Traceback (most recent call last):

 "/usr/local/bin/extract-paired-reads.py", line 5, in <module>
pkg_resources.run_script('khmer==1.3-rc3', 'extract-paired-reads.py')

 "build/bdist.linux-x86_64/egg/pkg_resources.py", line 528, in run_script
self.require(requires)[0].run_script(script_name, ns)

 "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1394, in run_script
execfile(script_filename, namespace, namespace)

 "/usr/local/lib/python2.7/dist-packages/khmer-1.3_rc3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/extract-paired-reads.py", line 154, in <module>
main()

 "/usr/local/lib/python2.7/dist-packages/khmer-1.3_rc3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/extract-paired-reads.py", line 86, in main
check_file_status(args.infile, args.force)

 "/usr/local/lib/python2.7/dist-packages/khmer-1.3_rc3-py2.7-linux-x86_64.egg/khmer/file.py", line 25, in check_file_status
mode = os.stat(file_path).st_modeOSError: [Errno 2] No such file or directory: '*.pe.*.abundfilt'
Traceback (most recent call last):


 "/opt/citoplus/local/lib/python2.7/site-packages/sphinx/cmdline.py", line 304, in main

app.build(args.force_all, filenames)


 "/opt/citoplus/local/lib/python2.7/site-packages/sphinx/application.py", line 331, in build

self.builder.build_update()


 "/opt/citoplus/local/lib/python2.7/site-packages/sphinx/builders/__init__.py", line 342, in build_update

'out of date' % len(to_build))


 "/opt/citoplus/local/lib/python2.7/site-packages/sphinx/builders/__init__.py", line 355, in build

updated_docnames = set(self.env.update(self.config, self.srcdir, self.doctreedir))


 "/opt/citoplus/local/lib/python2.7/site-packages/sphinx/environment/__init__.py", line 565, in update

self._read_serial(docnames, self.app)


 "/opt/citoplus/local/lib/python2.7/site-packages/sphinx/environment/__init__.py", line 584, in _read_serial

self.read_doc(docname, app)


 "/opt/citoplus/local/lib/python2.7/site-packages/sphinx/environment/__init__.py", line 659, in read_doc

doctree = read_doc(self.app, self, self.doc2path(docname))


 "/opt/citoplus/local/lib/python2.7/site-packages/sphinx/io.py", line 302, in read_doc

pub.publish()


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/core.py", line 217, in publish

self.settings)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/readers/__init__.py", line 72, in read

self.parse()


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/readers/__init__.py", line 78, in parse

self.parser.parse(self.input, document)


 "/opt/citoplus/local/lib/python2.7/site-packages/sphinx/parsers.py", line 85, in parse

self.statemachine.run(inputstring, document, inliner=self.inliner)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 171, in run

input_source=document['source'])


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/statemachine.py", line 239, in run

context, state, transitions)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/statemachine.py", line 460, in check_line

return method(match, context, next_state)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2753, in underline

self.section(title, source, style, lineno - 1, messages)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 327, in section

self.new_subsection(title, lineno, messages)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 395, in new_subsection

node=section_node, match_titles=True)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 282, in nested_parse

node=node, match_titles=match_titles)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 196, in run

results = StateMachineWS.run(self, input_lines, input_offset)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/statemachine.py", line 239, in run

context, state, transitions)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/statemachine.py", line 460, in check_line

return method(match, context, next_state)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2753, in underline

self.section(title, source, style, lineno - 1, messages)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 327, in section

self.new_subsection(title, lineno, messages)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 395, in new_subsection

node=section_node, match_titles=True)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 282, in nested_parse

node=node, match_titles=match_titles)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 196, in run

results = StateMachineWS.run(self, input_lines, input_offset)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/statemachine.py", line 239, in run

context, state, transitions)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/statemachine.py", line 460, in check_line

return method(match, context, next_state)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2326, in explicit_markup

nodelist, blank_finish = self.explicit_construct(match)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2338, in explicit_construct

return method(self, expmatch)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2081, in directive

directive_class, match, type_name, option_presets)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2130, in run_directive

result = directive_instance.run()


 "/opt/citoplus/local/lib/python2.7/site-packages/sphinx/ext/autodoc/directive.py", line 144, in run

result = parse_generated_content(self.state, params.result, documenter)


 "/opt/citoplus/local/lib/python2.7/site-packages/sphinx/ext/autodoc/directive.py", line 85, in parse_generated_content

nested_parse_with_titles(state, content, node)


 "/opt/citoplus/local/lib/python2.7/site-packages/sphinx/util/nodes.py", line 219, in nested_parse_with_titles

return state.nested_parse(content, 0, node, match_titles=1)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 282, in nested_parse

node=node, match_titles=match_titles)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 196, in run

results = StateMachineWS.run(self, input_lines, input_offset)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/statemachine.py", line 239, in run

context, state, transitions)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/statemachine.py", line 460, in check_line

return method(match, context, next_state)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2328, in explicit_markup

self.explicit_list(blank_finish)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2358, in explicit_list

match_titles=self.state_machine.match_titles)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 319, in nested_list_parse

node=node, match_titles=match_titles)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 196, in run

results = StateMachineWS.run(self, input_lines, input_offset)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/statemachine.py", line 239, in run

context, state, transitions)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/statemachine.py", line 460, in check_line

return method(match, context, next_state)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2631, in explicit_markup

nodelist, blank_finish = self.explicit_construct(match)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2338, in explicit_construct

return method(self, expmatch)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2081, in directive

directive_class, match, type_name, option_presets)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2130, in run_directive

result = directive_instance.run()


 "/opt/citoplus/local/lib/python2.7/site-packages/sphinx/domains/__init__.py", line 237, in run

return BaseDirective.run(self)


 "/opt/citoplus/local/lib/python2.7/site-packages/sphinx/directives/__init__.py", line 179, in run

self.state.nested_parse(self.content, self.content_offset, contentnode)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 282, in nested_parse

node=node, match_titles=match_titles)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 196, in run

results = StateMachineWS.run(self, input_lines, input_offset)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/statemachine.py", line 239, in run

context, state, transitions)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/statemachine.py", line 460, in check_line

return method(match, context, next_state)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 2767, in text

paragraph, literalnext = self.paragraph(lines, startline)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 418, in paragraph

textnodes, messages = self.inline_text(text, lineno)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 427, in inline_text

return self.inliner.parse(text, lineno, self.memo, self.parent)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 645, in parse

lineno)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 787, in interpreted_or_phrase_ref

lineno)


 "/opt/citoplus/local/lib/python2.7/site-packages/docutils/parsers/rst/states.py", line 871, in interpreted

nodes, messages2 = role_fn(role, rawsource, text, lineno, self)


 "/opt/citoplus/local/lib/python2.7/site-packages/django/contrib/admindocs/utils.py", line 126, in _role

inliner.document.settings.link_base,
AttributeError: Values instance has no attribute 'link_base'
