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


--
Bio-informatics consultant
QBCG (http://qbcg.uga.edu)
706-542-6092 (8-12 All week)
706-583-0442 (12-5 All week)



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