Troubleshooting

Nathan Mih edited this page Mar 2, 2018 · 18 revisions

Table of Contents

Install errors with pip

libxml library errors

Error

During pip install ssbio:

make sure the development packages of libxml2 and libxslt are installed

Solution

See: http://stackoverflow.com/questions/5178416/pip-install-lxml-error

  • For Ubuntu/Debian:

      sudo apt-get install python-dev libxml2-dev libxslt1-dev zlib1g-dev
    
  • For CentOS/Fedora/Red Hat:

      yum install libxslt-devel libxml2-devel
    

Missing glpsol

Error

During pip install ssbio:

subprocess.CalledProcessError: Command '['which', 'glpsol']' returned non-zero exit status 1.

Solution

pip install swiglpk --only-binary swiglpk

Installation tips

FreeSASA Python bindings

Some tips to enable Python bindings with FreeSASA. These bindings seem difficult to install with Python 3, so ssbio just provides wrappers to execute FreeSASA and parse the NACCESS formatted output files. However, if you want to use the bindings in Python 2, here are tips:

  • Download the latest tarball (see home page), expand it and run

      ./configure --enable-python-bindings CFLAGS="-fPIC -O2"
      make
    
  • If you have a user-specific Python executable (ie. through Anaconda), edit the freesasa-2.0/bindings/Makefile, lines 805, 809, 815 to change:

      python setup.py [...]
    

    to

      /path/to/anaconda/python setup.py [...]
    
  • Install with

      sudo make install
    

Issues with the Jupyter notebook

Tips for nglview

These are some tips I gathered on troubleshooting nglviewer in the Jupyter notebook. The easiest thing to do is just make sure everything's fresh and installed correctly...

Fresh install

  • Delete the folders

      rm -rf ~/anaconda3/share/jupyter/nbextensions/nglview-js-widgets/  # or wherever your python installation is, check /usr/local/share/jupyter/nbextensions or ~/.jupyter/nbextensions
      rm -rf ~/.local/share/jupyter/nbextensions/nglview-js-widgets/ 
    
  • Uninstall any installations of nglview, try multiple times just to be sure

      conda uninstall nglview 
      pip uninstall nglview 
    
  • Check your installations versions of widgetsnbextension, ipywidgets, and ipython

      conda list 
      
      widgetsnbextension        3.0.2            py36hd01bb71_1 
      ipywidgets                7.0.3                    py36_1    conda-forge 
      ipython                   6.1.0            py36hc72a948_1 
    
    • ipywidgets version 7 is compatible with widgetsnbextension 3
    • ipywidgets version 6 is compatible with widgetsnbextension 2
  • Double check if you are having two ipywidgets version (e.g: one installed via pip and one installed via conda)

    • To uninstall:

        conda remove ipywidgets --force 
        pip uninstall ipywidgets 
      
    • You can just try installing nglview next as it will install ipywidgets as a dependency

      • Or do:

          pip install ipywidgets 
        
      • Or:

          conda install -c conda-forge ipywidgets 
        
  • Reinstall nglview

      conda config --add channels conda-forge 
      conda install nglview -c bioconda 
    
    • Or..

        pip install nglview 
      
  • Check your enabled nbextensions

      jupyter-nbextension list 
    
  • Make sure widgets are enabled

      jupyter nbextension install widgetsnbextension --py --sys-prefix 
      jupyter nbextension enable --py --sys-prefix widgetsnbextension 
      jupyter-nbextension enable nglview --py --sys-prefix  # or: nglview enable
    
    • nglview_main seems to be disabled on mine
  • Restart everything

      kill $(pgrep jupyter)
      jupyter notebook 
    
  • Other testing things


Issues with external software

Running I-TASSER for a protein sequence

Error

    exp.dat: Line-XXX is missed !!!!!!

Explanation

  • I-TASSER4.4/bin/solve does not run properly on a 64-bit system, giving this error in your I-TASSER output files for a sequence.

  • If you try running it (/path/to/I-TASSER4.4/bin/solve) manually, you get this error:

      ./solve: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory
    

Solution 1

  • Try installing 32-bit libraries according to this link

Solution 2

  • Download this executable: solve, obtained from here.

  • Rename it from solve.pdf to solve

  • Replace I-TASSER4.4/bin/solve with the new file, and try running:

      ./solve
    
  • If you get this error you also might want to install STRIDE from source.

Sources

  1. Troubleshooting: http://zhanglab.ccmb.med.umich.edu/bbs/?q=node/3464#comment-3089
  2. Fixed solve: http://zhanglab.ccmb.med.umich.edu/bbs/?q=node/57#comment-181
  3. STRIDE: http://zhanglab.ccmb.med.umich.edu/bbs/?q=node/3760#comment-3617

EMBOSS

On Unix you may encounter:

   /usr/local/bin/embossupdate: error while loading shared libraries: libnucleus.so.6: cannot open shared object file: No such file or directory

Just run (according to https://www.biostars.org/p/86327/):

   sudo ldconfig

And try running an EMBOSS program, such as needle.

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