Hello everyone,
I have installed a local instance of Galaxy (release_16.07) on my CentOS (7.3.1611) server and added a custom tool for taxonomic analysis using qiime2.
When I run the tool I get the error:
UnicodeEncodeError: 'latin-1' codec can't encode character u'\u2018' in position 408: ordinal not in range(256)
but the job command line produced by the tool actually works when typed in the terminal.
I had noticed this type of behaviour in other different tools as well and noticed that when they produced an output like a warning or any additional output, Galaxy mistakes it as an error and produces the same error.
None of the tools have anything to do with MySQL, I think it’s some kind of internal error from Galaxy’s database or something.
So far I managed to get around that by redirecting stderr ( 2>/dev/null ) but in this case nothing works.
Could you help me out?
Thank you in advance,
The full error is the following:
Traceback (most recent call last):
File "/home/user/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/user/galaxy/lib/galaxy/jobs/__init__.py", line 1332, in finish
self.sa_session.flush()
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/scoping.py", line 150, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2004, in flush
self._flush(objects)
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2122, in _flush
transaction.rollback(_capture_exception=True)
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2086, in _flush
flush_context.execute()
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 373, in execute
rec.execute(self)
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 532, in execute
uow
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 170, in save_obj
mapper, table, update)
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 692, in _emit_update_statements
execute(statement, multiparams)
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 914, in execute
return meth(self, multiparams, params)
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement
compiled_sql, distilled_params
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1146, in _execute_context
context)
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1344, in _handle_dbapi_exception
util.reraise(*exc_info)
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1139, in _execute_context
context)
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 450, in do_execute
cursor.execute(statement, parameters)
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/cursors.py", line 187, in execute
query = query % tuple([db.literal(item) for item in args])
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 278, in literal
return self.escape(o, self.encoders)
File "/home/user/galaxy/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 208, in unicode_literal
return db.literal(u.encode(unicode_literal.charset))
UnicodeEncodeError: 'latin-1' codec can't encode character u'\u2018' in position 408: ordinal not in range(256)