Having trouble resolving this behavior in a Galaxy wrapper I'm working on. The tool runs to completion, and I can view the output file via shell. The problem is, the tool continues to go in to an ERROR state, thus the workflow does not continue. No errors from the tools, or from my wrapper, just the following in one of the logs.
Blockquote File "/home/groups/clinical/Galaxy/galaxy-dist/eggs/SQLAlchemy-1.0.0-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py", line 1226, in _safe_close_cursor cursor.close() InternalError: current transaction is aborted, commands ignored until end of transaction block
This error message is a little vague for me to determine the problem, though I'm sure the root cause must be something in my wrapper. All other tools continue to behave normally. I'm hoping perhaps someone has come across this in the past and might save me from the headache.