Troubleshooting

Compilation issues

If you encounter any compilation issue, please proceed the following instructions:

• check that you cloned the project with --recursive.
• if you recently pulled the project with git pull, use ./gitpull.sh instead (see the readme)

Running issues

If you encounter any issue when running ParGenes, please proceed the following instructions:

• check that you ran the install script.
• run the checker script. If there is an error, there is a good chance that the compilation of one binary failed.
• check that you have all the dependencies installed. On clusters, you might have to load the corresponding modules.
• try running the tests: cd tests && python run_tests.py. If the tests pass, then the issue is not related to your environment or to missing dependencies.

Reporting

If this page did not help solving your issue, please report it, either on the raxml google group, or open an issue on the present github repository.

When reporting an issue, please join a report file (report.txt in the ParGenes output directory).

If the file was not generated, you can generate it with: python pargenes/report.py <pargenes_directory> <pargenes_directory>/report.txt where <pargenes_directory> is ParGenes output directory (corresponds to the -o argument when you called ParGenes).