Using Biolinux and installed Ubuntu 16.04 but now qiime is not working

[dbrads...@fau.edu]

Dear Whom It May Concern,

I have also contacted the Biolinux mailing list but I am also wanted to see if anyone here know how to fix it. I upgraded to Ubuntu 16.04 and now there are items within qiime that are not working. I imagine I may have removed some essential items during the upgrade? What would be the best way to fix this? Below are some of the errors I am encountering.

Thank you for your time and help,

Sincerely,

David Bradshaw


microbiology@microbiology-OptiPlex-9020[microbiology] qiime           [ 1:35PM]
join_paired_ends.py
Setting up ZSH (/bin/zsh) environment to run QIIME commands.

You have QIIME version UNKNOWN.
Note that this will not produce identical results to the official QIIME release
as it uses updated versions of several tools.

Type 'help' for help, 'print_qiime_config_all' to see the current QIIME
settings, or 'exit' to return to regular shell.

microbiology@microbiology-OptiPlex-9020[microbiology]  qiime > print_qiime_config_all
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
Traceback (most recent call last):
  File "/usr/lib/qiime/bin/print_qiime_config.py", line 57, in <module>
    raise ImportError("%s\n%s" % (e, core_dependency_missing_msg))
ImportError: cannot import name OrdinationResults
See the QIIME Installation Guide: http://qiime.org/install/install.html

Here are the versions of the packages that QIIME depends on as reported by
the system package manager:

ampliconnoise             : 1.29-5build1
blast2                    : 1:2.2.26.20120620-10
bwa                       : 0.7.12-5
cd-hit                    : 4.6.4-1
chimeraslayer             : 20101212+dfsg1-1
clearcut                  : 1.0.9-1
clustalw                  : 2.1+lgpl-4
ea-utils                  : 1.1.2+dfsg-3
emperor                   : 0.9.51-0biolinux1
fasttree                  : 2.1.8-2
infernal                  : 1.1.1-3
mafft                     : 7.271-1
mothur                    : 1.36.1-1build1
muscle                    : 1:3.8.31+dfsg-1
parsinsert                : 1.04-1biolinux1.1
pynast                    : 1.2.2-1
python                    : 2.7.11-1
python-biom-format        : 2.1.5+dfsg-1
python-burrito            : 0.9.1-1
python-burrito-fillings   : 0.1.0-0biolinux4
python-cogent             : 1.5.3-10
python-matplotlib         : 1.5.1-1ubuntu1
python-mpi4py             : 1.3.1+hg20131106-2ubuntu5
python-numpy              : 1:1.11.0-1ubuntu1
python-pandas             : 0.17.1-3ubuntu2
python-qcli               : 0.1.0-1
python                    : 2.7.11-1
qiime-data                : 1.9.0+dfsg-0biolinux5
qiime-default-reference   : 0.1.1-0biolinux2
r-cran-optparse           : 1.3.0-1cran1ppa0
raxml                     : 8.2.4-1
rdp-classifier            : 2.10.2-1
seqprep                   : 1.1-4ubuntu1
sortmerna                 : 2.0-1
sumatra                   : 1.0.10-1
swarm                     : 2.1.6-1
vsearch                   : 1.1.3+dfsg-1

OK
microbiology@microbiology-OptiPlex-9020[microbiology]  qiime > join_paired_ends.py -f DCH2_062216/4653_C1S616-515wF-806bR_R1.fastq -r DCH2_062216/4653_C1S616-515wF-806bR_R2.fastq -o C1S616
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
Traceback (most recent call last):
  File "/usr/lib/qiime/bin/join_paired_ends.py", line 11, in <module>
    from qiime.join_paired_ends import (join_method_names,
  File "/usr/lib/python2.7/dist-packages/qiime/join_paired_ends.py", line 11, in <module>
    from skbio.parse.sequences import parse_fastq
ImportError: No module named parse.sequences

[Jai Ram Rideout]

Hi David,

First I want to note that the QIIME development group does not officially support Biolinux installations of QIIME. It looks like you have one or more incompatible versions of QIIME dependencies installed. It appears a newer version of scikit-bio is installed that doesn't work with QIIME. QIIME supports scikit-bio 0.2.3 only so you'll need to downgrade scikit-bio. Biolinux support should be able to help you with that process.

Best,

Jai

[dbrads...@fau.edu]

Dear Jai,

Thank you very much for the quick reply. Hopefully they will get back to me soon.

Sincerely,

David Bradshaw

[Colin Brislawn]

Hello David,

I'd like to 'qiime in' here and mention that you could also consider installing qiime with miniconda. This method will make a brand new copy of qiime, totally independant of other software on your system, and the miniconda installation is the officially recommended and supported install method. 

http://qiime.org/install/install.html 

Just a thought,

Colin

[dbrads...@fau.edu]

Dear Colin Brislawn,

Thank you for the suggestion, I am sorry I did not see this until now. I am trying to install MiniConda 3 but the conda command is not working after installation. Would you be able to assist with that or should I contact MiniConda? Thank you for your time and help.

