Quick start (with provided test dataset)

Once setup is done, you can run the ROADIES pipeline using the provided test dataset. Follow these steps for a 16-core machine:

Step 1: Go to ROADIES repository directory if not there:

cd ROADIES

Step 2: Create a directory for the test data and download the test datasets (using the following one line command):

mkdir -p test/test_data && cat test/input_genome_links.txt | xargs -I {} sh -c 'wget -O test/test_data/$(basename {}) {}'

Step 3: Run the pipeline with the following command (from ROADIES directory):

python run_roadies.py --cores 16

The second command will download the 11 Drosophila genomic datasets (links provided in test/input_genome_links.txt) and save them in the test/test_data directory. The third command will run ROADIES for those 11 Drosophila genomes and save the final newick tree as roadies.nwk in a separate output_files folder upon completion.

Running ROADIES with different modes of operation

To run ROADIES in various other modes of operation (fast, balanced, accurate) (description of these modes are mentioned in Modes of operation section), try the following commands:

python run_roadies.py --cores 16 --mode accurate

python run_roadies.py --cores 16 --mode balanced

python run_roadies.py --cores 16 --mode fast

Note

Accurate mode is the default mode of operation. If you don't specify any particular mode using --mode argument, default mode will run.

For each modes, the output species tree will be saved as roadies.nwk in a separate output_files folder.

Running ROADIES in converge mode

To run ROADIES with converge mode (details mentioned in convergence mechanism section), run the following command (notice the addition of --converge argument):

python run_roadies.py --cores 16 --converge

Try following commands for other modes:

python run_roadies.py --cores 16 --mode balanced --converge

python run_roadies.py --cores 16 --mode fast --converge

The output files for all iterations will be saved in a separate converge_files folder. output_files will save the results of the last iteration. Species tree for all iterations will be saved in converge_files folder with the nomenclature iteration_<iteration_number>.nwk.