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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