Hi all
Since updating to the latest Galaxy-dist version, I'm unable to run any
jobs.
galaxy.jobs.handler INFO 2012-11-20 12:22:09,018 (6403) Job dispatched
galaxy.objectstore CRITICAL 2012-11-20 12:22:15,362
/home/galaxy/galaxy-dist/database/job_working_directory/006/6403
delete error [Errno 2] No such file or directory:
'/home/galaxy/galaxy-dist/database/job_working_directory/006/6403'
CRITICAL 12:22:15
__init__.delete:322
/home/galaxy/galaxy-dist/database/job_working_directory/006/6403
delete error [Errno 2] No such file or directory:
'/home/galaxy/galaxy-dist/database/job_working_directory/006/6403'
galaxy.jobs.runners.local ERROR 2012-11-20 12:22:15,363 failure running job 6403
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py",
line 129, in run_job
stdout_file.close()
File "/usr/lib/python2.7/tempfile.py", line 410, in close
self.unlink(self.name)
OSError: [Errno 2] No such file or directory:
'/home/galaxy/galaxy-dist/database/job_working_directory/006/6403/tmpKuTwAJ_stdout'
ERROR 12:22:15 local.run_job:134 failure running job 6403
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py",
line 129, in run_job
stdout_file.close()
File "/usr/lib/python2.7/tempfile.py", line 410, in close
self.unlink(self.name)
OSError: [Errno 2] No such file or directory:
'/home/galaxy/galaxy-dist/database/job_working_directory/006/6403/tmpKuTwAJ_stdout'
Exception OSError: (2, 'No such file or directory',
'/home/galaxy/galaxy-dist/database/job_working_directory/006/6403/tmpK7i5n4_stderr')
in <bound method _TemporaryFileWrapper.__del__ of <closed file
'<fdopen>', mode 'w+b' at 0x55b8f60>> ignored
galaxy.objectstore CRITICAL 2012-11-20 12:22:15,723
/home/galaxy/galaxy-dist/database/job_working_directory/006/6404
delete error [Errno 2] No such file or directory:
'/home/galaxy/galaxy-dist/database/job_working_directory/006/6404'
CRITICAL 12:22:15
__init__.delete:322
/home/galaxy/galaxy-dist/database/job_working_directory/006/6404
delete error [Errno 2] No such file or directory:
'/home/galaxy/galaxy-dist/database/job_working_directory/006/6404'
I'm running the version from ~Nov 6th: 8153:5dcbbdfe1087 tip | Allow rerun
to access hidden datasets.
I already found this recent issue on the maillinglist which appeared
similar, but my problems involve running jobs, not uploading datasets:
http://dev.list.galaxyproject.org/Re-Galaxy-at-Duke-td4656946.html
My setup involves 1 runner instance and 2 web instances, all inside the
same VM, as per my configuration files here:
https://trac.nbic.nl/brs2010p33/browser/trunk/galaxy-dist/
The folder /work/project is an sshfs mount to the server running the VM.
sshfs#backup@192.168.122.1:/work/odose/ /work/project/ fuse
defaults,idmap=user,allow_other,cache=no 0 0
I've setup the following paths to that mounted folder:
# Dataset files are stored in this directory.
file_path = /work/project/galaxy-dist/database/files
# Temporary files are stored in this directory.
new_file_path = /work/project/galaxy-dist/database/tmp
The job_working_directory is a normal folder in the VM, but I still get the
above error.
Can anyone tell me what I should do to be able to run jobs in Galaxy again?
Best,
Tim
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