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
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.koski@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:
galaxy-dev@lists.galaxyproject.org
-
James Taylor -
Liisa Koski