Issues installing and running Qiime

[nlh15]

Hello,

I am having issues installing and running qiime on my desktop. I install everything using sudo and following the basic install on qiime.org. The end of the install process generates the following text:

no previously-included directories found matching 'doc/build' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution
Successfully installed numpy scipy pynast biom-format scikit-bio

And when i try to verify my installation with the print_qiime_config.py -t command I get the following error message:


cedb@bio-edi[cedb] print_qiime_config.py -t [ 4:05PM]
Traceback (most recent call last): File "/usr/local/bin/print_qiime_config.py", line 40, in <module> raise ImportError("%s\n%s" % (e, core_dependency_missing_msg)) ImportError: libqhull.so.5: cannot open shared object file: No such file or directory

I have tried installing libqhull and all other dependencies that appear to be missing but with no results. Ive used the synaptic package manager to install qiime as well as done it via the terminal and I still get the same error message. Can anyone tell me what I am doing wrong here?

// Nine

[Jenya Kopylov]

Hello,

A few questions to help figure out the issues you're seeing:

Are you trying to install QIIME on linux or Mac?

Can you point me to the exact instructions you used for installing QIIME?

What version are you trying to install and where did you download the package from?

The libqhull library is used my Matplotlib (maybe other tools too), do you know if that was installed correctly?

You can check with:

$ python -c "import matplotlib; print matplotlib.__version__"

Jenya

[nlh15]

I used the synaptic package manager to do all the installations. After i posted this i switched desktops and installed ubuntu 15.10 on it and tried installing qiime again. Now im facing the following problem:

cedbuwf@cedbuwf-OptiPlex-9020:~/Desktop/Init3125/Merged$ print_qiime_config.py -t

Traceback (most recent call last):

  File "/usr/local/bin/print_qiime_config.py", line 57, in <module>

    raise ImportError("%s\n%s" % (e, core_dependency_missing_msg))

ImportError: cannot import name DenseTable

I cant find anything like DenseTable anywhere and its screwing with my attempts to run validate_mapping_file.py. Any ideas?

[Jenya Kopylov]

Hello,

The "ImportError: cannot import name DenseTable" error relates to BIOM (a QIIME dependency) not being installed. You can check that with the command:

$ python -c "import biom; print biom.__version__"

What version of QIIME are you trying to install?

Have you taken a look at similar threads regarding QIIME installation on Linux, like this?

However, the easiest way to install QIIME (and all its dependencies) would be through pip (see this thread),

$ pip install https://github.com/biocore/qiime/archive/1.9.1.tar.gz

Jenya

[nlh15]

According to the synaptic package manager I have qiime 1.8 installed already but the print_qiime_config.py command still generates the same error about core dependencies Dense Table missing. I tried using your pip install link but it generated the following message:

cedbuwf@cedbuwf-OptiPlex-9020:~$ pip install https://github.com/biocore/qiime/archive/1.9.1.tar.gz
Downloading/unpacking https://github.com/biocore/qiime/archive/1.9.1.tar.gz
Cleaning up...
Exception:

Traceback (most recent call last):

  File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 122, in main
    status = self.run(options, args)
  File "/usr/lib/python2.7/dist-packages/pip/commands/install.py", line 304, in run
    requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1198, in prepare_files
    do_download,
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1376, in unpack_url
    self.session,
  File "/usr/lib/python2.7/dist-packages/pip/download.py", line 546, in unpack_http_url
    resp = session.get(target_url, stream=True)
  File "/usr/lib/python2.7/dist-packages/requests/sessions.py", line 477, in get
    return self.request('GET', url, **kwargs)
  File "/usr/lib/python2.7/dist-packages/pip/download.py", line 237, in request
    return super(PipSession, self).request(method, url, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/requests/sessions.py", line 465, in request
    resp = self.send(prep, **send_kwargs)
  File "/usr/lib/python2.7/dist-packages/requests/sessions.py", line 573, in send
    r = adapter.send(request, **kwargs)
  File "/usr/lib/python2.7/dist-packages/requests/adapters.py", line 370, in send
    timeout=timeout
  File "/usr/lib/python2.7/dist-packages/urllib3/connectionpool.py", line 557, in urlopen
    body=body, headers=headers)
  File "/usr/lib/python2.7/dist-packages/urllib3/connectionpool.py", line 388, in _make_request
    assert_header_parsing(httplib_response.msg)
  File "/usr/lib/python2.7/dist-packages/urllib3/util/response.py", line 49, in assert_header_parsing
    if not isinstance(headers, httplib.HTTPMessage):
AttributeError: 'module' object has no attribute 'HTTPMessage'

Storing debug log for failure in /tmp/tmpKMPkFs

The other command generated the following:

cedbuwf@cedbuwf-OptiPlex-9020:~$ python -c "import biom; print biom.__version__"
2.1

my python version is 2.7.10, is this in any way related to inconsistencies in dependency versions?

