Having issues with AttributeError: ZipFile(path) as file

[xsharkbaitx]

I'm trying to get extract-paired-reads.py to work and am having the following issue: Traceback (most recent call last): File "/usr/bin/extract-paired-reads.py", line 4, in import pkg_resources File "/usr/lib/python2.6/site-packages/pkg_resources/init.py", line 3147, in @_call_aside File "/usr/lib/python2.6/site-packages/pkg_resources/init.py", line 3131, in _call_aside f(*args, **kwargs) File "/usr/lib/python2.6/site-packages/pkg_resources/init.py", line 3160, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/usr/lib/python2.6/site-packages/pkg_resources/init.py", line 657, in _build_master ws = cls() File "/usr/lib/python2.6/site-packages/pkg_resources/init.py", line 650, in init self.add_entry(entry) File "/usr/lib/python2.6/site-packages/pkg_resources/init.py", line 706, in add_entry for dist in find_distributions(entry, True): File "/usr/lib/python2.6/site-packages/pkg_resources/init.py", line 1966, in find_eggs_in_zip if metadata.has_metadata('PKG-INFO'): File "/usr/lib/python2.6/site-packages/pkg_resources/init.py", line 1488, in has_metadata return self.egg_info and self._has(self._fn(self.egg_info, name)) File "/usr/lib/python2.6/site-packages/pkg_resources/init.py", line 1840, in _has return zip_path in self.zipinfo or zip_path in self._index() File "/usr/lib/python2.6/site-packages/pkg_resources/init.py", line 1717, in zipinfo return self._zip_manifests.load(self.loader.archive) File "/usr/lib/python2.6/site-packages/pkg_resources/init.py", line 1677, in load manifest = self.build(path) File "/usr/lib/python2.6/site-packages/pkg_resources/init.py", line 1650, in build with zipfile.ZipFile(path) as zfile: AttributeError: ZipFile instance has no attribute 'exit'

We are running python 2.7.6 on our server and the input files are trimmed, qc'd, fasta files. Thanks in advance.

[standage]

Hi, thanks for the report. It looks like it's almost certainly a conflict between different versions of Python on your system. You say Python 2.7.6 is installed, yet all the file paths in the stack trace point to modules in a Python 2.6 installation. Also, if you're using a recent version of khmer installed directly from Github, Python 2.7 is no longer supported and you'll need to upgrade to Python 3 in order to use khmer.

If you have admin privileges on the server, you should be able to follow the following installation instructions. If not, I would suggest installing the Anaconda Python distribution in your server's home directory and installing khmer in a conda virtual environment (instructions included in the link above).

[xsharkbaitx]

Thanks for the feedback on the issue.

[standage]

Did this resolve your issues @xsharkbaitx?