Running Sample Data

Exploring the AXIOME Commands

First, ensure the AXIOME command is available by typing the command axiome -h. You should get the following:

usage: axiome [-h] {ui,process,utility} ...

optional arguments:
   -h, --help            show this help message and exit

subcommands:
  the following subcommands are possible: ui, process, utility

  {ui,process,utility}

Let's look at the axiome utility command by using axiome utility -h:

usage: axiome utility [-h] {mapping_template,sample_data}

positional arguments:
  {mapping_template,sample_data}
                        mapping_template: generates a file mapping template in
                        the current directory, which can be opened in a
                        spreadsheet program; sample_data: copies AXIOME sample
                        data into the current directory

optional arguments:
  -h, --help            show this help message and exit

We can get the sample data with the command axiome utility sample_data.

Successfully copied sample.ax to current directory
Run `axiome process -i sample.ax` to process sample file

As the output suggests, we can now process the .ax AXIOME control file with axiome process -i sample.ax:

AXIOME file processed
Directory 'sample.axiome' created
Run command `make` in directory 'sample.axiome'

Running the Analysis

Move into the .axiome folder with cd sample.axiome. Start the analysis with make | tee -a log.txt. AXIOME's commands will be printed to the terminal (it will probably scroll very quickly). The tee command will send a copy to log.txt.

If installation of QIIME is complete, it will complete all of the steps. If there are issues, the on screen output will help debug which parts of QIIME are not configured correctly. For example, it may fail at the classification step if RDP was not installed correctly. Once it is installed correctly, re-run make | tee -a log.txt. This will start the pipeline from where it left off.

Viewing the Results

A file called "report.html" is created when the axiome process command is invoked. This HTML document can be opened in any web browser on your system (if you have graphical access), and will provide links to important analysis files. If you do not have graphical access, you can download the sample.axiome directory to a local machine and the report.html file can be used to navigate the results.

The subdirectories in the sample.axiome folder are all organized by pipeline step. Inside each of these directories are the directories for the submodule that was invoked for that step, and its resultant files. For example, in the created_otu_table folder, there is a qiime0 folder. This indicates that the "qiime" submodule was used to create the OTU table. Inside the qiime0 directory is a otu_table.biom file. This is the BIOM formatted OTU table.