Hi I just blew everything up, I have no idea why. Galaxy doesn't start anymore. When I run the run.sh script, it stops after loading the converters and just crashes. Here's the traceback: Traceback (most recent call last): File "/home/galaxy/galaxy-dev/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dev/lib/galaxy/app.py", line 52, in __init__ load_history_imp_exp_tools( self.toolbox ) File "/home/galaxy/galaxy-dev/lib/galaxy/tools/imp_exp/__init__.py", line 34, in load_history_imp_exp_tools history_exp_tool = toolbox.load_tool( tmp_name.name ) File "/home/galaxy/galaxy-dev/lib/galaxy/tools/__init__.py", line 131, in load_tool tree = util.parse_xml( config_file ) File "/home/galaxy/galaxy-dev/lib/galaxy/util/__init__.py", line 104, in parse_xml tree = ElementTree.parse(fname) File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 584, in parse self._root = parser.close() File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 1251, in close self._parser.Parse("", 1) # end of data ExpatError: no element found: line 1, column 0 Exception IOError: (28, 'No space left on device') in <bound method _TemporaryFileWrapper.__del__ of <closed file '<fdopen>', mode 'w+b' at 0x8539a50>> ignored Since the message is not really self-explanatory, I have no idea as to what's gone wrong. The only thing I know is that the file referred by tmp_name.name is empty. Do you have an idea where I should be looking? I really can't relate that to anything I did recently, I just modified some parameter labels in two tools, which should be really harmless, and the display name of a reference genome, which shouldn't make any difference either. Thanks, L-A
Hey, I am guessing that the disk space on your Galaxy hosted machine is empty. Check df -h on your shell HTH, Vipin Hi
I just blew everything up, I have no idea why. Galaxy doesn't start anymore. When I run the run.sh script, it stops after loading the converters and just crashes. Here's the traceback:
Traceback (most recent call last): File "/home/galaxy/galaxy-dev/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dev/lib/galaxy/app.py", line 52, in __init__ load_history_imp_exp_tools( self.toolbox ) File "/home/galaxy/galaxy-dev/lib/galaxy/tools/imp_exp/__init__.py", line 34, in load_history_imp_exp_tools history_exp_tool = toolbox.load_tool( tmp_name.name ) File "/home/galaxy/galaxy-dev/lib/galaxy/tools/__init__.py", line 131, in load_tool tree = util.parse_xml( config_file ) File "/home/galaxy/galaxy-dev/lib/galaxy/util/__init__.py", line 104, in parse_xml tree = ElementTree.parse(fname) File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 584, in parse self._root = parser.close() File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 1251, in close self._parser.Parse("", 1) # end of data ExpatError: no element found: line 1, column 0 Exception IOError: (28, 'No space left on device') in <bound method _TemporaryFileWrapper.__del__ of <closed file '<fdopen>', mode 'w+b' at 0x8539a50>> ignored
Since the message is not really self-explanatory, I have no idea as to what's gone wrong. The only thing I know is that the file referred by tmp_name.name is empty. Do you have an idea where I should be looking?
I really can't relate that to anything I did recently, I just modified some parameter labels in two tools, which should be really harmless, and the display name of a reference genome, which shouldn't make any difference either.
Thanks, L-A ___________________________________________________________ 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:
2011/6/3 Louise-Amélie Schmitt <louise-amelie.schmitt@embl.de>:
Hi
I just blew everything up, I have no idea why. Galaxy doesn't start anymore. When I run the run.sh script, it stops after loading the converters and just crashes. Here's the traceback:
Traceback (most recent call last): File "/home/galaxy/galaxy-dev/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dev/lib/galaxy/app.py", line 52, in __init__ load_history_imp_exp_tools( self.toolbox ) File "/home/galaxy/galaxy-dev/lib/galaxy/tools/imp_exp/__init__.py", line 34, in load_history_imp_exp_tools history_exp_tool = toolbox.load_tool( tmp_name.name ) File "/home/galaxy/galaxy-dev/lib/galaxy/tools/__init__.py", line 131, in load_tool tree = util.parse_xml( config_file ) File "/home/galaxy/galaxy-dev/lib/galaxy/util/__init__.py", line 104, in parse_xml tree = ElementTree.parse(fname) File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 584, in parse self._root = parser.close() File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 1251, in close self._parser.Parse("", 1) # end of data ExpatError: no element found: line 1, column 0 Exception IOError: (28, 'No space left on device') in <bound method _TemporaryFileWrapper.__del__ of <closed file '<fdopen>', mode 'w+b' at 0x8539a50>> ignored
Since the message is not really self-explanatory, I have no idea as to what's gone wrong. The only thing I know is that the file referred by tmp_name.name is empty. Do you have an idea where I should be looking?
I really can't relate that to anything I did recently, I just modified some parameter labels in two tools, which should be really harmless, and the display name of a reference genome, which shouldn't make any difference either.
The message looks self explanatory to me, 'No space left on device' means the disk is full. The fact that this is from a temporary file suggests it might not be the partition/disk where Galaxy is installed, but the system temp folder which is often a different partition. So check both, and also if you have any user disk quote in place, check that. Peter
Le 03/06/2011 15:19, Peter Cock a écrit :
2011/6/3 Louise-Amélie Schmitt<louise-amelie.schmitt@embl.de>:
Hi
I just blew everything up, I have no idea why. Galaxy doesn't start anymore. When I run the run.sh script, it stops after loading the converters and just crashes. Here's the traceback:
Traceback (most recent call last): File "/home/galaxy/galaxy-dev/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dev/lib/galaxy/app.py", line 52, in __init__ load_history_imp_exp_tools( self.toolbox ) File "/home/galaxy/galaxy-dev/lib/galaxy/tools/imp_exp/__init__.py", line 34, in load_history_imp_exp_tools history_exp_tool = toolbox.load_tool( tmp_name.name ) File "/home/galaxy/galaxy-dev/lib/galaxy/tools/__init__.py", line 131, in load_tool tree = util.parse_xml( config_file ) File "/home/galaxy/galaxy-dev/lib/galaxy/util/__init__.py", line 104, in parse_xml tree = ElementTree.parse(fname) File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 584, in parse self._root = parser.close() File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 1251, in close self._parser.Parse("", 1) # end of data ExpatError: no element found: line 1, column 0 Exception IOError: (28, 'No space left on device') in<bound method _TemporaryFileWrapper.__del__ of<closed file '<fdopen>', mode 'w+b' at 0x8539a50>> ignored
Since the message is not really self-explanatory, I have no idea as to what's gone wrong. The only thing I know is that the file referred by tmp_name.name is empty. Do you have an idea where I should be looking?
I really can't relate that to anything I did recently, I just modified some parameter labels in two tools, which should be really harmless, and the display name of a reference genome, which shouldn't make any difference either. The message looks self explanatory to me, 'No space left on device' means the disk is full. The fact that this is from a temporary file suggests it might not be the partition/disk where Galaxy is installed, but the system temp folder which is often a different partition. So check both, and also if you have any user disk quote in place, check that.
Peter
Yes you're right, I kinda misread this part in the panic... Sorry for being an idiot again :) Thanks a lot! L-A
participants (3)
-
Louise-Amélie Schmitt -
Peter Cock -
Vipin TS