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



--
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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