bz2 error and An error occurred running this job: Job output not returned from cluster
import bz2 print bz2.__doc__ The python bz2 module provides a comprehensive interface for
Hello, I am trying to fix something that I see in my paster.log file. At the end of the file, after everything has been loaded and the server is running, I get an error message saying that bz2 cannot be imported. When I start a python interpreter session and type in "import bz2" it runs without incident. I can even get the doc info. I am also getting the error An error occurred running this job: Job output not returned from cluster when I run an "add column" to a basic data set from the text manipulation tools file. I'm wondering if they are related. We are currently trying to check our queueing system to make sure it can correctly deliver these back from the execution hosts to our filesystem. -Robert Chase Similar bugs appears here: http://gmod.827538.n3.nabble.com/Job-output-not-returned-from-cluster-td3420... http://osdir.com/ml/galaxy-source-control/2009-03/msg00015.html Python 2.7.1 (r271:86832, Mar 13 2012, 17:18:00) [GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2 Type "help", "copyright", "credits" or "license" for more information. the bz2 compression library. It implements a complete file interface, one shot (de)compression functions, and types for sequential (de)compression. 7.0.0.1:8080 Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 218, in run result = self.command() File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 413, in get_context section) File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/share/shared/galaxy-dist/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/share/shared/galaxy-dist/lib/galaxy/web/buildapp.py", line 19, in <module> from galaxy import config, jobs, util, tools File "/share/shared/galaxy-dist/lib/galaxy/jobs/__init__.py", line 4, in <module> from galaxy import util, model File "/share/shared/galaxy-dist/lib/galaxy/model/__init__.py", line 13, in <module> import galaxy.datatypes.registry File "/share/shared/galaxy-dist/lib/galaxy/datatypes/registry.py", line 5, in <module> import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex, wsf File "/share/shared/galaxy-dist/lib/galaxy/datatypes/tabular.py", line 15, in <module> from sniff import * File "/share/shared/galaxy-dist/lib/galaxy/datatypes/sniff.py", line 7, in <module> from galaxy.datatypes.checkers import * File "/share/shared/galaxy-dist/lib/galaxy/datatypes/checkers.py", line 1, in <module> import os, gzip, re, gzip, zipfile, binascii, bz2, imghdr ImportError: No module named bz2
On Apr 2, 2012, at 1:43 PM, Robert Chase wrote:
Hello,
I am trying to fix something that I see in my paster.log file. At the end of the file, after everything has been loaded and the server is running, I get an error message saying that bz2 cannot be imported. When I start a python interpreter session and type in "import bz2" it runs without incident. I can even get the doc info.
I am also getting the error An error occurred running this job: Job output not returned from cluster when I run an "add column" to a basic data set from the text manipulation tools file. I'm wondering if they are related.
We are currently trying to check our queueing system to make sure it can correctly deliver these back from the execution hosts to our filesystem.
-Robert Chase
Similar bugs appears here:
http://gmod.827538.n3.nabble.com/Job-output-not-returned-from-cluster-td3420...
http://osdir.com/ml/galaxy-source-control/2009-03/msg00015.html
import bz2 print bz2.__doc__ The python bz2 module provides a comprehensive interface for
Python 2.7.1 (r271:86832, Mar 13 2012, 17:18:00) [GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2 Type "help", "copyright", "credits" or "license" for more information. the bz2 compression library. It implements a complete file interface, one shot (de)compression functions, and types for sequential (de)compression.
Could you also do:
bz2
Which should show the path to the module. Also, printing sys.path from the interactive interpreter and from within the file that fails (lib/galaxy/datatypes/checkers.py) would give a few more hints. Thanks, --nate
7.0.0.1:8080 Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 218, in run result = self.command() File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 413, in get_context section) File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/share/shared/galaxy-dist/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/share/shared/galaxy-dist/lib/galaxy/web/buildapp.py", line 19, in <module> from galaxy import config, jobs, util, tools File "/share/shared/galaxy-dist/lib/galaxy/jobs/__init__.py", line 4, in <module> from galaxy import util, model File "/share/shared/galaxy-dist/lib/galaxy/model/__init__.py", line 13, in <module> import galaxy.datatypes.registry File "/share/shared/galaxy-dist/lib/galaxy/datatypes/registry.py", line 5, in <module> import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex, wsf File "/share/shared/galaxy-dist/lib/galaxy/datatypes/tabular.py", line 15, in <module> from sniff import * File "/share/shared/galaxy-dist/lib/galaxy/datatypes/sniff.py", line 7, in <module> from galaxy.datatypes.checkers import * File "/share/shared/galaxy-dist/lib/galaxy/datatypes/checkers.py", line 1, in <module> import os, gzip, re, gzip, zipfile, binascii, bz2, imghdr ImportError: No module named bz2 ___________________________________________________________ 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:
participants (2)
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Nate Coraor -
Robert Chase