check

This command of HATCHet verifies that dependencies that are unique to specific parts of HATCHet are correctly installed. The relevant commands with dependencies are count-reads, phase-snps, and compute-cn.

All checks can be run simultaneously via hatchet check, or an individual command can be checked via, e.g., hatchet check compute-cn.

The check for compute-cn runs the step on a set of small data files (.bbc/.seg) pre-packaged with HATCHet, and is a quick way to verify if your solver is working correctly. If you are unable to run this command, it likely indicates a licensing issue with default (Gurobi) solver. To use alternative solvers, see the Using a different Pyomo-supported solver section of the README for more details.

Input

This command takes no inputs.

Output

This command produces debugging output from the solver as well as other dependency checks. For compute-cn, look for the message towards the end of the output:

# Your current solver ... seems to be working correctly

to verify if your selected solver works correctly.