Frequently Asked Questions (FAQs)

This is a collection of FAQs for BacterialTyper tutorial and interpretation of results.

See also

Please read further information on each section following the links provided or the main User Guide for BacterialTyper.

Installation

  • What is required for the installation?

In order to correctly install BacterialTyper, it is necessary to have python3 and python development and virtual environment libraries installed. See additional details in section System requirements.

  • Why does the script env/create_python_environment.sh or the script env/activate_python_environment.sh report source and pip not found?

Sometimes, the script to create or activate a python environment do not execute and update the content of the virtual environment created.

The common error messages are:

For the env/create_python_environment.sh script:

env/create_python_environment.sh: 16 env/create_python_environment.sh: source: not found
env/create_python_environment.sh: 23 env/create_python_environment.sh: pip: not found

For the env/activate_python_environment.sh script:

env/activate_python_environment.sh: 16 env/create_python_environment.sh: source: not found

These error messages are because they are not correctly executed or they might have lost execution permissions.

To fix this error and follow with BacterialTyper installation provide execution permission using chmod and execute appropriately the shell scripts command as follows:

For the create_python_environment.sh script:

chmod +x env/create_python_environment.sh
source env/create_python_environment.sh

Or for the activate_python_environment.sh script:

chmod +x env/activate_python_environment.sh
source env/activate_python_environment.sh

  • How do I know the python environment is activated?

Once you execute the activation of the environment, either using the script activate_python_environment.sh or by executing source env/BacterialTyper/bin/activate, you should see a tag in the command-line prompt as shown in the following image.

../_images/environment.png

Once you deactivate the environment this tag should disappear.

Read additional details in python environment official documentation website.

  • What is CPAN?

CPAN is the Comprehensive Perl Archive Network, a large collection of perl software and documentation. You can begin exploring from either http://www.cpan.org/ or any of the mirrors listed at http://www.cpan.org/SITES.html.

CPAN is also the name of a perl module, CPAN.pm, which is used to download and install perl software from the CPAN archive. Read further information at https://metacpan.org/pod/CPAN.

Database

  • Why does the database module take so much time?

Some files, specially KMA databases are very big files (Gbytes) and it might take a long time. Please be patient.

Here we show an example of the size of the different KMA databases.

../_images/KMA_databases_ftp_dir.png

Quality control

  • Why do raw read length values vary for each sample?

This is generally a result of the trimming generated by default in the raw data from a Illumina MiSeq run. The software bcl2fastq [10] performs base calling and writes the sequence and quality scores into two FASTQ files per sample (one for R1 and one for R2), after separating de-multiplexing mixed samples from the library pool by bar code indices.

It also performs the trimming of adapter sequence in the reads beyond the genomic insert. If so, the corresponding base calls beyond the match will be changed to N in the resultant FASTQ file or trimmed, generating variable lengths for each read.

  • Why is there a drop in quality with read length?

As an example of a Multiqc image of quality control of our samples, there is a progressive drop in quality with read length, less pronounced in R1 than in R2, causing R2 reads with lower mean base quality [11], which is expected from 300 nt long paired end reads