Can you send some additional lines of the error? The important part is to see what part of the stack is repeating. Based on what you have it suggests recursion in trying to do a datatype conversion. Have you modified datatypes_conf.xml and is it possible there is a problem there? Thanks!
-- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Jan 25, 2013 at 2:47 PM, Liisa Koski <liisa.ko...@basf.com> wrote: > Hi, > I'm running a local instance of Galaxy and no matter what tool I run I get > the following error: > > Error executing tool: maximum recursion depth exceeded while calling a > Python object > > In the log file: > > galaxy.tools ERROR 2013-01-25 14:06:54,375 Exception caught while attempting > tool execution: > Traceback (most recent call last): > File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1776, in > handle_input > _, out_data = self.execute( trans, incoming=params, history=history ) > File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 2103, in > execute > return self.tool_action.execute( self, trans, incoming=incoming, > set_output_hid=set_output_hid, history=history, **kwargs ) > File "/Galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py", line 203, > in execute > chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' > ).file_name > File "/Galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 1161, in > get_converted_dataset > new_dataset = self.datatype.convert_dataset( trans, self, target_ext, > return_output=True, visible=False, deps=deps, set_output_history=False > ).values()[0] > File "/Galaxy/galaxy_dist/lib/galaxy/datatypes/data.py", line 467, in > convert_dataset > converted_dataset = converter.execute( trans, incoming=params, > set_output_hid=visible, set_output_history=set_output_history)[1] > File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 2103, in > execute > return self.tool_action.execute( self, trans, incoming=incoming, > set_output_hid=set_output_hid, history=history, **kwargs ) > File "/Galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py", line 203, > in execute > chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' > ).file_name > File "/Galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 1161, in > get_converted_dataset > new_dataset = self.datatype.convert_dataset( trans, self, target_ext, > return_output=True, visible=False, deps=deps, set_output_history=False > ).values()[0] > File "/Galaxy/galaxy_dist/lib/galaxy/datatypes/data.py", line 467, in > convert_dataset > converted_dataset = converter.execute( trans, incoming=params, > set_output_hid=visible, set_output_history=set_output_history)[1] > File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 2103, in > execute > return self.tool_action.execute( self, trans, incoming=incoming, > set_output_hid=set_output_hid, history=history, **kwargs ) > File "/Galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py", line 203, > in execute > chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' > ).file_name > File "/Galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 1161, in > get_converted_dataset > new_dataset = self.datatype.convert_dataset( trans, self, target_ext, > return_output=True, visible=False, deps=deps, set_output_history=False > ).values()[0] > File "/Galaxy/galaxy_dist/lib/galaxy/datatypes/data.py", line 467, in > convert_dataset > converted_dataset = converter.execute( trans, incoming=params, > set_output_hid=visible, set_output_history=set_output_history)[1] > File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 2103, in > execute > return self.tool_action.execute( self, trans, incoming=incoming, > set_output_hid=set_output_hid, history=history, **kwargs ) > > thousands of lines here...ending with... > > File > "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", > line 760, in _make_proxy > selectable.columns.add(c) > File > "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/expression.py", > line 1668, in add > self[column.key] = column > File > "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/expression.py", > line 1671, in __setitem__ > if key in self: > File > "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/expression.py", > line 1702, in __contains__ > return util.OrderedProperties.__contains__(self, other) > File > "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/util.py", > line 652, in __contains__ > return key in self._data > RuntimeError: maximum recursion depth exceeded while calling a Python object > > > Any help would be much appreciated, > Thanks in advance, > Liisa > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
