How to restart a gubbins run using the --resume flag

[mattbird567]

Hello,

As the tite suggests i am trying to restart a run using the --resume flag as i had to stop my inital run on a HPC. I am confused as to what the resume flag needs to restart the run? I am currently running the following command:

run_gubbins.py --resume path/to/last/generated/t25_tree.iteration_1.treefile --threads 16 --tree-builder iqtree /path/to/corresponding/alignment.iteration_1

However, when i run this i am getting an error telling me that the t25_tree.iteration_1.treefile.phylip isn't detected. Now a .phylip file is being created although its called alignment.iteration_1.phylip. Can't seem to think what i'm doing wrong to restart this run i would assume i'm just missing something obvious. Any help would be great.

[nickjcroucher]

There should be a .tre/.phylip pair to resume from? See #406 for the current state of this functionality.