12. FAQS

12.2. 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 but those two lines should be sufficient to install most of the dependencies with conda:

conda install --file https://raw.githubusercontent.com/sequana/sequana/master/requirements.txt
conda install --file https://raw.githubusercontent.com/sequana/sequana/master/requirements_pipelines.txt

Additional tools such as prokka, busco, canu and future heavy software will be maintained in this specific requirements for now:

conda install --file https://raw.githubusercontent.com/sequana/sequana/master/requirements_pipelines_extra.txt

12.3. 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.

12.3.1. quast

http://quast.bioinf.spbau.ru/manual.html#sec1

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

12.3.2. 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

12.3.3. 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.

12.3.4. pysam / samtools / bzip2

We have experienced few issues with pysam and samtools. Here are some solutions.

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

Another error know for pysam version 0.11.2.2 raises this error:

ImportError: libbz2.so.1.0: cannot open shared object file: No such file or
directory

Downgrading to version 0.11.2.1 and upgrading to working version solves the problem:

conda install pysam=0.11.2.1

but one reason was also related to the order of the channel in the .condarc file. You may get bzip2 from the default channel and not from conda-forge (reference: https://github.com/bioconda/bioconda-recipes/issues/5188)

conda install --override-channels -c conda-forge bzip2

12.3.5. 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

12.3.6. libselinux

If you get this error (using conda install sequana):

ImportError: libselinux.so.1: cannot open shared object file: No such file or directory

it looks like you need to install libselinux on your environment as reported here.

12.4. 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:

PREFIX_R1_.fastq.gz

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.

12.6. 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.

12.7. 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:

http://sequana.readthedocs.io/en/master/tutorial.html#new-in-v0-10

12.8. Singularity

If you use the singularity container and get this kind of error:

singularity shell sequana-sequana-master.img
ERROR  : Base home directory does not exist within the container: /pasteur
ABORT  : Retval = 255

it means the container does not know about the Base home directory.

If you have sudo access, add the missing path as follows:

sudo singularity shell --writable sequana-sequana-master.img
mkdir /pasteur
exit

If you do not have sudo permissions, copy the image on a computer where you have such permission, use the same code as above and copy back the new image on the computer where you had the issue.

Finally, try to use the container again using this code:

singularity shell sequana-sequana-master.img