Hi Jeremy,

Thanks for you assistance. I would love to try your suggestions, but Galaxy won't start anymore.

I have found the root cause of the problems: my home partition has become too small, due to a fat 'job_working_directory'. I didn't expect it to become so big (especially with tophat output). Now I have the job_working_directory mounted on our network share. So I restart Galaxy, and got this error:

Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 36, in app_factory
   app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 85, in __init__ self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 84, in __init__
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 236, in load_integrated_tool_panel_keys
   tree = util.parse_xml( self.integrated_tool_panel_config )
File "/home/galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 143, in parse_xml
   tree = ElementTree.parse(fname)
File "/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse
   tree.parse(source, parser)
File "/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 584, in parse
   self._root = parser.close()
File "/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 1251, in close
   self._parser.Parse("", 1) # end of data
ExpatError: unclosed token: line 109, column 4
Removing PID file main.pid

Before dragging up my backup, any idea how to fix this otherwise? I suspect that mercurial could not pull all changes in, is that possible?


On Wed 14 Nov 2012 04:25:53 AM CET, Jeremy Goecks wrote:
One dataset I want to view in Trackster has an error
ConverterDependencyException: 'A dependency (bgzip) was in an error state.

I've seen this once or twice before but haven't been able to track down the 
issue yet.

Here are two workaround that may help you out:

(1) Add the dataset to a new/saved visualization and then click 'try again' to 
try reindexing the dataset;

(2) copy the dataset using History Options --> Copy Datasets, then delete the 
failing dataset and try indexing the new dataset.

If the dataset continues to fail, please make it available to me and I'll take 
a look.


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