After some investigating I think the problem is at the line: converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] in File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/datatypes/data.py", line 483, in convert_dataset -Raj On Fri Aug 2 00:51:39 2013, Raj Ayyampalayam wrote:

Here is the first part of the error (Traceback):

galaxy.tools ERROR 2013-08-01 22:56:16,590 Exception caught while attempting tool execution: Traceback (most recent call last): File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/__init__.py", line 1936, in handle_input _, out_data = self.execute( trans, incoming=params, history=history ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/__init__.py", line 2264, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 213, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/model/__init__.py", line 1308, 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 "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/datatypes/data.py", line 483, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/__init__.py", line 2264, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 213, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/model/__init__.py", line 1308, 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 "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/datatypes/data.py", line 483, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/__init__.py", line 2264, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 213, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/model/__init__.py", line 1308, 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 "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/datatypes/data.py", line 483, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/__init__.py", line 2264, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 213, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/model/__init__.py", line 1308, 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 "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/datatypes/data.py", line 483, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/__init__.py", line 2264, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 213, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/model/__init__.py", line 1308, 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 "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/datatypes/data.py", line 483, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/__init__.py", line 2264, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 213, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/model/__init__.py", line 1308, 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 "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/datatypes/data.py", line 483, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/__init__.py", line 2264, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 213, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/model/__init__.py", line 1308, 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 "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/datatypes/data.py", line 483, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/__init__.py", line 2264, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 213, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/model/__init__.py", line 1308, 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 "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/datatypes/data.py", line 483, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/__init__.py", line 2264, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 213, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name

Seems like it is dying at chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name

Thanks, -Raj On 8/2/13 12:00 AM, Raj Ayyampalayam wrote:

...

Hello,

My local cluster based galaxy installation was running fine till this evening. Later I decided to test some workflows and got an error with massive stack trace. I can't make any sense of this. Here is the last part of the error. The stack trace is literally 1000's of lines. Can somebody throw some light on this?

Thanks, -Raj

File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/datatypes/data.py", line 483, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/__init__.py", line 2264, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 201, in execute db_dataset = trans.db_dataset_for( input_dbkey ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 1046, in db_dataset_for for ds in datasets: File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py", line 2227, in __iter__ return self._execute_and_instances(context) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py", line 2242, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1449, in execute params) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1576, in _execute_clauseelement inline=len(distilled_params) > 1) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/expression.py", line 1778, in compile return self._compiler(dialect, bind=bind, **kw) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/expression.py", line 1784, in _compiler return dialect.statement_compiler(dialect, self, **kw) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 276, in __init__ engine.Compiled.__init__(self, dialect, statement, **kwargs) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 705, in __init__ self.string = self.process(self.statement) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 724, in process return obj._compiler_dispatch(self, **kwargs) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/visitors.py", line 72, in _compiler_dispatch return getter(visitor)(self, **kw) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 997, in visit_select t = select._whereclause._compiler_dispatch(self, **kwargs) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/visitors.py", line 72, in _compiler_dispatch return getter(visitor)(self, **kw) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 498, in visit_clauselist for c in clauselist.clauses) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 496, in <genexpr> s for s in File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 498, in <genexpr> for c in clauselist.clauses) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/visitors.py", line 72, in _compiler_dispatch return getter(visitor)(self, **kw) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 618, in visit_binary **kw File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 663, in _operator_dispatch return fn(OPERATORS[operator]) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 617, in <lambda> self, **kw), File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/visitors.py", line 72, in _compiler_dispatch return getter(visitor)(self, **kw) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 679, in visit_bindparam name = self._truncate_bindparam(bindparam) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 743, in _truncate_bindparam bind_name = self._truncated_identifier("bindparam", bind_name) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 754, in _truncated_identifier anonname = name.apply_map(self.anon_map) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/expression.py", line 1325, in apply_map return self % map_ RuntimeError: maximum recursion depth exceeded

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