Created
August 16, 2018 15:25
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error on wrapper
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galaxy.jobs.runners.drmaa DEBUG 2018-08-16 15:10:25,560 (29) submitting file /export/galaxy-central/database/job_working_directory/000/29/galaxy_29.sh | |
galaxy.jobs.runners.drmaa DEBUG 2018-08-16 15:10:25,560 (29) native specification is: --ntasks=1 --share | |
galaxy.jobs.runners.drmaa INFO 2018-08-16 15:10:25,565 (29) queued as 30 | |
galaxy.jobs DEBUG 2018-08-16 15:10:25,566 (29) Persisting job destination (destination id: slurm_cluster) | |
galaxy.jobs.runners.drmaa DEBUG 2018-08-16 15:10:25,879 (29/30) state change: job is running | |
galaxy.jobs.runners.drmaa DEBUG 2018-08-16 15:10:51,484 (29/30) state change: job finished normally | |
galaxy.model.metadata DEBUG 2018-08-16 15:10:51,839 loading metadata from file for: HistoryDatasetAssociation 39 | |
galaxy.jobs.runners ERROR 2018-08-16 15:10:51,851 (29/30) Job wrapper finish method failed | |
Traceback (most recent call last): | |
File "/galaxy-central/lib/galaxy/jobs/runners/__init__.py", line 690, in finish_job | |
self._finish_or_resubmit_job(job_state, stdout, stderr, exit_code) | |
File "/galaxy-central/lib/galaxy/jobs/runners/__init__.py", line 433, in _finish_or_resubmit_job | |
job_state.job_wrapper.finish(stdout, stderr, exit_code, check_output_detected_state=check_output_detected_state) | |
File "/galaxy-central/lib/galaxy/jobs/__init__.py", line 1364, in finish | |
self.sa_session.flush() | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/scoping.py", line 153, in do | |
return getattr(self.registry(), name)(*args, **kwargs) | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2254, in flush | |
self._flush(objects) | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2380, in _flush | |
transaction.rollback(_capture_exception=True) | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 66, in __exit__ | |
compat.reraise(exc_type, exc_value, exc_tb) | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2344, in _flush | |
flush_context.execute() | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 386, in execute | |
n.execute_aggregate(self, set_) | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 668, in execute_aggregate | |
uow) | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 177, in save_obj | |
mapper, table, update) | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 768, in _emit_update_statements | |
execute(statement, multiparams) | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute | |
return meth(self, multiparams, params) | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection | |
return connection._execute_clauseelement(self, multiparams, params) | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement | |
compiled_sql, distilled_params | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context | |
context) | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1416, in _handle_dbapi_exception | |
util.reraise(*exc_info) | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context | |
context) | |
File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute | |
cursor.execute(statement, parameters) | |
ValueError: A string literal cannot contain NUL (0x00) characters. | |
galaxy.tools.error_reports DEBUG 2018-08-16 15:10:53,588 Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7f1a1e525190> generated response None |
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