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