[Jai Ram Rideout]

Hi Nine,

I'm not sure what exactly is going wrong, but I suspect it is an issue with having two versions of QIIME installed (one via synaptic, one via pip). We do not maintain or support the synaptic versions of QIIME, and the synaptic version is old (1.8.0), so I recommend uninstalling it with:

sudo apt-get purge --auto-remove qiime

Let's also remove your QIIME pip installation:

sudo pip uninstall qiime

Now, assuming those commands executed successfully, let's install QIIME following these instructions:

sudo apt-get install build-essential python-dev python-pip

sudo pip install numpy
sudo pip install qiime

Can you try that and let me know how it goes?

Jai

[nlh15]

yJai,

managed to uninstall all and installed qiime according to your instructions and it worked! My only problem is that I am having issues getting uclust to work for me now. I downloaded the file and moved it to my usr/local/bin directory. Then I utilized chmod a+x to set the permissions and created a link (uclust). Uclust is however showing up in red when I ls the directory and when i try print_qiime_config i get the following error message:

FAIL: test_uclust_supported_version (__main__.QIIMEDependencyBase)
uclust is in path and version is supported
----------------------------------------------------------------------

Traceback (most recent call last):

  File "/usr/local/bin/print_qiime_config.py", line 322, in test_uclust_supported_version
    "which components of QIIME you plan to use.")
AssertionError: uclust not found. This may or may not be a problem depending on which components of QIIME you plan to use.

I attempted to chmod a+x uclust as well but it wouldnt let me use that command on a link. Any advice?
Very much appreciate your help!

[Jai Ram Rideout]

Great, glad to hear the install worked! That's strange that uclust isn't working for you, it should have been downloaded and installed as part of the "pip install qiime" command. Can you remove the uclust binary and link that you created in /usr/local/bin, rerun "sudo pip install qiime", and then run "print_qiime_config.py -t"? If that doesn't work I'll help guide you through a manual uclust install.

Jai

[nlh15]

Managed to install it by switching to a 32 version. I just realized that the system im working with is a 32 bit ubuntu version. I know the recommended system is 64 bit, how will this affect qiime running and working properly? Should I just go ahead and replace this ubuntu installation with a 64 bit version? Trying to weigh my options..

[Colin Brislawn]

Good afternoon,

Using 32 bit programs will limit the amount of memory (RAM) programs can use. 32 bits of memory is about enough to address 4gb of so of RAM, so databases or data sets larger than that will fail. 

Almost all modern operating systems, processors, and software is compiled in 64-bits so that it can handle large files. Your computer can probably run 64 bit ubuntu, so I would recommend taking the free the upgrade. 

Colin

[Jai Ram Rideout]

To add to Colin's response: as of QIIME 1.2.0 we no longer support 32-bit systems so I highly recommend upgrading to 64-bit Ubuntu.

Jai

[nlh15]

I wiped the comp and installed a 14.04 64 bit version of ubuntu. Despite following previous instructions I am now getting the following error message when trying to pip install qiime:

 Can't roll back scipy; was not uninstalled
Cleaning up...
Command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_root/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-xFxhqT-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /tmp/pip_build_root/scipy

Traceback (most recent call last):

  File "/usr/local/bin/pip", line 9, in <module>
    load_entry_point('pip==1.5.4', 'console_scripts', 'pip')()
  File "/usr/lib/python2.7/dist-packages/pip/__init__.py", line 235, in main
    return command.main(cmd_args)
  File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 161, in main
    text = '\n'.join(complete_log)
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 72: ordinal not in range(128)

Help please..

[Jai Ram Rideout]

Hello,

Can you please post the exact commands you ran, including the complete output that's generated by those commands? I'm not sure what the problem is from the snippet you posted (it seems to be an issue with installing scipy, one of QIIME's dependencies).

Thanks,

Jai