11. FAQS

11.2. What are the dependencies

There are two kind of dependencies. First, the Python libraries such as matplotlib or Pandas. Second, the external tools such as BWA (alignment) or Kraken (taxonomy). The first kind of tools can be installed using Anaconda and the default conda channel. For instance:

conda install pandas

The second kind of tools can also be installed using another conda channel called bioconda. For instance:

conda install bwa

The full list of dependencies will be maintained in the Installation section.

11.3. Installation issues

As explained in the previous section, most of the dependencies can be installed via Conda. If not, pip is recommended. Yet there are still a few dependencies that needs manual installation.

11.3.1. quast


wget https://downloads.sourceforge.net/project/quast/quast-4.2.tar.gz
tar -xzf quast-4.2.tar.gz
cd quast-4.2

Alternatively, get the source code from their GitHub (takes a while):

git clone https://github.com/ablab/quast
cd quast
python setup.py install

11.3.2. graphviz

graphviz provides an executable called dot. If you type dot in a shell and get this error message:

Warning: Could not load
...lib/graphviz/libgvplugin_gd.so.6" - file not found

This may be solved by re-installation graphviz using the main anaconda channel (instead of bioconda):

conda install --override-channels -c anaconda graphviz=2.38.0
Update April 2017:
 replace anaconda with conda-forge

11.3.3. matplotlib

If you get errors related to the X connection, you may need to change the backend of matplotlib. To do so, go in your home directory and in this directory

/home/user/.config/matplotlib ,

add a file called matplotlibrc with the following content:

backend: Agg

Save, exit the shell, start a new shell.

11.3.4. pysam

from pysam.libchtslib import *
...ImportError: libhts.so.1: cannot open shared object file: No such file or directory

This may be solved by removing conda installation and using pip instead:

conda remove pysam
pip install pysam

11.3.5. qt

from PyQt5.QtWebKitWidgets import QWebView
...ImportError: libQt5WebKitWidgets.so.5: cannot open shared object file: No such file or directory

This may be solved by re-installation qt using the main anaconda channel (instead of bioconda):

conda install --override-channels -c anaconda qt

11.4. Expected input format

Most of the pipelines and standalone expect FastQ files with the extension fastq.gz meaning that files are gzipped.

Besides, the filename convention is as follows:


that is _R1_ and _R2_ indicates the paired or single-ended files and the PREFIX is used to create directories or reports; it must be present.

New in version 0.2: more flexible tags are now possible in sequana pipelines and sequanix using e.g. _R[12] in the input_readtag in the configuration file of the pipelines.

11.6. QXcbConnection issue

If you get this error:

QXcbConnection: Could not connect to display localhost:10.0

this is an issue with your Qt backend. You need to change it to Agg.

11.7. Variant Calling pipeline

If snpeff fails with this type of errors:

java.lang.RuntimeException: Error reading file 'null'
java.lang.RuntimeException: Cannot find sequence for 'LN831026.gbk'

this may be because your genbank does not contain the sequences.

Another type of errors is that the sequence and genbank are not synchrone. We would recommend to use the code here to download the Fasta and genbank: