PackageNotFoundError: Package missing in current linux-64 channels¶

The installation of ddRAGE fails with the error:

me@machine:~$ conda create -n ddrage ddrage
Fetching package metadata .........

PackageNotFoundError: Package missing in current linux-64 channels:
  - ddrage

In this case, the bioconda channel is missing. You can either tell conda to use it with the -c parameter:

me@machine:~$ conda create -n ddrage -c bioconda ddrage

or permanently add it to your .condarc as described in the bioconda documentation.

conda: command not found¶

After installing conda, the conda command is not available. This can be due to the fact, that the path to the conda executable(s) has not been added to the PATH variable.

During the installation, the script asks, if it should add a line to the .bashrc to solve this:

Do you wish the installer to prepend the Miniconda3 install location to PATH in your .bashrc? [yes|no]
[no] >>>

Choose ‘yes’ and start a new shell or source the .bashrc. The conda executable should be available now.

You can also add the following line manually to your .bashrc:

export PATH="/home/<user>/miniconda3/bin:$PATH"

Where <user> is your user name. If you chose a different installation path, find the /bin folder in your chosen path and replace the path with your custom path.

Many reads are removed by the analysis tool¶

While this can have many reasons, most likely this is due to the fact that some analysis tools can not handle modified FASTQ name lines. Since ddRAGE adds annotations to the end of the name line, all reads get discarded.

To solve this, remove the annotation with the remove_annotation script as described in the tools chapter. Then try the analysis using the files without annotations (with the _noheader suffix).

Address already in use¶

Visualizing the BBD parameters using the visualize_bbd script does fail with the error:

(ddrage)me@machine:~$ visualize_bbd
Traceback (most recent call last):
  File "bbd_visualization.py", line 215, in <module>
    main_standalone()
  File "bbd_visualization.py", line 219, in main_standalone
    server = Server({'/': bokeh_app}, io_loop=io_loop)
  File "/home/me/miniconda3/envs/rad/lib/python3.5/site-packages/bokeh/server/server.py", line 121, in __init__
    sockets, self._port = _bind_sockets(self._address, port)
  File "/home/me/miniconda3/envs/rad/lib/python3.5/site-packages/bokeh/server/server.py", line 60, in _bind_sockets
    ss = netutil.bind_sockets(port=port or 0, address=address)
  File "/home/me/miniconda3/envs/rad/lib/python3.5/site-packages/tornado/netutil.py", line 194, in bind_sockets
    sock.bind(sockaddr)
OSError: [Errno 98] Address already in use

This problem occurs, when an instance of the bokeh server is already running. Make sure you closed all browser tabs showing the visualization and retry.

If you already closed all browser windows, stop the python process visualizing the server either using you process management (like top or htop), by closing the terminal in which you ran visualize_bbd or by killing the process. As a last resort you can also stop ALL python processes using

(ddrage)me@machine:~$ killall python

However, make sure that no other python process that you (or others) want to keep is running on your machine.

If this does not solve the problem, make sure that no other process is using port 5006.

ImportError: No module named ‘bokeh’¶

Starting the visualize_bbd script fails with the error:

(ddrage) me@machine:~$ visualize_bbd
Traceback (most recent call last):
  File "/home/me/miniconda3/envs/ddrage/bin/visualize_bbd", line 4, in <module>
    import ddrage.tools.bbd_visualization
  File "/home/me/miniconda3/envs/ddrage/lib/python3.5/site-packages/ddrage/tools/bbd_visualization.py", line 13, in <module>
    from bokeh.application.handlers import FunctionHandler
ImportError: No module named 'bokeh'

This means that bokeh, the plotting library used to visualize the BBD (which is not a hard dependency of ddRAGE), needs to be installed. Depending on the installation kind you used, install bokeh either by using conda:

(ddrage)me@machine:~$ conda install bokeh

or using pip:

(ddrage)me@machine:~$ pip install bokeh

ModuleNotFoundError: No module named ‘tornado’¶

Starting the visualize_bbd script fails with the error:

(ddrage) me@machine:~$ visualize_bbd
Traceback (most recent call last):
  File "/vol/home/me/miniconda3/envs/ddrage/bin/visualize_bbd", line 4, in <module>
    import ddrage.tools.bbd_visualization
  File "/vol/home/me/miniconda3/envs/ddrage/lib/python3.6/site-packages/ddrage/tools/bbd_visualization.py", line 11, in <module>
    from tornado.ioloop import IOLoop
ModuleNotFoundError: No module named 'tornado'

This means, that the tornado web-server, which is required by bokeh, is not installed. Normally it should be installed as a dependency of bokeh. So if you are using conda try (re-)installing bokeh:

(ddrage)me@machine:~$ conda install bokeh

If you are using pip, try the same:

(ddrage)me@machine:~$ pip install bokeh

If the dependencies are not handled automatically, try installing tornado directly:

(ddrage)me@machine:~$ pip install tornado

However, in this case you might need to install all dependencies of bokeh this way.