Sincerely,

David Bradshaw

[dbrads...@fau.edu]

Dear Colin Brislawn or Whom It May Concern,

Sorry here is the command line and error

microbiology@microbiology-OptiPlex-9020[microbiology] conda           [ 4:27PM]
zsh: command not found: conda

I followed the installation prompt and said yes to everything.

[Jai Ram Rideout]

Hi David,

Feel free to post the exact commands you ran to install Miniconda3 and we will do our best to help, if not we can refer you to the conda developers.

Best,

Jai

[Jai Ram Rideout]

Hi David,

I'm guessing that Miniconda3 installed correctly but you're not finding the installed commands due to your PATH environment variable. First thing to try: log out of your cluster and log back in in a new terminal, then try running "conda". If that doesn't work:

The Miniconda3 installer should have added a line to $HOME/.bashrc that sets your PATH variable. It'll look similar to mine:

# added by Miniconda3 4.0.5 installer

export PATH="/Users/jairideout/miniconda3/bin:$PATH"

I wonder if this line needs to be added to a different startup file? You're using zsh instead of bash, so you may need to add it to a different shell startup file (e.g. $HOME/.zshrc). You may want to contact your cluster administrator to see if they can help you get conda installed since there may be cluster-specific configuration affecting the Miniconda3 install. We basically need the PATH setting command to be run when you log into the cluster (or when a module is loaded, if that's how your cluster administrator wants to install conda).

Best,

Jai

[dbrads...@fau.edu]

Dear Jai,

Here are the scripts I ran. Strangely I do not have a .bashrc file in my Home file, at least visually, so I do not know what it is prepending it to? Thank you for your time and help.

Sincerely,

David Bradshaw

microbiology@microbiology-OptiPlex-9020[microbiology] bash Miniconda3-latest-Linux-x86_64.sh

Welcome to Miniconda3 4.1.11 (by Continuum Analytics, Inc.)

In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>>
=================
Miniconda License
=================

Deleted this for the post

Do you approve the license terms? [yes|no]
>>> yes

Miniconda3 will now be installed into this location:
/home/microbiology/miniconda3

  - Press ENTER to confirm the location
  - Press CTRL-C to abort the installation
  - Or specify a different location below

Pressed ENTER

[/home/microbiology/miniconda3] >>>
PREFIX=/home/microbiology/miniconda3
installing: python-3.5.2-0 ...
installing: conda-env-2.5.2-py35_0 ...
installing: openssl-1.0.2h-1 ...
installing: pycosat-0.6.1-py35_1 ...
installing: pyyaml-3.11-py35_4 ...
installing: readline-6.2-2 ...
installing: requests-2.10.0-py35_0 ...
installing: ruamel_yaml-0.11.14-py35_0 ...
installing: sqlite-3.13.0-0 ...
installing: tk-8.5.18-0 ...
installing: xz-5.2.2-0 ...
installing: yaml-0.1.6-0 ...
installing: zlib-1.2.8-3 ...
installing: conda-4.1.11-py35_0 ...
installing: pycrypto-2.6.1-py35_4 ...
installing: pip-8.1.2-py35_0 ...
installing: wheel-0.29.0-py35_0 ...
installing: setuptools-23.0.0-py35_0 ...
Python 3.5.2 :: Continuum Analytics, Inc.
creating default environment...
installation finished.
Do you wish the installer to prepend the Miniconda3 install location
to PATH in your /home/microbiology/.bashrc ? [yes|no]
[no] >>> yes  

Prepending PATH=/home/microbiology/miniconda3/bin to PATH in /home/microbiology/.bashrc
A backup will be made to: /home/microbiology/.bashrc-miniconda3.bak


For this change to become active, you have to open a new terminal.

Thank you for installing Miniconda3!

Share your notebooks and packages on Anaconda Cloud!
Sign up for free: https://anaconda.org

microbiology@microbiology-OptiPlex-9020[microbiology]    

Then I closed the terminal and restarted it.

microbiology@microbiology-OptiPlex-9020[microbiology] conda           [ 5:20PM]

zsh: command not found: conda

microbiology@microbiology-OptiPlex-9020[microbiology]                 [ 5:20PM]

[Jai Ram Rideout]

Hi David,

It looks like your default shell is zsh, but Miniconda3 was installed with bash so it added the PATH line to /home/microbiology/.bashrc. Files that start with a period are hidden when you "ls" a directory. If you run "ls -a" that will show you all files in the directory.

I think what you need to do is add that PATH line to /home/microbiology/.zshrc, then open a new terminal and log in. If that doesn't work I recommend contacting your cluster administrator to help you install conda.

Best,

Jai

[dbrads...@fau.edu]

Dear Jai,

I just switched from the zsh to the bash shell terminal and it started working. Thank you very much for all your help. Sorry for all the questions, I am still very new to qiime, ubuntu, using the terminal etc..I did not even know what bash and zsh were until did more research. I will test out this new qiime system now. All the best. Thank you for your time and help.

Sincerely,

David Bradshaw

[Jai Ram Rideout]

Hi David,

Great, thanks for following up with your solution! In general QIIME should work better using bash as your shell instead of zsh, so you may want to make bash your default shell going forward. I'll follow up on the other thread you created about aligning sequences now that you have a functioning QIIME installation.

Best,

Jai