBUG 2013-02-06 17:51:49,591 Stopping job 296: galaxy.jobs.handler DEBUG 2013-02-06 17:51:49,592 stopping job 296 in local runner galaxy.jobs.runners.local WARNING 2013-02-06 17:51:49,613 stop_job(): 296: no PID in database for job, unable to stop /steno-internal/projects/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from csamtools import * Do you have any idea why this would happen? Regards, Nikos
On Feb 6, 2013, at 12:19 PM, Nikoloas Sidiropoulos wrote:
Hi all!
When user tried to run Phantom Peak, the job was assigned to a handler by the manager but it keeps hanging. No messages appear on the handler.log file.
As an admin I can use the tool successfully with no abnormal behavior.
Hi Nikos, When you run the job as an admin, does it run in the same handler as you're expecting the job to run in when initiated by the user? Can you verify that you are tracking jobs in the database? --nate
When the user deleted the job, the following message appeared on the handler.log
galaxy.jobs.handler DEBUG 2013-02-06 17:51:49,591 Stopping job 296: galaxy.jobs.handler DEBUG 2013-02-06 17:51:49,592 stopping job 296 in local runner galaxy.jobs.runners.local WARNING 2013-02-06 17:51:49,613 stop_job(): 296: no PID in database for job, unable to stop /steno-internal/projects/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from csamtools import *
Do you have any idea why this would happen?
Regards, Nikos
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participants (2)
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Nate Coraor -
Nikoloas Sidiropoulos