Question: tophat failure job
0
gravatar for 1603.neha
2.3 years ago by
1603.neha70
1603.neha70 wrote:

i have run fastqgroomer again on the sra sequences and waiting for it to complete. its result i plan to use for tophat.as my previous tophat is not running i plan to do it again. my last tophat job says job resumed and is running for past 8 hours.what should i do.

tophat • 561 views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by 1603.neha70
0
gravatar for 1603.neha
2.3 years ago by
1603.neha70
1603.neha70 wrote:

this is the error message i have received. galaxy team i need help.

info url: https://usegalaxy.org/datasets/bbd44e69cb8906b561fa3f7c441de73b/show_params job id: 12604972 (bbd44e69cb8906b5498919c36178e348) tool id: toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9 tool version: 0.9 job pid or drm id: None

job tool version: None

job command line:

None

job stderr:


job stdout:


job info:

failure preparing job

job traceback: Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/jobs/runners/pulsar.py", line 307, in __prepare_job remote_job_config = client.setuptool.id, tool.version) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/client/client.py", line 75, in setup return self.setup_handler.setup(setup_args) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/client/setup_handler.py", line 68, in setup return self.client.remote_setup(setup_args) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/client/decorators.py", line 13, in replacement response = func(args, kwargs) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/client/client.py", line 168, in remote_setup return self._raw_execute("setup", setup_args) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/client/client.py", line 218, in _raw_execute return self.job_manager_interface.execute(command, args, data, input_path, output_path) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/client/interface.py", line 142, in execute result = action(args) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/web/routes.py", line 47, in setup return __setup(manager, job_id, tool_id=tool_id, tool_version=tool_version, use_metadata=use_metadata) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/web/routes.py", line 52, in __setup response = setup_job(manager, job_id, tool_id, tool_version, use_metadata) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/manager_endpoint_util.py", line 108, in setup_job job_id = manager.setup_job(job_id, tool_id, tool_version) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/managers/stateful.py", line 60, in setup_job job_id = self._proxied_manager.setup_job(args, *kwargs) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/managers/base/external.py", line 31, in setup_job return self._setup_job_for_job_id(job_id, tool_id, tool_version) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/managers/base/directory.py", line 48, in _setup_job_for_job_id self._setup_job_directory(job_id) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/managers/base/__init__.py", line 145, in _setup_job_directory job_directory.setup() File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/managers/base/__init__.py", line 278, in setup self._directory_maker.make(self.job_directory) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/pulsar/managers/base/__init__.py", line 397, in make os.mkdir(makedir_args) OSError: [Errno 28] No space left on device: '/jetstream/tacc-scratch0/main/jobs/12604972'

ADD COMMENTlink written 2.3 years ago by 1603.neha70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 153 users visited in the last hour